Starting phenix.real_space_refine on Thu Jan 18 15:36:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tps_10544/01_2024/6tps_10544.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tps_10544/01_2024/6tps_10544.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tps_10544/01_2024/6tps_10544.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tps_10544/01_2024/6tps_10544.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tps_10544/01_2024/6tps_10544.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tps_10544/01_2024/6tps_10544.pdb" } resolution = 3.54 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9640 atoms to isotropic. 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 7 6.06 5 P 78 5.49 5 Mg 1 5.21 5 S 228 5.16 5 C 31603 2.51 5 N 8630 2.21 5 O 9523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 10": "OE1" <-> "OE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 131": "OD1" <-> "OD2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 353": "OD1" <-> "OD2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A PHE 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 433": "OD1" <-> "OD2" Residue "A ASP 439": "OD1" <-> "OD2" Residue "A PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 631": "OD1" <-> "OD2" Residue "A GLU 766": "OE1" <-> "OE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 773": "OD1" <-> "OD2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 804": "OE1" <-> "OE2" Residue "A GLU 881": "OE1" <-> "OE2" Residue "A ASP 885": "OD1" <-> "OD2" Residue "A GLU 1004": "OE1" <-> "OE2" Residue "A ASP 1040": "OD1" <-> "OD2" Residue "A PHE 1048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1053": "OD1" <-> "OD2" Residue "A PHE 1068": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1071": "OD1" <-> "OD2" Residue "A GLU 1092": "OE1" <-> "OE2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A TYR 1127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1224": "OE1" <-> "OE2" Residue "A ASP 1248": "OD1" <-> "OD2" Residue "A TYR 1290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1311": "OE1" <-> "OE2" Residue "A ASP 1463": "OD1" <-> "OD2" Residue "A GLU 1465": "OE1" <-> "OE2" Residue "A PHE 1472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1491": "OE1" <-> "OE2" Residue "A GLU 1533": "OE1" <-> "OE2" Residue "A ASP 1545": "OD1" <-> "OD2" Residue "A TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1654": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 54": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B GLU 70": "OE1" <-> "OE2" Residue "B PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 111": "OD1" <-> "OD2" Residue "B TYR 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 301": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 388": "OE1" <-> "OE2" Residue "B ASP 418": "OD1" <-> "OD2" Residue "B GLU 489": "OE1" <-> "OE2" Residue "B ASP 557": "OD1" <-> "OD2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B GLU 599": "OE1" <-> "OE2" Residue "B TYR 641": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "B PHE 667": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 671": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 757": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 765": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 804": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 810": "OD1" <-> "OD2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B PHE 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 838": "OE1" <-> "OE2" Residue "B GLU 878": "OE1" <-> "OE2" Residue "B GLU 883": "OE1" <-> "OE2" Residue "B GLU 884": "OE1" <-> "OE2" Residue "B ASP 890": "OD1" <-> "OD2" Residue "B GLU 998": "OE1" <-> "OE2" Residue "B TYR 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1021": "OE1" <-> "OE2" Residue "B ASP 1042": "OD1" <-> "OD2" Residue "B PHE 1044": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "B TYR 1098": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1137": "OD1" <-> "OD2" Residue "B PHE 1152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1154": "OD1" <-> "OD2" Residue "B ASP 1161": "OD1" <-> "OD2" Residue "B GLU 1172": "OE1" <-> "OE2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C GLU 81": "OE1" <-> "OE2" Residue "C TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C ASP 122": "OD1" <-> "OD2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C ASP 145": "OD1" <-> "OD2" Residue "C ASP 152": "OD1" <-> "OD2" Residue "C PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C GLU 201": "OE1" <-> "OE2" Residue "C GLU 242": "OE1" <-> "OE2" Residue "C PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 273": "OD1" <-> "OD2" Residue "D GLU 41": "OE1" <-> "OE2" Residue "D ASP 45": "OD1" <-> "OD2" Residue "D ASP 95": "OD1" <-> "OD2" Residue "E PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "G TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 55": "OE1" <-> "OE2" Residue "G ASP 99": "OD1" <-> "OD2" Residue "G TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 151": "OD1" <-> "OD2" Residue "G ASP 246": "OD1" <-> "OD2" Residue "H PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 110": "OD1" <-> "OD2" Residue "H TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 68": "OE1" <-> "OE2" Residue "K ASP 69": "OD1" <-> "OD2" Residue "K PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 11": "OE1" <-> "OE2" Residue "M PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 35": "OD1" <-> "OD2" Residue "M TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 50": "OE1" <-> "OE2" Residue "M TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 149": "OD1" <-> "OD2" Residue "N TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 64": "OD1" <-> "OD2" Residue "O ASP 67": "OD1" <-> "OD2" Residue "O PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 247": "OE1" <-> "OE2" Residue "O ASP 333": "OD1" <-> "OD2" Residue "O GLU 344": "OE1" <-> "OE2" Residue "O PHE 361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 394": "OE1" <-> "OE2" Residue "O PHE 408": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 415": "OE1" <-> "OE2" Residue "O TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 587": "OD1" <-> "OD2" Residue "O PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 595": "OD1" <-> "OD2" Residue "P ASP 53": "OD1" <-> "OD2" Residue "P ARG 194": "NH1" <-> "NH2" Residue "P TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 221": "NH1" <-> "NH2" Residue "P ARG 257": "NH1" <-> "NH2" Residue "P PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 299": "OD1" <-> "OD2" Residue "P ASP 304": "OD1" <-> "OD2" Residue "P PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 345": "OD1" <-> "OD2" Residue "P GLU 355": "OE1" <-> "OE2" Residue "P PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 407": "NH1" <-> "NH2" Residue "P ARG 419": "NH1" <-> "NH2" Residue "P PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 472": "NH1" <-> "NH2" Residue "P TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 484": "NH1" <-> "NH2" Residue "P GLU 509": "OE1" <-> "OE2" Residue "P PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 542": "NH1" <-> "NH2" Residue "P TYR 549": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 550": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 570": "OD1" <-> "OD2" Residue "P PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 583": "OE1" <-> "OE2" Residue "P GLU 587": "OE1" <-> "OE2" Residue "P ARG 603": "NH1" <-> "NH2" Residue "P GLU 674": "OE1" <-> "OE2" Residue "P ASP 680": "OD1" <-> "OD2" Residue "P PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 693": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 697": "OE1" <-> "OE2" Residue "P ARG 746": "NH1" <-> "NH2" Residue "P PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 762": "NH1" <-> "NH2" Residue "P ASP 778": "OD1" <-> "OD2" Residue "P ASP 779": "OD1" <-> "OD2" Residue "Q PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ASP 38": "OD1" <-> "OD2" Residue "Q ASP 44": "OD1" <-> "OD2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q GLU 150": "OE1" <-> "OE2" Residue "Q TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 291": "OD1" <-> "OD2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q PHE 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q GLU 346": "OE1" <-> "OE2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q ASP 359": "OD1" <-> "OD2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 372": "OE1" <-> "OE2" Residue "Q PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q GLU 440": "OE1" <-> "OE2" Residue "Q ASP 441": "OD1" <-> "OD2" Residue "Q GLU 444": "OE1" <-> "OE2" Residue "Q PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q PHE 491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 196": "OE1" <-> "OE2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 363": "OE1" <-> "OE2" Residue "R ASP 420": "OD1" <-> "OD2" Residue "R GLU 439": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 50070 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 11659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1475, 11659 Classifications: {'peptide': 1475} Link IDs: {'PCIS': 5, 'PTRANS': 54, 'TRANS': 1415} Chain breaks: 5 Chain: "B" Number of atoms: 9350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1177, 9350 Classifications: {'peptide': 1177} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1117} Chain breaks: 2 Chain: "C" Number of atoms: 2423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2423 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 285} Chain: "D" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 459 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain breaks: 1 Chain: "E" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1735 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 199} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1520 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 180} Chain breaks: 1 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: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1052 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 542 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 3, 'TRANS': 69} Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 793 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "L" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 340 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "M" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 833 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "N" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1151 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 9, 'TRANS': 135} Chain breaks: 2 Chain: "O" Number of atoms: 3811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3811 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 449} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "P" Number of atoms: 4840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4840 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 19, 'TRANS': 575} Chain breaks: 5 Chain: "Q" Number of atoms: 3839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 461, 3839 Classifications: {'peptide': 461} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 440} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "R" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2725 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain breaks: 3 Chain: "S" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 567 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 539 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "U" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 264 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "V" Number of atoms: 228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 228 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 461 SG CYS A 62 111.250 117.333 115.380 1.00 63.22 S ATOM 480 SG CYS A 65 109.568 118.335 119.634 1.00 62.66 S ATOM 535 SG CYS A 72 108.397 115.725 117.308 1.00 61.63 S ATOM 20302 SG CYS B1104 98.830 130.730 121.877 1.00 60.53 S ATOM 20328 SG CYS B1107 98.280 130.537 117.687 1.00 60.18 S ATOM 20475 SG CYS B1128 101.709 129.398 119.305 1.00 64.48 S ATOM 20503 SG CYS B1131 100.127 133.334 119.748 1.00 72.44 S ATOM 29084 SG CYS I 10 74.726 105.533 26.955 1.00 99.09 S ATOM 29106 SG CYS I 13 77.770 105.284 28.883 1.00100.43 S ATOM 29226 SG CYS I 30 77.890 108.897 28.820 1.00 98.32 S ATOM 29247 SG CYS I 33 77.784 106.918 25.637 1.00101.54 S ATOM 29617 SG CYS J 7 74.342 53.517 112.124 1.00 29.97 S ATOM 29640 SG CYS J 10 72.765 51.604 114.754 1.00 27.79 S ATOM 29920 SG CYS J 45 70.130 52.601 112.557 1.00 31.88 S ATOM 30968 SG CYS L 31 114.070 61.821 93.194 1.00 49.88 S ATOM 30988 SG CYS L 34 115.060 58.652 91.869 1.00 50.28 S ATOM 31092 SG CYS L 48 117.851 60.509 93.376 1.00 59.65 S ATOM 41962 SG CYS Q 10 110.276 99.422 132.094 1.00 86.57 S ATOM 41995 SG CYS Q 15 110.435 97.454 135.238 1.00 68.95 S ATOM 42115 SG CYS Q 29 108.147 95.597 133.341 1.00 65.57 S Time building chain proxies: 19.64, per 1000 atoms: 0.39 Number of scatterers: 50070 At special positions: 0 Unit cell: (207.1, 176.58, 204.92, 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 7 29.99 S 228 16.00 P 78 15.00 Mg 1 11.99 O 9523 8.00 N 8630 7.00 C 31603 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: 14.83 Conformation dependent library (CDL) restraints added in 7.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1701 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 65 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 72 " pdb="ZN ZN A1701 " - pdb=" SG CYS A 62 " pdb="ZN ZN A1701 " - pdb=" NE2 HIS A 75 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1107 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1104 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1131 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1128 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 30 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 33 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 13 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 34 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 15 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 29 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 10 " Number of angles added : 15 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11454 Finding SS restraints... Secondary structure from input PDB file: 214 helices and 58 sheets defined 38.5% alpha, 15.1% beta 34 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 13.17 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 removed outlier: 3.680A pdb=" N ARG A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASN A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 27 " --> pdb=" O GLU A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 99 removed outlier: 3.690A pdb=" N TYR A 97 " --> pdb=" O GLN A 93 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG A 99 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.656A pdb=" N HIS A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 135 removed outlier: 3.580A pdb=" N TYR A 134 " --> pdb=" O ILE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 196 removed outlier: 3.833A pdb=" N SER A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 226 removed outlier: 3.573A pdb=" N ARG A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 267 removed outlier: 3.619A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 331 removed outlier: 3.564A pdb=" N LEU A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 5.359A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.596A pdb=" N PHE A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.683A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 390 " --> pdb=" O LEU A 386 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N SER A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 422 through 439 removed outlier: 3.940A pdb=" N VAL A 428 " --> pdb=" O MET A 424 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN A 431 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASP A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP A 439 " --> pdb=" O ASN A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 460 Processing helix chain 'A' and resid 515 through 525 removed outlier: 3.966A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 removed outlier: 3.512A pdb=" N ALA A 556 " --> pdb=" O GLU A 552 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN A 559 " --> pdb=" O LYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 removed outlier: 3.743A pdb=" N MET A 600 " --> pdb=" O LYS A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 622 removed outlier: 4.090A pdb=" N GLY A 622 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 650 removed outlier: 3.989A pdb=" N ALA A 647 " --> pdb=" O ALA A 643 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU A 648 " --> pdb=" O ARG A 644 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 650 " --> pdb=" O GLU A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.589A pdb=" N GLY A 677 " --> pdb=" O HIS A 673 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 701 removed outlier: 3.533A pdb=" N GLN A 693 " --> pdb=" O ARG A 689 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 740 removed outlier: 3.545A pdb=" N THR A 740 " --> pdb=" O LEU A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 760 removed outlier: 3.555A pdb=" N TYR A 759 " --> pdb=" O LYS A 756 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP A 760 " --> pdb=" O ASN A 757 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 756 through 760' Processing helix chain 'A' and resid 782 through 787 removed outlier: 3.566A pdb=" N TYR A 786 " --> pdb=" O ASP A 782 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 801 removed outlier: 3.759A pdb=" N SER A 796 " --> pdb=" O GLY A 792 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 820 removed outlier: 3.840A pdb=" N LYS A 808 " --> pdb=" O GLU A 804 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER A 811 " --> pdb=" O ALA A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.651A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 849 removed outlier: 3.668A pdb=" N ILE A 846 " --> pdb=" O TRP A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 863 removed outlier: 3.515A pdb=" N GLU A 860 " --> pdb=" O GLU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 884 removed outlier: 3.870A pdb=" N LYS A 877 " --> pdb=" O PRO A 873 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ARG A 884 " --> pdb=" O GLN A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.534A pdb=" N SER A 889 " --> pdb=" O ASP A 885 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE A 891 " --> pdb=" O ASN A 887 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 892 " --> pdb=" O LYS A 888 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN A 906 " --> pdb=" O ALA A 902 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 907 " --> pdb=" O ILE A 903 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 910 " --> pdb=" O GLN A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 931 removed outlier: 3.727A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 945 removed outlier: 3.883A pdb=" N ILE A 943 " --> pdb=" O ASN A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1010 removed outlier: 3.613A pdb=" N TYR A 996 " --> pdb=" O PRO A 992 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU A1004 " --> pdb=" O MET A1000 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1027 removed outlier: 3.680A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.532A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 removed outlier: 3.510A pdb=" N CYS A1069 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1072 through 1081 removed outlier: 3.706A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A1079 " --> pdb=" O ALA A1075 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A1080 " --> pdb=" O LEU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1089 removed outlier: 3.592A pdb=" N LEU A1085 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU A1087 " --> pdb=" O ALA A1084 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A1088 " --> pdb=" O LEU A1085 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A1089 " --> pdb=" O ILE A1086 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1082 through 1089' Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.846A pdb=" N TYR A1097 " --> pdb=" O SER A1093 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A1099 " --> pdb=" O LEU A1095 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A1105 " --> pdb=" O THR A1101 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1112 through 1116 removed outlier: 4.029A pdb=" N GLN A1116 " --> pdb=" O HIS A1113 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.967A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1149 removed outlier: 3.766A pdb=" N PHE A1147 " --> pdb=" O LYS A1143 " (cutoff:3.500A) Processing helix chain 'A' and resid 1162 through 1177 removed outlier: 3.735A pdb=" N GLN A1171 " --> pdb=" O ARG A1167 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR A1174 " --> pdb=" O MET A1170 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N MET A1175 " --> pdb=" O GLN A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1191 removed outlier: 3.610A pdb=" N ILE A1188 " --> pdb=" O ALA A1184 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER A1190 " --> pdb=" O GLY A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.896A pdb=" N MET A1200 " --> pdb=" O SER A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1226 removed outlier: 3.993A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A1225 " --> pdb=" O ARG A1221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL A1226 " --> pdb=" O LEU A1222 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1258 removed outlier: 3.505A pdb=" N ILE A1258 " --> pdb=" O PHE A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 3.544A pdb=" N SER A1303 " --> pdb=" O ASN A1299 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU A1304 " --> pdb=" O ASN A1300 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR A1306 " --> pdb=" O TYR A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1320 removed outlier: 3.769A pdb=" N ASN A1315 " --> pdb=" O GLU A1311 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL A1316 " --> pdb=" O GLU A1312 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ILE A1317 " --> pdb=" O LEU A1313 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1335 removed outlier: 3.511A pdb=" N ALA A1327 " --> pdb=" O HIS A1323 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1338 No H-bonds generated for 'chain 'A' and resid 1336 through 1338' Processing helix chain 'A' and resid 1441 through 1453 removed outlier: 3.515A pdb=" N SER A1448 " --> pdb=" O ARG A1444 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N SER A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N HIS A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1485 through 1494 removed outlier: 3.754A pdb=" N GLU A1491 " --> pdb=" O ASN A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.084A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1531 removed outlier: 3.990A pdb=" N ASP A1531 " --> pdb=" O GLN A1527 " (cutoff:3.500A) Processing helix chain 'A' and resid 1548 through 1553 Processing helix chain 'A' and resid 1555 through 1573 removed outlier: 3.591A pdb=" N ASN A1560 " --> pdb=" O GLU A1556 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL A1563 " --> pdb=" O ARG A1559 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASN A1564 " --> pdb=" O ASN A1560 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR A1573 " --> pdb=" O VAL A1569 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1587 removed outlier: 3.819A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 removed outlier: 3.574A pdb=" N GLU A1604 " --> pdb=" O ARG A1600 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1614 removed outlier: 3.783A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N SER A1614 " --> pdb=" O PHE A1610 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1629 removed outlier: 3.512A pdb=" N PHE A1621 " --> pdb=" O THR A1617 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A1625 " --> pdb=" O PHE A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1638 through 1644 removed outlier: 3.651A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1649 through 1652 removed outlier: 3.871A pdb=" N GLY A1652 " --> pdb=" O VAL A1649 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1649 through 1652' Processing helix chain 'B' and resid 17 through 27 removed outlier: 3.603A pdb=" N ASN B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 Processing helix chain 'B' and resid 42 through 47 Processing helix chain 'B' and resid 58 through 67 removed outlier: 4.453A pdb=" N ASN B 62 " --> pdb=" O GLY B 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 63 " --> pdb=" O GLY B 59 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 129 removed outlier: 3.679A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN B 128 " --> pdb=" O SER B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 removed outlier: 3.625A pdb=" N VAL B 181 " --> pdb=" O PRO B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.282A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.659A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE B 289 " --> pdb=" O ASP B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 removed outlier: 3.516A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 3.847A pdb=" N VAL B 326 " --> pdb=" O ASN B 322 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY B 331 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS B 333 " --> pdb=" O TYR B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 357 removed outlier: 3.774A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 363 Processing helix chain 'B' and resid 368 through 386 removed outlier: 3.650A pdb=" N ARG B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET B 373 " --> pdb=" O ASP B 369 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE B 378 " --> pdb=" O LEU B 374 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU B 381 " --> pdb=" O MET B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 398 No H-bonds generated for 'chain 'B' and resid 396 through 398' Processing helix chain 'B' and resid 405 through 433 removed outlier: 3.650A pdb=" N LEU B 413 " --> pdb=" O TYR B 409 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET B 430 " --> pdb=" O ALA B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 450 removed outlier: 3.885A pdb=" N ARG B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU B 450 " --> pdb=" O MET B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.610A pdb=" N GLN B 462 " --> pdb=" O GLY B 458 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N TYR B 463 " --> pdb=" O SER B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.595A pdb=" N PHE B 496 " --> pdb=" O ASN B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 510 removed outlier: 3.512A pdb=" N ALA B 510 " --> pdb=" O SER B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 567 removed outlier: 3.691A pdb=" N ILE B 564 " --> pdb=" O ARG B 560 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER B 567 " --> pdb=" O SER B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 615 removed outlier: 3.517A pdb=" N LYS B 602 " --> pdb=" O HIS B 598 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 610 " --> pdb=" O ASP B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 670 removed outlier: 3.555A pdb=" N GLN B 669 " --> pdb=" O PRO B 666 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL B 670 " --> pdb=" O PHE B 667 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 666 through 670' Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.771A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.944A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.539A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N CYS B 719 " --> pdb=" O ASN B 715 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.892A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 791 through 795 Processing helix chain 'B' and resid 932 through 936 removed outlier: 3.754A pdb=" N MET B 936 " --> pdb=" O THR B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 952 No H-bonds generated for 'chain 'B' and resid 950 through 952' Processing helix chain 'B' and resid 953 through 958 removed outlier: 3.848A pdb=" N ARG B 957 " --> pdb=" O ALA B 953 " (cutoff:3.500A) Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.635A pdb=" N VAL B 964 " --> pdb=" O ILE B 960 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 966 " --> pdb=" O MET B 962 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS B 970 " --> pdb=" O SER B 966 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 974 " --> pdb=" O LYS B 970 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1003 removed outlier: 3.884A pdb=" N GLU B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B1000 " --> pdb=" O PHE B 996 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA B1003 " --> pdb=" O GLN B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1039 through 1043 Processing helix chain 'B' and resid 1073 through 1082 removed outlier: 3.795A pdb=" N ASP B1077 " --> pdb=" O GLU B1073 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU B1079 " --> pdb=" O GLU B1075 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLY B1081 " --> pdb=" O ASP B1077 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1093 Processing helix chain 'B' and resid 1135 through 1139 Processing helix chain 'B' and resid 1180 through 1192 removed outlier: 3.932A pdb=" N MET B1192 " --> pdb=" O GLU B1188 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 38 Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.727A pdb=" N ALA C 66 " --> pdb=" O SER C 62 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG C 68 " --> pdb=" O ALA C 64 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 removed outlier: 3.622A pdb=" N GLY C 102 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU C 103 " --> pdb=" O HIS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 179 Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.819A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 309 through 329 removed outlier: 3.768A pdb=" N PHE C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 45 removed outlier: 3.689A pdb=" N ILE D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 98 removed outlier: 4.066A pdb=" N GLN D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS D 97 " --> pdb=" O GLN D 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 26 removed outlier: 3.730A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 35 Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.838A pdb=" N LYS E 45 " --> pdb=" O ASP E 41 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS E 47 " --> pdb=" O LYS E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 58 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.674A pdb=" N ILE E 69 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 102 removed outlier: 3.606A pdb=" N GLN E 101 " --> pdb=" O VAL E 97 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU E 102 " --> pdb=" O ILE E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 127 removed outlier: 3.670A pdb=" N LYS E 122 " --> pdb=" O SER E 119 " (cutoff:3.500A) Proline residue: E 125 - end of helix Processing helix chain 'E' and resid 137 through 141 removed outlier: 4.221A pdb=" N VAL E 141 " --> pdb=" O ALA E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 165 removed outlier: 3.735A pdb=" N ARG E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.625A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 56 through 73 removed outlier: 3.956A pdb=" N ILE F 64 " --> pdb=" O GLN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 4.053A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 103 removed outlier: 3.589A pdb=" N ALA F 91 " --> pdb=" O LYS F 87 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA F 98 " --> pdb=" O LEU F 94 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET F 103 " --> pdb=" O LEU F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 126 removed outlier: 3.506A pdb=" N ALA F 121 " --> pdb=" O PRO F 117 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA F 126 " --> pdb=" O MET F 122 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 removed outlier: 3.972A pdb=" N HIS G 20 " --> pdb=" O ILE G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 63 Processing helix chain 'G' and resid 66 through 70 Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.543A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 56 removed outlier: 3.908A pdb=" N ALA I 55 " --> pdb=" O ALA I 52 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE I 56 " --> pdb=" O ASP I 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 52 through 56' Processing helix chain 'I' and resid 58 through 63 Processing helix chain 'J' and resid 17 through 25 Processing helix chain 'J' and resid 32 through 39 removed outlier: 3.920A pdb=" N LEU J 36 " --> pdb=" O GLU J 32 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER J 37 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU J 39 " --> pdb=" O ALA J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 52 removed outlier: 4.107A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 removed outlier: 3.585A pdb=" N PHE J 60 " --> pdb=" O LEU J 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.932A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR K 78 " --> pdb=" O ASN K 74 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET K 81 " --> pdb=" O ARG K 77 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 126 removed outlier: 3.513A pdb=" N ALA K 116 " --> pdb=" O THR K 112 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY K 120 " --> pdb=" O ALA K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 141 removed outlier: 3.733A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLU K 137 " --> pdb=" O SER K 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS K 138 " --> pdb=" O LYS K 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 69 through 73 removed outlier: 3.529A pdb=" N SER M 73 " --> pdb=" O SER M 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 69 through 73' Processing helix chain 'O' and resid 50 through 65 removed outlier: 3.790A pdb=" N ASP O 62 " --> pdb=" O SER O 58 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP O 64 " --> pdb=" O LEU O 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 79 Processing helix chain 'O' and resid 89 through 102 removed outlier: 3.713A pdb=" N ILE O 95 " --> pdb=" O LYS O 91 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP O 98 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 121 Processing helix chain 'O' and resid 124 through 128 removed outlier: 3.534A pdb=" N GLU O 127 " --> pdb=" O LYS O 124 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU O 128 " --> pdb=" O TRP O 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 124 through 128' Processing helix chain 'O' and resid 132 through 147 removed outlier: 3.572A pdb=" N TYR O 138 " --> pdb=" O SER O 134 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 161 removed outlier: 3.743A pdb=" N VAL O 154 " --> pdb=" O TRP O 150 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 165 through 169 Processing helix chain 'O' and resid 171 through 183 removed outlier: 3.795A pdb=" N MET O 175 " --> pdb=" O CYS O 171 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS O 177 " --> pdb=" O HIS O 173 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG O 181 " --> pdb=" O LYS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 188 removed outlier: 3.691A pdb=" N GLY O 188 " --> pdb=" O SER O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 189 through 197 removed outlier: 3.565A pdb=" N TYR O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE O 197 " --> pdb=" O TYR O 193 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 220 removed outlier: 3.552A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL O 209 " --> pdb=" O ARG O 205 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 247 removed outlier: 3.656A pdb=" N TRP O 230 " --> pdb=" O GLY O 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU O 235 " --> pdb=" O SER O 231 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE O 238 " --> pdb=" O ILE O 234 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL O 242 " --> pdb=" O ILE O 238 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU O 244 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 347 removed outlier: 3.711A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASP O 333 " --> pdb=" O SER O 329 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N SER O 334 " --> pdb=" O THR O 330 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE O 335 " --> pdb=" O LYS O 331 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER O 340 " --> pdb=" O LEU O 336 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N HIS O 342 " --> pdb=" O LEU O 338 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU O 345 " --> pdb=" O THR O 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 348 through 352 removed outlier: 3.840A pdb=" N LEU O 352 " --> pdb=" O PRO O 349 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 371 removed outlier: 3.642A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS O 369 " --> pdb=" O THR O 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 381 through 385 Processing helix chain 'O' and resid 392 through 406 removed outlier: 3.963A pdb=" N MET O 396 " --> pdb=" O GLN O 392 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP O 405 " --> pdb=" O VAL O 401 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE O 406 " --> pdb=" O THR O 402 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 429 removed outlier: 3.602A pdb=" N LYS O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU O 421 " --> pdb=" O LYS O 417 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR O 427 " --> pdb=" O TYR O 423 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE O 428 " --> pdb=" O LEU O 424 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA O 429 " --> pdb=" O GLY O 425 " (cutoff:3.500A) Processing helix chain 'O' and resid 438 through 452 removed outlier: 3.573A pdb=" N TYR O 445 " --> pdb=" O PHE O 441 " (cutoff:3.500A) Processing helix chain 'O' and resid 452 through 457 removed outlier: 4.030A pdb=" N GLU O 456 " --> pdb=" O ARG O 452 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG O 457 " --> pdb=" O TYR O 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 452 through 457' Processing helix chain 'O' and resid 466 through 469 removed outlier: 3.787A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 469' Processing helix chain 'O' and resid 470 through 484 removed outlier: 3.585A pdb=" N ALA O 479 " --> pdb=" O ALA O 475 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU O 480 " --> pdb=" O ALA O 476 " (cutoff:3.500A) Processing helix chain 'O' and resid 487 through 492 removed outlier: 3.659A pdb=" N PHE O 491 " --> pdb=" O ARG O 487 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG O 492 " --> pdb=" O HIS O 488 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 487 through 492' Processing helix chain 'O' and resid 527 through 533 removed outlier: 3.733A pdb=" N GLN O 533 " --> pdb=" O ALA O 529 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 551 removed outlier: 3.583A pdb=" N ASN O 548 " --> pdb=" O ILE O 544 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN O 549 " --> pdb=" O GLU O 545 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG O 551 " --> pdb=" O ASN O 547 " (cutoff:3.500A) Processing helix chain 'O' and resid 582 through 587 removed outlier: 3.501A pdb=" N ASP O 587 " --> pdb=" O GLN O 583 " (cutoff:3.500A) Processing helix chain 'O' and resid 600 through 606 Processing helix chain 'P' and resid 189 through 194 removed outlier: 3.933A pdb=" N ARG P 194 " --> pdb=" O ALA P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 574 through 578 removed outlier: 3.506A pdb=" N LEU P 577 " --> pdb=" O TRP P 574 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE P 578 " --> pdb=" O ALA P 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 574 through 578' Processing helix chain 'P' and resid 583 through 609 removed outlier: 4.224A pdb=" N SER P 588 " --> pdb=" O ARG P 584 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ILE P 589 " --> pdb=" O GLU P 585 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER P 594 " --> pdb=" O GLY P 590 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER P 605 " --> pdb=" O ARG P 601 " (cutoff:3.500A) Processing helix chain 'P' and resid 610 through 613 Processing helix chain 'P' and resid 616 through 644 removed outlier: 3.708A pdb=" N GLN P 624 " --> pdb=" O ASP P 620 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE P 632 " --> pdb=" O TYR P 628 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR P 644 " --> pdb=" O SER P 640 " (cutoff:3.500A) Processing helix chain 'P' and resid 671 through 686 Processing helix chain 'P' and resid 695 through 700 removed outlier: 3.579A pdb=" N LEU P 700 " --> pdb=" O PHE P 696 " (cutoff:3.500A) Processing helix chain 'P' and resid 701 through 704 Processing helix chain 'P' and resid 712 through 723 removed outlier: 3.506A pdb=" N LEU P 718 " --> pdb=" O PHE P 714 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N CYS P 721 " --> pdb=" O LYS P 717 " (cutoff:3.500A) Processing helix chain 'P' and resid 728 through 743 removed outlier: 4.213A pdb=" N LEU P 732 " --> pdb=" O GLN P 728 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE P 741 " --> pdb=" O VAL P 737 " (cutoff:3.500A) Processing helix chain 'P' and resid 754 through 766 removed outlier: 3.732A pdb=" N ASN P 758 " --> pdb=" O GLU P 754 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE P 760 " --> pdb=" O ILE P 756 " (cutoff:3.500A) Processing helix chain 'P' and resid 767 through 772 removed outlier: 3.591A pdb=" N ILE P 771 " --> pdb=" O PRO P 767 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE P 772 " --> pdb=" O TYR P 768 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 767 through 772' Processing helix chain 'Q' and resid 79 through 93 removed outlier: 3.707A pdb=" N GLN Q 85 " --> pdb=" O LEU Q 81 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG Q 86 " --> pdb=" O GLN Q 82 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS Q 90 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE Q 92 " --> pdb=" O SER Q 88 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS Q 93 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 120 removed outlier: 3.502A pdb=" N SER Q 107 " --> pdb=" O LEU Q 103 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE Q 110 " --> pdb=" O LYS Q 106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN Q 115 " --> pdb=" O ILE Q 111 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 145 removed outlier: 3.863A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU Q 138 " --> pdb=" O LYS Q 134 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 172 removed outlier: 3.700A pdb=" N THR Q 161 " --> pdb=" O HIS Q 157 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE Q 162 " --> pdb=" O MET Q 158 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N SER Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 186 removed outlier: 3.661A pdb=" N TYR Q 181 " --> pdb=" O TYR Q 177 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE Q 182 " --> pdb=" O THR Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 216 removed outlier: 3.544A pdb=" N ILE Q 214 " --> pdb=" O TYR Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 230 removed outlier: 3.646A pdb=" N ASN Q 228 " --> pdb=" O GLY Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 230 through 235 Processing helix chain 'Q' and resid 248 through 260 removed outlier: 3.657A pdb=" N VAL Q 257 " --> pdb=" O LEU Q 253 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 3.931A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN Q 272 " --> pdb=" O PHE Q 268 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL Q 273 " --> pdb=" O TYR Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.539A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 340 removed outlier: 3.512A pdb=" N THR Q 339 " --> pdb=" O THR Q 335 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN Q 340 " --> pdb=" O GLU Q 336 " (cutoff:3.500A) Processing helix chain 'Q' and resid 344 through 356 removed outlier: 4.172A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL Q 356 " --> pdb=" O ILE Q 352 " (cutoff:3.500A) Processing helix chain 'Q' and resid 363 through 367 removed outlier: 3.687A pdb=" N TYR Q 366 " --> pdb=" O SER Q 363 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 363 through 367' Processing helix chain 'Q' and resid 370 through 385 removed outlier: 3.659A pdb=" N THR Q 374 " --> pdb=" O SER Q 370 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU Q 375 " --> pdb=" O GLU Q 371 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS Q 383 " --> pdb=" O LYS Q 379 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 417 removed outlier: 3.647A pdb=" N LYS Q 415 " --> pdb=" O ARG Q 411 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE Q 416 " --> pdb=" O LYS Q 412 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE Q 417 " --> pdb=" O LEU Q 413 " (cutoff:3.500A) Processing helix chain 'Q' and resid 439 through 449 removed outlier: 4.239A pdb=" N GLN Q 449 " --> pdb=" O ARG Q 445 " (cutoff:3.500A) Processing helix chain 'Q' and resid 471 through 490 removed outlier: 3.873A pdb=" N ALA Q 475 " --> pdb=" O ALA Q 471 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU Q 479 " --> pdb=" O ALA Q 475 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR Q 481 " --> pdb=" O GLY Q 477 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS Q 482 " --> pdb=" O ARG Q 478 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA Q 484 " --> pdb=" O LEU Q 480 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 511 removed outlier: 3.911A pdb=" N LYS Q 499 " --> pdb=" O LYS Q 495 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU Q 510 " --> pdb=" O LYS Q 506 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 35 removed outlier: 3.598A pdb=" N LYS R 18 " --> pdb=" O ALA R 14 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 131 removed outlier: 3.594A pdb=" N PHE R 127 " --> pdb=" O GLU R 123 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS R 130 " --> pdb=" O LYS R 126 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR R 131 " --> pdb=" O PHE R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 175 removed outlier: 4.179A pdb=" N ILE R 168 " --> pdb=" O LYS R 164 " (cutoff:3.500A) Proline residue: R 169 - end of helix removed outlier: 4.029A pdb=" N ILE R 175 " --> pdb=" O ARG R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 193 removed outlier: 3.668A pdb=" N GLN R 189 " --> pdb=" O LYS R 185 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N SER R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 205 removed outlier: 3.947A pdb=" N GLU R 204 " --> pdb=" O SER R 201 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL R 205 " --> pdb=" O THR R 202 " (cutoff:3.500A) Processing helix chain 'R' and resid 207 through 226 removed outlier: 3.699A pdb=" N HIS R 212 " --> pdb=" O TYR R 208 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR R 215 " --> pdb=" O ARG R 211 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.799A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 251 through 261 removed outlier: 3.833A pdb=" N ILE R 257 " --> pdb=" O ILE R 253 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU R 261 " --> pdb=" O ILE R 257 " (cutoff:3.500A) Processing helix chain 'R' and resid 266 through 278 removed outlier: 3.750A pdb=" N PHE R 270 " --> pdb=" O SER R 266 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS R 275 " --> pdb=" O LEU R 271 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE R 277 " --> pdb=" O TRP R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 322 removed outlier: 3.666A pdb=" N THR R 311 " --> pdb=" O LYS R 307 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS R 322 " --> pdb=" O ILE R 318 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 355 removed outlier: 3.560A pdb=" N LEU R 354 " --> pdb=" O SER R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 382 removed outlier: 3.721A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER R 380 " --> pdb=" O ALA R 376 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG R 381 " --> pdb=" O ASP R 377 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN R 382 " --> pdb=" O THR R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 418 removed outlier: 3.752A pdb=" N ILE R 405 " --> pdb=" O ILE R 401 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS R 406 " --> pdb=" O ASN R 402 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS R 407 " --> pdb=" O GLN R 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR R 413 " --> pdb=" O HIS R 409 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) Processing helix chain 'R' and resid 429 through 440 removed outlier: 3.549A pdb=" N GLN R 434 " --> pdb=" O LEU R 430 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU R 435 " --> pdb=" O ILE R 431 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER R 437 " --> pdb=" O ASN R 433 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 15 removed outlier: 6.898A pdb=" N ASN B1199 " --> pdb=" O THR A 12 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N VAL A 14 " --> pdb=" O ARG B1197 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ARG B1197 " --> pdb=" O VAL A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 3.588A pdb=" N GLY A 77 " --> pdb=" O VAL A 362 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.652A pdb=" N LYS A 242 " --> pdb=" O THR A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 371 through 373 removed outlier: 3.507A pdb=" N SER A 371 " --> pdb=" O HIS A 378 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N VAL A 377 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 3.758A pdb=" N ASN A 590 " --> pdb=" O ASN A 634 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N ILE A 495 " --> pdb=" O ARG A 606 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 506 through 510 removed outlier: 6.688A pdb=" N LYS A 576 " --> pdb=" O ILE A 536 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ILE A 536 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR A 578 " --> pdb=" O THR A 534 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 544 " --> pdb=" O ILE A 536 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AA8, first strand: chain 'A' and resid 749 through 751 removed outlier: 3.993A pdb=" N CYS A 778 " --> pdb=" O LEU A 770 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB1, first strand: chain 'A' and resid 1031 through 1032 Processing sheet with id=AB2, first strand: chain 'A' and resid 1507 through 1508 removed outlier: 3.625A pdb=" N VAL A1520 " --> pdb=" O VAL A1508 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1260 through 1262 removed outlier: 6.882A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1457 through 1462 removed outlier: 5.527A pdb=" N ILE A1457 " --> pdb=" O GLU A1475 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N GLU A1475 " --> pdb=" O ILE A1457 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS A1459 " --> pdb=" O LYS A1473 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A1473 " --> pdb=" O LYS A1459 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A1288 " --> pdb=" O LEU A1476 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A1275 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A1272 " --> pdb=" O THR I 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A1274 " --> pdb=" O VAL I 47 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 21 through 24 removed outlier: 4.059A pdb=" N VAL D 21 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR G 46 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG F 136 " --> pdb=" O GLU F 144 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 29 through 30 removed outlier: 5.737A pdb=" N HIS G 119 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N GLY G 86 " --> pdb=" O HIS G 119 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASN G 121 " --> pdb=" O TYR G 84 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR G 84 " --> pdb=" O ASN G 121 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N TYR G 123 " --> pdb=" O LEU G 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 73 removed outlier: 3.591A pdb=" N VAL B 97 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 73 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 71 through 73 removed outlier: 3.591A pdb=" N VAL B 97 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE B 73 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC1, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC2, first strand: chain 'B' and resid 206 through 209 Processing sheet with id=AC3, first strand: chain 'B' and resid 215 through 217 removed outlier: 5.129A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 571 through 572 removed outlier: 6.858A pdb=" N VAL B 586 " --> pdb=" O ILE B 593 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N TRP B 595 " --> pdb=" O CYS B 584 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N CYS B 584 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLY B 639 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 625 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 664 removed outlier: 3.563A pdb=" N ALA B 675 " --> pdb=" O HIS B 688 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.285A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU B 884 " --> pdb=" O LYS B 904 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AC8, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 4.260A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 823 through 825 Processing sheet with id=AD1, first strand: chain 'B' and resid 851 through 852 Processing sheet with id=AD2, first strand: chain 'B' and resid 857 through 859 removed outlier: 6.930A pdb=" N LYS B 872 " --> pdb=" O ILE B 858 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1099 through 1104 Processing sheet with id=AD4, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AD5, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AD6, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.878A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 301 " --> pdb=" O SER C 226 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER C 226 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR C 224 " --> pdb=" O GLU C 303 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.878A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LEU C 47 " --> pdb=" O GLU C 51 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLU C 51 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS C 290 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 234 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LEU C 230 " --> pdb=" O VAL C 294 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 168 through 170 removed outlier: 4.091A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLU C 201 " --> pdb=" O ASN C 88 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ASN C 88 " --> pdb=" O GLU C 201 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N SER C 203 " --> pdb=" O PHE C 86 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR C 82 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ILE C 209 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA C 80 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N GLY C 211 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL C 78 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL L 65 " --> pdb=" O PHE C 85 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'C' and resid 161 through 162 removed outlier: 3.530A pdb=" N ALA C 194 " --> pdb=" O VAL C 162 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 256 through 258 Processing sheet with id=AE3, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AE4, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.869A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 132 through 140 removed outlier: 5.412A pdb=" N ILE G 137 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU G 148 " --> pdb=" O ILE G 137 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE G 139 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY G 135 " --> pdb=" O LEU G 229 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 167 through 169 Processing sheet with id=AE7, first strand: chain 'H' and resid 4 through 7 removed outlier: 6.528A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 145 " --> pdb=" O THR H 56 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA H 60 " --> pdb=" O TYR H 141 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU H 142 " --> pdb=" O MET H 97 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU H 121 " --> pdb=" O PHE H 118 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 27 through 29 Processing sheet with id=AE9, first strand: chain 'K' and resid 47 through 54 removed outlier: 5.132A pdb=" N SER K 62 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N GLN K 52 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 10.870A pdb=" N SER K 60 " --> pdb=" O GLN K 52 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE K 103 " --> pdb=" O PHE K 63 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'M' and resid 11 through 14 removed outlier: 6.823A pdb=" N LEU M 90 " --> pdb=" O GLU M 13 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLY M 79 " --> pdb=" O TRP N 54 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU N 55 " --> pdb=" O LYS N 135 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'M' and resid 65 through 66 removed outlier: 3.871A pdb=" N TYR M 65 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL M 97 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 38 " --> pdb=" O LEU N 119 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR M 62 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 65 through 66 removed outlier: 3.871A pdb=" N TYR M 65 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL M 97 " --> pdb=" O TYR M 65 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE M 38 " --> pdb=" O LEU N 119 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 79 through 82 removed outlier: 3.738A pdb=" N TYR N 87 " --> pdb=" O MET N 80 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'P' and resid 59 through 66 removed outlier: 7.001A pdb=" N VAL P 547 " --> pdb=" O LEU P 65 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL P 539 " --> pdb=" O TYR P 548 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N ASP P 536 " --> pdb=" O THR P 510 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N THR P 510 " --> pdb=" O ASP P 536 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU P 538 " --> pdb=" O ILE P 508 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ILE P 508 " --> pdb=" O LEU P 538 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LYS P 540 " --> pdb=" O THR P 506 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 173 through 174 removed outlier: 3.629A pdb=" N TRP P 174 " --> pdb=" O GLU R 196 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU R 196 " --> pdb=" O TRP P 174 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'P' and resid 182 through 183 removed outlier: 4.587A pdb=" N GLU P 201 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE P 203 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA P 217 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER P 207 " --> pdb=" O VAL P 213 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 186 through 187 removed outlier: 3.513A pdb=" N THR P 200 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N GLU P 201 " --> pdb=" O LEU P 219 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE P 203 " --> pdb=" O ALA P 217 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA P 217 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER P 207 " --> pdb=" O VAL P 213 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR P 234 " --> pdb=" O ILE P 216 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'P' and resid 242 through 246 removed outlier: 5.612A pdb=" N ILE P 274 " --> pdb=" O SER P 287 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N SER P 287 " --> pdb=" O ILE P 274 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N SER P 276 " --> pdb=" O MET P 285 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N MET P 285 " --> pdb=" O SER P 276 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 300 through 304 removed outlier: 6.999A pdb=" N ASP P 319 " --> pdb=" O GLN P 301 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL P 303 " --> pdb=" O ILE P 317 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE P 317 " --> pdb=" O VAL P 303 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER P 325 " --> pdb=" O ILE P 318 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'P' and resid 361 through 365 removed outlier: 3.604A pdb=" N TRP P 389 " --> pdb=" O ASP P 384 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'P' and resid 406 through 407 removed outlier: 3.746A pdb=" N ILE P 421 " --> pdb=" O SER P 418 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'P' and resid 449 through 457 removed outlier: 3.515A pdb=" N TYR P 477 " --> pdb=" O VAL P 468 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N SER P 470 " --> pdb=" O ARG P 475 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG P 475 " --> pdb=" O SER P 470 " (cutoff:3.500A) 1583 hydrogen bonds defined for protein. 4383 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 20.27 Time building geometry restraints manager: 16.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9021 1.32 - 1.44: 13076 1.44 - 1.57: 28634 1.57 - 1.69: 152 1.69 - 1.81: 359 Bond restraints: 51242 Sorted by residual: bond pdb=" C VAL B 121 " pdb=" N TYR B 122 " ideal model delta sigma weight residual 1.329 1.198 0.130 3.03e-02 1.09e+03 1.85e+01 bond pdb=" C ARG B 909 " pdb=" N THR B 910 " ideal model delta sigma weight residual 1.331 1.260 0.071 2.07e-02 2.33e+03 1.17e+01 bond pdb=" C THR Q 450 " pdb=" N PRO Q 451 " ideal model delta sigma weight residual 1.334 1.393 -0.059 2.34e-02 1.83e+03 6.36e+00 bond pdb=" C ILE P 500 " pdb=" N PRO P 501 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.73e+00 bond pdb=" CB VAL C 222 " pdb=" CG1 VAL C 222 " ideal model delta sigma weight residual 1.521 1.445 0.076 3.30e-02 9.18e+02 5.30e+00 ... (remaining 51237 not shown) Histogram of bond angle deviations from ideal: 94.24 - 106.01: 1515 106.01 - 117.78: 36857 117.78 - 129.55: 30844 129.55 - 141.33: 348 141.33 - 153.10: 1 Bond angle restraints: 69565 Sorted by residual: angle pdb=" C CYS Q 15 " pdb=" N PRO Q 16 " pdb=" CD PRO Q 16 " ideal model delta sigma weight residual 120.60 94.24 26.36 2.20e+00 2.07e-01 1.44e+02 angle pdb=" C CYS Q 15 " pdb=" N PRO Q 16 " pdb=" CA PRO Q 16 " ideal model delta sigma weight residual 127.00 153.10 -26.10 2.40e+00 1.74e-01 1.18e+02 angle pdb=" C GLY B1062 " pdb=" N ARG B1063 " pdb=" CA ARG B1063 " ideal model delta sigma weight residual 121.54 133.54 -12.00 1.91e+00 2.74e-01 3.95e+01 angle pdb=" C PRO A 84 " pdb=" N CYS A 85 " pdb=" CA CYS A 85 " ideal model delta sigma weight residual 121.54 132.70 -11.16 1.91e+00 2.74e-01 3.41e+01 angle pdb=" C GLN E 113 " pdb=" N ASN E 114 " pdb=" CA ASN E 114 " ideal model delta sigma weight residual 121.54 132.02 -10.48 1.91e+00 2.74e-01 3.01e+01 ... (remaining 69560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.53: 29872 35.53 - 71.06: 1035 71.06 - 106.59: 58 106.59 - 142.12: 0 142.12 - 177.65: 2 Dihedral angle restraints: 30967 sinusoidal: 13309 harmonic: 17658 Sorted by residual: dihedral pdb=" CA VAL R 426 " pdb=" C VAL R 426 " pdb=" N PRO R 427 " pdb=" CA PRO R 427 " ideal model delta harmonic sigma weight residual 180.00 120.10 59.90 0 5.00e+00 4.00e-02 1.44e+02 dihedral pdb=" CA ALA B 116 " pdb=" C ALA B 116 " pdb=" N VAL B 117 " pdb=" CA VAL B 117 " ideal model delta harmonic sigma weight residual 180.00 -132.48 -47.52 0 5.00e+00 4.00e-02 9.03e+01 dihedral pdb=" CA ASP Q 280 " pdb=" C ASP Q 280 " pdb=" N ILE Q 281 " pdb=" CA ILE Q 281 " ideal model delta harmonic sigma weight residual 180.00 -134.38 -45.62 0 5.00e+00 4.00e-02 8.32e+01 ... (remaining 30964 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 7311 0.111 - 0.222: 440 0.222 - 0.333: 16 0.333 - 0.444: 2 0.444 - 0.555: 1 Chirality restraints: 7770 Sorted by residual: chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" CB ILE P 351 " pdb=" CA ILE P 351 " pdb=" CG1 ILE P 351 " pdb=" CG2 ILE P 351 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.37 2.00e-01 2.50e+01 3.39e+00 chirality pdb=" CB VAL P 393 " pdb=" CA VAL P 393 " pdb=" CG1 VAL P 393 " pdb=" CG2 VAL P 393 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 7767 not shown) Planarity restraints: 8639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 426 " 0.077 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO R 427 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO R 427 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO R 427 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP P 443 " -0.059 5.00e-02 4.00e+02 8.86e-02 1.26e+01 pdb=" N PRO P 444 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO P 444 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO P 444 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Q 386 " 0.054 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO Q 387 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO Q 387 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO Q 387 " 0.047 5.00e-02 4.00e+02 ... (remaining 8636 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 873 2.64 - 3.21: 42470 3.21 - 3.77: 74541 3.77 - 4.34: 102441 4.34 - 4.90: 169953 Nonbonded interactions: 390278 Sorted by model distance: nonbonded pdb=" OD1 ASP A 627 " pdb="MG MG A1703 " model vdw 2.081 2.170 nonbonded pdb=" OD1 ASP A 631 " pdb="MG MG A1703 " model vdw 2.203 2.170 nonbonded pdb=" OD2 ASP O 241 " pdb=" OG1 THR O 378 " model vdw 2.226 2.440 nonbonded pdb=" O GLU A 258 " pdb=" OG1 THR A 262 " model vdw 2.257 2.440 nonbonded pdb=" OG1 THR A 12 " pdb=" OE1 GLU B1201 " model vdw 2.268 2.440 ... (remaining 390273 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.330 Construct map_model_manager: 0.050 Extract box with map and model: 17.160 Check model and map are aligned: 0.560 Set scattering table: 0.350 Process input model: 121.050 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.160 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:2.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 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 : 0.009 0.130 51242 Z= 0.607 Angle : 0.984 26.361 69565 Z= 0.544 Chirality : 0.058 0.555 7770 Planarity : 0.007 0.116 8639 Dihedral : 17.255 177.651 19513 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.10 % Rotamer: Outliers : 0.59 % Allowed : 12.37 % Favored : 87.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.95 % Twisted General : 0.35 % 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: -5.18 (0.08), residues: 5943 helix: -4.43 (0.05), residues: 2016 sheet: -2.60 (0.16), residues: 801 loop : -2.97 (0.09), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 174 HIS 0.019 0.002 HIS P 58 PHE 0.030 0.003 PHE A 57 TYR 0.045 0.003 TYR B1033 ARG 0.009 0.001 ARG R 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 671 time to evaluate : 4.507 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: A 433 ASP cc_start: 0.6676 (t0) cc_final: 0.6269 (t0) REVERT: A 646 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 917 MET cc_start: 0.9127 (ttp) cc_final: 0.8919 (ttp) REVERT: A 928 MET cc_start: 0.8902 (mtm) cc_final: 0.8676 (mtp) REVERT: B 217 ILE cc_start: 0.8926 (mm) cc_final: 0.8583 (tt) REVERT: B 287 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7789 (mt-10) REVERT: B 430 MET cc_start: 0.7629 (ttp) cc_final: 0.7387 (ttt) REVERT: B 434 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7003 (mtt180) REVERT: B 461 MET cc_start: 0.8827 (mmm) cc_final: 0.8104 (mmm) REVERT: B 1139 LYS cc_start: 0.8253 (mtpt) cc_final: 0.8025 (ttpt) REVERT: C 81 GLU cc_start: 0.7252 (tp30) cc_final: 0.7026 (tp30) REVERT: D 47 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8109 (mmtt) REVERT: E 93 MET cc_start: 0.7656 (tpp) cc_final: 0.7401 (tpt) REVERT: E 182 ASP cc_start: 0.8935 (t70) cc_final: 0.8617 (t0) REVERT: F 60 GLN cc_start: 0.8042 (tt0) cc_final: 0.7403 (tp40) REVERT: G 151 ASP cc_start: 0.6769 (t0) cc_final: 0.6539 (t0) REVERT: K 81 MET cc_start: 0.8751 (mmm) cc_final: 0.8281 (mmt) REVERT: K 103 ILE cc_start: 0.9494 (mm) cc_final: 0.9208 (mm) REVERT: M 18 GLN cc_start: 0.7800 (mm110) cc_final: 0.7562 (mm110) REVERT: M 51 PHE cc_start: 0.8046 (m-80) cc_final: 0.7824 (m-10) REVERT: M 97 VAL cc_start: 0.9316 (t) cc_final: 0.9051 (m) REVERT: M 101 VAL cc_start: 0.8269 (t) cc_final: 0.7953 (p) REVERT: O 467 MET cc_start: 0.7053 (mmt) cc_final: 0.6712 (mpp) REVERT: O 527 MET cc_start: 0.7911 (tpp) cc_final: 0.7653 (tpp) REVERT: P 419 ARG cc_start: 0.6690 (tmt170) cc_final: 0.5190 (ttp-170) REVERT: P 471 MET cc_start: 0.8439 (mtt) cc_final: 0.8002 (mtm) REVERT: Q 158 MET cc_start: 0.8160 (mmm) cc_final: 0.7867 (mmm) REVERT: Q 360 LYS cc_start: 0.8754 (mttt) cc_final: 0.7960 (mptt) outliers start: 32 outliers final: 22 residues processed: 701 average time/residue: 0.5540 time to fit residues: 622.9901 Evaluate side-chains 478 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 456 time to evaluate : 4.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain Q residue 419 LEU Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 294 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 508 optimal weight: 6.9990 chunk 456 optimal weight: 0.0040 chunk 253 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 307 optimal weight: 0.0050 chunk 243 optimal weight: 0.9980 chunk 471 optimal weight: 8.9990 chunk 182 optimal weight: 0.7980 chunk 286 optimal weight: 0.7980 chunk 351 optimal weight: 4.9990 chunk 546 optimal weight: 20.0000 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 378 HIS A 400 ASN A 458 GLN ** A 610 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 GLN ** A1141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1514 ASN A1564 ASN A1567 ASN B 50 ASN B 80 ASN B 197 ASN B 248 ASN B 321 GLN B 422 GLN B 469 ASN B 547 HIS B 598 HIS B 669 GLN B 683 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 ASN B 921 HIS B1089 GLN B1171 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 HIS C 207 HIS C 301 ASN C 330 ASN D 81 ASN E 115 ASN H 52 GLN H 137 GLN H 139 ASN I 27 ASN M 16 GLN N 51 GLN N 52 GLN O 77 GLN ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 362 ASN O 422 GLN O 451 ASN ** P 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 348 HIS P 401 ASN P 487 ASN P 554 ASN P 571 HIS P 687 GLN ** P 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN Q 85 GLN ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 155 GLN Q 250 GLN Q 368 GLN Q 389 GLN Q 435 GLN Q 507 ASN R 189 GLN R 223 ASN R 298 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 51242 Z= 0.167 Angle : 0.601 13.286 69565 Z= 0.323 Chirality : 0.043 0.311 7770 Planarity : 0.005 0.109 8639 Dihedral : 13.398 179.635 7440 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 1.64 % Allowed : 16.13 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.83 (0.09), residues: 5943 helix: -2.73 (0.08), residues: 2141 sheet: -1.93 (0.18), residues: 788 loop : -2.55 (0.10), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 203 HIS 0.010 0.001 HIS R 304 PHE 0.025 0.001 PHE O 505 TYR 0.019 0.001 TYR A1302 ARG 0.009 0.000 ARG Q 512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 645 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 556 time to evaluate : 4.474 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: A 928 MET cc_start: 0.8862 (mtm) cc_final: 0.8542 (mtp) REVERT: B 287 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7657 (mt-10) REVERT: B 461 MET cc_start: 0.8691 (mmm) cc_final: 0.7895 (mmm) REVERT: B 941 THR cc_start: 0.8875 (OUTLIER) cc_final: 0.8604 (p) REVERT: C 81 GLU cc_start: 0.7157 (tp30) cc_final: 0.6937 (tp30) REVERT: D 47 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8033 (mmtt) REVERT: D 89 LEU cc_start: 0.9342 (mt) cc_final: 0.9100 (mt) REVERT: D 91 ARG cc_start: 0.8796 (mtm110) cc_final: 0.8502 (mtp180) REVERT: E 25 ASP cc_start: 0.8374 (m-30) cc_final: 0.8073 (m-30) REVERT: E 58 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8040 (ttm) REVERT: E 93 MET cc_start: 0.7896 (tpp) cc_final: 0.7576 (tpt) REVERT: G 151 ASP cc_start: 0.6585 (t0) cc_final: 0.6338 (t0) REVERT: H 105 GLU cc_start: 0.6802 (pt0) cc_final: 0.6563 (pt0) REVERT: K 81 MET cc_start: 0.8754 (mmm) cc_final: 0.8443 (mmt) REVERT: M 18 GLN cc_start: 0.7786 (mm110) cc_final: 0.7548 (mm110) REVERT: M 97 VAL cc_start: 0.9239 (t) cc_final: 0.9014 (m) REVERT: O 424 LEU cc_start: 0.8934 (tp) cc_final: 0.8719 (tp) REVERT: O 467 MET cc_start: 0.6930 (mmt) cc_final: 0.6566 (mpp) REVERT: P 419 ARG cc_start: 0.6479 (tmt170) cc_final: 0.3943 (ttp80) REVERT: P 471 MET cc_start: 0.7982 (mtt) cc_final: 0.7392 (ptp) REVERT: Q 155 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.7052 (mm110) REVERT: Q 317 MET cc_start: 0.7588 (tmm) cc_final: 0.7193 (tmm) REVERT: Q 336 GLU cc_start: 0.8368 (mm-30) cc_final: 0.7613 (mm-30) REVERT: Q 360 LYS cc_start: 0.8735 (mttt) cc_final: 0.8120 (mptt) outliers start: 89 outliers final: 51 residues processed: 625 average time/residue: 0.4892 time to fit residues: 514.5260 Evaluate side-chains 505 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 451 time to evaluate : 4.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain I residue 27 ASN Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain Q residue 155 GLN Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 303 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 454 optimal weight: 6.9990 chunk 372 optimal weight: 0.9980 chunk 150 optimal weight: 0.8980 chunk 547 optimal weight: 10.0000 chunk 591 optimal weight: 10.0000 chunk 487 optimal weight: 10.0000 chunk 543 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 439 optimal weight: 10.0000 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS A 694 GLN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1141 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 543 ASN ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 899 GLN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN F 59 GLN I 27 ASN N 51 GLN ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 117 GLN P 543 ASN P 635 ASN ** P 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 194 GLN Q 482 HIS R 260 ASN R 402 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 51242 Z= 0.370 Angle : 0.652 11.589 69565 Z= 0.344 Chirality : 0.046 0.256 7770 Planarity : 0.005 0.108 8639 Dihedral : 13.359 178.673 7431 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.08 % Favored : 91.84 % Rotamer: Outliers : 2.87 % Allowed : 18.54 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.13 (0.10), residues: 5943 helix: -1.72 (0.10), residues: 2114 sheet: -1.84 (0.18), residues: 800 loop : -2.41 (0.10), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP Q 20 HIS 0.009 0.001 HIS B1038 PHE 0.022 0.002 PHE R 162 TYR 0.027 0.002 TYR O 445 ARG 0.007 0.000 ARG O 530 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 461 time to evaluate : 4.519 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: A 928 MET cc_start: 0.8931 (mtm) cc_final: 0.8699 (mtp) REVERT: B 147 ASN cc_start: 0.7409 (OUTLIER) cc_final: 0.7191 (t0) REVERT: B 287 GLU cc_start: 0.8023 (mt-10) cc_final: 0.7675 (mt-10) REVERT: B 307 GLU cc_start: 0.7522 (tm-30) cc_final: 0.7204 (tm-30) REVERT: B 461 MET cc_start: 0.8801 (mmm) cc_final: 0.8046 (mmm) REVERT: B 767 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8355 (t0) REVERT: B 941 THR cc_start: 0.9074 (OUTLIER) cc_final: 0.8781 (p) REVERT: C 81 GLU cc_start: 0.7267 (tp30) cc_final: 0.7064 (tp30) REVERT: D 91 ARG cc_start: 0.8913 (mtm110) cc_final: 0.8301 (mtp180) REVERT: E 25 ASP cc_start: 0.8418 (m-30) cc_final: 0.8099 (m-30) REVERT: E 58 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8306 (ttm) REVERT: E 93 MET cc_start: 0.8134 (tpp) cc_final: 0.7792 (tpt) REVERT: G 151 ASP cc_start: 0.6566 (t0) cc_final: 0.6087 (t0) REVERT: H 105 GLU cc_start: 0.6728 (pt0) cc_final: 0.6474 (pt0) REVERT: K 81 MET cc_start: 0.8789 (mmm) cc_final: 0.8378 (mmt) REVERT: L 42 ARG cc_start: 0.6402 (ttm110) cc_final: 0.5221 (tpt-90) REVERT: M 18 GLN cc_start: 0.7798 (mm110) cc_final: 0.7586 (mm110) REVERT: M 97 VAL cc_start: 0.9252 (t) cc_final: 0.9046 (m) REVERT: N 178 GLU cc_start: 0.7617 (pm20) cc_final: 0.7413 (pm20) REVERT: O 467 MET cc_start: 0.7031 (mmt) cc_final: 0.6750 (mpp) REVERT: P 195 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.6410 (p0) REVERT: P 419 ARG cc_start: 0.6484 (tmt170) cc_final: 0.4187 (ttp80) REVERT: P 471 MET cc_start: 0.8059 (mtt) cc_final: 0.7692 (mtm) REVERT: Q 360 LYS cc_start: 0.8796 (mttt) cc_final: 0.8265 (mptt) outliers start: 156 outliers final: 108 residues processed: 582 average time/residue: 0.4729 time to fit residues: 468.7106 Evaluate side-chains 542 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 429 time to evaluate : 4.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 727 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1332 GLU Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 184 ASN Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 418 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 541 optimal weight: 20.0000 chunk 411 optimal weight: 0.9980 chunk 284 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 261 optimal weight: 6.9990 chunk 367 optimal weight: 1.9990 chunk 549 optimal weight: 10.0000 chunk 581 optimal weight: 0.9990 chunk 287 optimal weight: 5.9990 chunk 520 optimal weight: 8.9990 chunk 156 optimal weight: 0.2980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 ASN ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1191 GLN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 ASN ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 769 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 384 GLN R 287 ASN R 298 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 51242 Z= 0.164 Angle : 0.541 9.555 69565 Z= 0.288 Chirality : 0.042 0.244 7770 Planarity : 0.004 0.108 8639 Dihedral : 13.020 178.068 7431 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 2.63 % Allowed : 19.63 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.10), residues: 5943 helix: -1.04 (0.11), residues: 2133 sheet: -1.55 (0.18), residues: 808 loop : -2.20 (0.11), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 20 HIS 0.006 0.001 HIS P 58 PHE 0.032 0.001 PHE R 438 TYR 0.031 0.001 TYR O 445 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 497 time to evaluate : 4.511 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: A 646 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7831 (tt0) REVERT: A 808 LYS cc_start: 0.7764 (tptt) cc_final: 0.7189 (tptt) REVERT: B 287 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7692 (mt-10) REVERT: B 307 GLU cc_start: 0.7459 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 461 MET cc_start: 0.8724 (mmm) cc_final: 0.7930 (mmm) REVERT: B 783 MET cc_start: 0.8595 (mtm) cc_final: 0.8225 (mtm) REVERT: B 941 THR cc_start: 0.9030 (OUTLIER) cc_final: 0.8773 (p) REVERT: C 81 GLU cc_start: 0.7227 (tp30) cc_final: 0.6997 (tp30) REVERT: D 91 ARG cc_start: 0.8820 (mtm110) cc_final: 0.8182 (mtp180) REVERT: E 25 ASP cc_start: 0.8373 (m-30) cc_final: 0.8033 (m-30) REVERT: E 58 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8206 (ttm) REVERT: E 93 MET cc_start: 0.8149 (tpp) cc_final: 0.7674 (tpt) REVERT: G 151 ASP cc_start: 0.6539 (t0) cc_final: 0.6207 (t0) REVERT: I 27 ASN cc_start: 0.6715 (m-40) cc_final: 0.6438 (t0) REVERT: K 81 MET cc_start: 0.8747 (mmm) cc_final: 0.8466 (mmt) REVERT: L 42 ARG cc_start: 0.6303 (ttm110) cc_final: 0.5115 (tpt-90) REVERT: M 18 GLN cc_start: 0.7792 (mm110) cc_final: 0.7569 (mm110) REVERT: M 97 VAL cc_start: 0.9233 (t) cc_final: 0.9005 (m) REVERT: N 176 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6982 (p0) REVERT: O 467 MET cc_start: 0.7004 (mmt) cc_final: 0.6655 (mpp) REVERT: O 602 TYR cc_start: 0.7647 (OUTLIER) cc_final: 0.6865 (m-80) REVERT: P 419 ARG cc_start: 0.6527 (tmt170) cc_final: 0.4416 (ttp80) REVERT: P 471 MET cc_start: 0.7939 (mtt) cc_final: 0.7405 (ptp) REVERT: P 693 PHE cc_start: 0.5726 (m-80) cc_final: 0.5328 (m-80) REVERT: Q 360 LYS cc_start: 0.8815 (mttt) cc_final: 0.8284 (mptt) REVERT: R 246 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7366 (pm20) outliers start: 143 outliers final: 86 residues processed: 608 average time/residue: 0.4820 time to fit residues: 497.3343 Evaluate side-chains 541 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 450 time to evaluate : 4.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1165 ASN Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain O residue 602 TYR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 10 CYS Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 419 LEU Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 246 GLN Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 484 optimal weight: 10.0000 chunk 330 optimal weight: 0.0010 chunk 8 optimal weight: 4.9990 chunk 433 optimal weight: 20.0000 chunk 240 optimal weight: 0.9980 chunk 496 optimal weight: 10.0000 chunk 402 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 297 optimal weight: 8.9990 chunk 522 optimal weight: 10.0000 chunk 146 optimal weight: 3.9990 overall best weight: 2.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 694 GLN ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1089 GLN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN E 115 ASN ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 635 ASN P 769 GLN Q 145 ASN Q 384 GLN R 298 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 51242 Z= 0.325 Angle : 0.602 10.302 69565 Z= 0.317 Chirality : 0.045 0.249 7770 Planarity : 0.005 0.110 8639 Dihedral : 13.069 179.192 7428 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.93 % Favored : 92.02 % Rotamer: Outliers : 3.44 % Allowed : 20.66 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.10), residues: 5943 helix: -0.80 (0.11), residues: 2126 sheet: -1.57 (0.18), residues: 796 loop : -2.16 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 365 HIS 0.008 0.001 HIS B1038 PHE 0.023 0.002 PHE R 438 TYR 0.028 0.002 TYR O 445 ARG 0.007 0.000 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 451 time to evaluate : 4.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 LYS cc_start: 0.8660 (pttm) cc_final: 0.8385 (pttp) REVERT: B 217 ILE cc_start: 0.8830 (mm) cc_final: 0.8588 (tt) REVERT: B 287 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7727 (mt-10) REVERT: B 307 GLU cc_start: 0.7464 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 461 MET cc_start: 0.8800 (mmm) cc_final: 0.8022 (mmm) REVERT: B 767 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8410 (t0) REVERT: B 941 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8836 (p) REVERT: C 81 GLU cc_start: 0.7278 (tp30) cc_final: 0.7056 (tp30) REVERT: C 188 ASP cc_start: 0.7706 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: D 91 ARG cc_start: 0.8808 (mtm110) cc_final: 0.8096 (mtp180) REVERT: E 25 ASP cc_start: 0.8405 (m-30) cc_final: 0.8077 (m-30) REVERT: E 58 MET cc_start: 0.8724 (OUTLIER) cc_final: 0.8370 (ttm) REVERT: E 93 MET cc_start: 0.8180 (tpp) cc_final: 0.7688 (tpt) REVERT: G 151 ASP cc_start: 0.6645 (t0) cc_final: 0.6276 (t0) REVERT: K 81 MET cc_start: 0.8773 (mmm) cc_final: 0.8402 (mmt) REVERT: L 57 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8827 (mt) REVERT: M 18 GLN cc_start: 0.7830 (mm110) cc_final: 0.7600 (mm110) REVERT: M 81 PHE cc_start: 0.6335 (t80) cc_final: 0.6134 (t80) REVERT: N 176 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6431 (p0) REVERT: N 178 GLU cc_start: 0.7442 (pm20) cc_final: 0.7176 (pm20) REVERT: O 467 MET cc_start: 0.7005 (mmt) cc_final: 0.6649 (mpp) REVERT: O 483 ILE cc_start: 0.7254 (OUTLIER) cc_final: 0.6933 (pt) REVERT: O 602 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.6916 (m-80) REVERT: P 195 ASN cc_start: 0.7497 (OUTLIER) cc_final: 0.6940 (p0) REVERT: P 201 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5038 (mp0) REVERT: P 419 ARG cc_start: 0.6384 (tmt170) cc_final: 0.4449 (ttp80) REVERT: P 681 GLN cc_start: 0.7562 (tp-100) cc_final: 0.6756 (tm-30) REVERT: P 769 GLN cc_start: 0.3391 (OUTLIER) cc_final: 0.2043 (tt0) REVERT: Q 360 LYS cc_start: 0.8901 (mttt) cc_final: 0.8372 (mptt) REVERT: R 165 ILE cc_start: 0.6277 (OUTLIER) cc_final: 0.6046 (tt) REVERT: R 246 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7529 (pm20) outliers start: 187 outliers final: 139 residues processed: 601 average time/residue: 0.4708 time to fit residues: 484.8928 Evaluate side-chains 587 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 435 time to evaluate : 4.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 767 ASN Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 176 ASP Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 483 ILE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 602 TYR Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 201 GLU Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 579 ASN Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain P residue 769 GLN Chi-restraints excluded: chain P residue 778 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 10 CYS Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 23 ILE Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 184 ASN Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 246 GLN Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 195 optimal weight: 2.9990 chunk 524 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 341 optimal weight: 0.9990 chunk 143 optimal weight: 6.9990 chunk 582 optimal weight: 6.9990 chunk 483 optimal weight: 10.0000 chunk 269 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 192 optimal weight: 10.0000 chunk 305 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 767 ASN ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN E 115 ASN G 75 ASN G 161 ASN N 51 GLN N 101 GLN P 278 HIS ** Q 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 HIS R 298 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 51242 Z= 0.461 Angle : 0.684 9.373 69565 Z= 0.359 Chirality : 0.047 0.249 7770 Planarity : 0.005 0.111 8639 Dihedral : 13.229 179.791 7428 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.17 % Favored : 90.76 % Rotamer: Outliers : 4.49 % Allowed : 20.66 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.10), residues: 5943 helix: -0.82 (0.11), residues: 2126 sheet: -1.70 (0.18), residues: 802 loop : -2.19 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 365 HIS 0.010 0.001 HIS B1038 PHE 0.022 0.002 PHE R 162 TYR 0.030 0.002 TYR O 445 ARG 0.007 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 684 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 440 time to evaluate : 5.137 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: A 358 ASP cc_start: 0.6942 (OUTLIER) cc_final: 0.6490 (m-30) REVERT: A 462 LYS cc_start: 0.8676 (pttm) cc_final: 0.8400 (pttp) REVERT: A 574 ASN cc_start: 0.9018 (OUTLIER) cc_final: 0.8791 (p0) REVERT: A 672 ASP cc_start: 0.8547 (m-30) cc_final: 0.8192 (m-30) REVERT: A 928 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8628 (mtp) REVERT: B 217 ILE cc_start: 0.8851 (mm) cc_final: 0.8560 (tt) REVERT: B 287 GLU cc_start: 0.8054 (mt-10) cc_final: 0.7736 (mt-10) REVERT: B 307 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7315 (tp30) REVERT: B 461 MET cc_start: 0.8844 (mmm) cc_final: 0.8039 (mmm) REVERT: B 941 THR cc_start: 0.9185 (OUTLIER) cc_final: 0.8880 (p) REVERT: C 81 GLU cc_start: 0.7336 (tp30) cc_final: 0.7086 (tp30) REVERT: C 188 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.6924 (m-30) REVERT: E 58 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8476 (ttm) REVERT: E 93 MET cc_start: 0.8302 (tpp) cc_final: 0.7753 (tpt) REVERT: G 151 ASP cc_start: 0.6734 (t0) cc_final: 0.6490 (t0) REVERT: K 81 MET cc_start: 0.8811 (mmm) cc_final: 0.8422 (mmt) REVERT: L 57 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8814 (mt) REVERT: M 18 GLN cc_start: 0.7841 (mm110) cc_final: 0.7615 (mm110) REVERT: M 81 PHE cc_start: 0.6364 (t80) cc_final: 0.6065 (t80) REVERT: O 467 MET cc_start: 0.7084 (mmt) cc_final: 0.6790 (mpp) REVERT: O 602 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.6919 (m-80) REVERT: P 195 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.6987 (p0) REVERT: P 201 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5077 (mp0) REVERT: P 419 ARG cc_start: 0.6352 (tmt170) cc_final: 0.4242 (ttp80) REVERT: P 471 MET cc_start: 0.7868 (mtt) cc_final: 0.7526 (ptp) REVERT: P 681 GLN cc_start: 0.7555 (tp-100) cc_final: 0.6728 (tm-30) REVERT: Q 360 LYS cc_start: 0.8885 (mttt) cc_final: 0.8394 (mptt) REVERT: Q 385 PHE cc_start: 0.7638 (OUTLIER) cc_final: 0.6833 (m-80) REVERT: R 165 ILE cc_start: 0.6320 (OUTLIER) cc_final: 0.6077 (tt) outliers start: 244 outliers final: 185 residues processed: 641 average time/residue: 0.4516 time to fit residues: 503.4577 Evaluate side-chains 619 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 422 time to evaluate : 4.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 326 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 896 THR Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 938 VAL Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 941 SER Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1118 VAL Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1193 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 132 SER Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 806 THR Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 VAL Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 89 LEU Chi-restraints excluded: chain E residue 22 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 88 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 29 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain I residue 49 THR Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 56 LEU Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 173 THR Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 64 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 439 ILE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 602 TYR Chi-restraints excluded: chain O residue 611 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 201 GLU Chi-restraints excluded: chain P residue 213 VAL Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 247 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 439 LYS Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 579 ASN Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain P residue 778 ASP Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 10 CYS Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 23 ILE Chi-restraints excluded: chain Q residue 28 THR Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 385 PHE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain Q residue 416 ILE Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain R residue 165 ILE Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 184 ASN Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 352 TRP Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 438 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 561 optimal weight: 10.0000 chunk 65 optimal weight: 0.8980 chunk 331 optimal weight: 7.9990 chunk 425 optimal weight: 1.9990 chunk 329 optimal weight: 0.8980 chunk 490 optimal weight: 8.9990 chunk 325 optimal weight: 5.9990 chunk 580 optimal weight: 0.9980 chunk 363 optimal weight: 6.9990 chunk 353 optimal weight: 0.7980 chunk 267 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 433 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 745 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 893 ASN D 23 HIS E 115 ASN G 161 ASN ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 384 GLN R 298 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 51242 Z= 0.160 Angle : 0.553 11.033 69565 Z= 0.292 Chirality : 0.043 0.241 7770 Planarity : 0.004 0.110 8639 Dihedral : 12.934 178.212 7428 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.40 % Rotamer: Outliers : 3.15 % Allowed : 22.30 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.11), residues: 5943 helix: -0.39 (0.11), residues: 2135 sheet: -1.49 (0.18), residues: 815 loop : -2.00 (0.11), residues: 2993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP P 365 HIS 0.006 0.001 HIS P 58 PHE 0.031 0.001 PHE P 675 TYR 0.034 0.001 TYR E 112 ARG 0.007 0.000 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 473 time to evaluate : 4.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8331 (t80) cc_final: 0.7861 (t80) REVERT: A 462 LYS cc_start: 0.8575 (pttm) cc_final: 0.8320 (pttp) REVERT: A 574 ASN cc_start: 0.8995 (OUTLIER) cc_final: 0.8764 (p0) REVERT: A 672 ASP cc_start: 0.7958 (m-30) cc_final: 0.7659 (m-30) REVERT: A 808 LYS cc_start: 0.7855 (tptt) cc_final: 0.7194 (tptt) REVERT: A 928 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8688 (mtp) REVERT: B 94 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7565 (tttp) REVERT: B 217 ILE cc_start: 0.8857 (mm) cc_final: 0.8591 (tt) REVERT: B 287 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7664 (mt-10) REVERT: B 461 MET cc_start: 0.8751 (mmm) cc_final: 0.8340 (mmt) REVERT: B 941 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8809 (p) REVERT: D 91 ARG cc_start: 0.8778 (mtm110) cc_final: 0.8070 (mtp180) REVERT: E 25 ASP cc_start: 0.8371 (m-30) cc_final: 0.8050 (m-30) REVERT: E 93 MET cc_start: 0.8218 (tpp) cc_final: 0.7837 (tpt) REVERT: G 151 ASP cc_start: 0.6654 (t0) cc_final: 0.6339 (t0) REVERT: I 27 ASN cc_start: 0.6539 (m-40) cc_final: 0.6284 (t0) REVERT: K 81 MET cc_start: 0.8757 (mmm) cc_final: 0.8483 (mmt) REVERT: M 18 GLN cc_start: 0.7760 (mm110) cc_final: 0.7533 (mm110) REVERT: O 51 MET cc_start: 0.7116 (tpp) cc_final: 0.6798 (tpt) REVERT: O 467 MET cc_start: 0.6984 (mmt) cc_final: 0.6619 (mpp) REVERT: O 602 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.7011 (m-80) REVERT: P 195 ASN cc_start: 0.7782 (OUTLIER) cc_final: 0.6866 (p0) REVERT: P 201 GLU cc_start: 0.6288 (OUTLIER) cc_final: 0.4823 (mp0) REVERT: P 419 ARG cc_start: 0.6204 (tmt170) cc_final: 0.4311 (ttp80) REVERT: P 471 MET cc_start: 0.7852 (mtt) cc_final: 0.7457 (ptp) REVERT: P 681 GLN cc_start: 0.7531 (tp-100) cc_final: 0.6812 (tm-30) REVERT: P 693 PHE cc_start: 0.5785 (m-80) cc_final: 0.5337 (m-80) REVERT: Q 360 LYS cc_start: 0.8757 (mttt) cc_final: 0.8220 (mptt) REVERT: Q 385 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6684 (m-80) REVERT: R 227 HIS cc_start: 0.7185 (m90) cc_final: 0.6808 (m90) outliers start: 171 outliers final: 127 residues processed: 610 average time/residue: 0.4759 time to fit residues: 497.3352 Evaluate side-chains 573 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 438 time to evaluate : 4.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1121 ASP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 94 LYS Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 893 ASN Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 602 TYR Chi-restraints excluded: chain O residue 611 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 201 GLU Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 372 ILE Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 439 LYS Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 579 ASN Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain P residue 778 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 10 CYS Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 385 PHE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 352 TRP Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 358 optimal weight: 6.9990 chunk 231 optimal weight: 5.9990 chunk 346 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 112 optimal weight: 0.0070 chunk 368 optimal weight: 0.0670 chunk 395 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 456 optimal weight: 6.9990 overall best weight: 1.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 745 GLN B 893 ASN ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 51 GLN ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 51242 Z= 0.212 Angle : 0.562 12.565 69565 Z= 0.295 Chirality : 0.043 0.245 7770 Planarity : 0.004 0.109 8639 Dihedral : 12.864 178.669 7428 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.87 % Favored : 93.08 % Rotamer: Outliers : 3.22 % Allowed : 22.70 % Favored : 74.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.11), residues: 5943 helix: -0.26 (0.11), residues: 2145 sheet: -1.44 (0.18), residues: 819 loop : -1.94 (0.11), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP O 125 HIS 0.008 0.001 HIS P 58 PHE 0.041 0.001 PHE R 438 TYR 0.030 0.001 TYR O 445 ARG 0.008 0.000 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 446 time to evaluate : 4.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8309 (t80) cc_final: 0.7802 (t80) REVERT: A 462 LYS cc_start: 0.8553 (pttm) cc_final: 0.8308 (pttp) REVERT: A 574 ASN cc_start: 0.9009 (OUTLIER) cc_final: 0.8782 (p0) REVERT: A 808 LYS cc_start: 0.7875 (tptt) cc_final: 0.7192 (tptt) REVERT: A 928 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8694 (mtp) REVERT: B 217 ILE cc_start: 0.8884 (mm) cc_final: 0.8620 (tt) REVERT: B 287 GLU cc_start: 0.7896 (mt-10) cc_final: 0.7625 (mt-10) REVERT: B 461 MET cc_start: 0.8776 (mmm) cc_final: 0.7950 (mmm) REVERT: B 941 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8832 (p) REVERT: E 93 MET cc_start: 0.8336 (tpp) cc_final: 0.7959 (tpt) REVERT: I 27 ASN cc_start: 0.6640 (m-40) cc_final: 0.6370 (t0) REVERT: K 81 MET cc_start: 0.8778 (mmm) cc_final: 0.8499 (mmt) REVERT: M 18 GLN cc_start: 0.7835 (mm110) cc_final: 0.7625 (mm110) REVERT: O 467 MET cc_start: 0.7024 (mmt) cc_final: 0.6659 (mpp) REVERT: O 602 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.6992 (m-80) REVERT: P 195 ASN cc_start: 0.7799 (OUTLIER) cc_final: 0.7278 (p0) REVERT: P 201 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.4915 (mp0) REVERT: P 419 ARG cc_start: 0.6250 (tmt170) cc_final: 0.4395 (ttp80) REVERT: P 471 MET cc_start: 0.7820 (mtt) cc_final: 0.7480 (ptp) REVERT: P 681 GLN cc_start: 0.7591 (tp-100) cc_final: 0.7373 (mm110) REVERT: P 693 PHE cc_start: 0.5824 (m-80) cc_final: 0.5414 (m-80) REVERT: Q 360 LYS cc_start: 0.8732 (mttt) cc_final: 0.8211 (mptt) REVERT: Q 385 PHE cc_start: 0.7544 (OUTLIER) cc_final: 0.6715 (m-80) REVERT: R 227 HIS cc_start: 0.7231 (m90) cc_final: 0.6863 (m90) REVERT: R 438 PHE cc_start: 0.7664 (OUTLIER) cc_final: 0.5917 (m-80) outliers start: 175 outliers final: 144 residues processed: 590 average time/residue: 0.4659 time to fit residues: 475.4701 Evaluate side-chains 589 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 437 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 PHE Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 703 GLU Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1203 ASN Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 832 TRP Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1036 LEU Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1181 VAL Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 378 THR Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 602 TYR Chi-restraints excluded: chain O residue 611 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 201 GLU Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 320 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 372 ILE Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 427 SER Chi-restraints excluded: chain P residue 439 LYS Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 579 ASN Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain P residue 778 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 10 CYS Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 23 ILE Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 385 PHE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 293 ILE Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 438 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 527 optimal weight: 8.9990 chunk 555 optimal weight: 8.9990 chunk 507 optimal weight: 20.0000 chunk 540 optimal weight: 20.0000 chunk 325 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 424 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 488 optimal weight: 5.9990 chunk 511 optimal weight: 2.9990 chunk 538 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN A 639 GLN ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1065 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** G 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 161 ASN N 51 GLN ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 51242 Z= 0.493 Angle : 0.712 12.313 69565 Z= 0.371 Chirality : 0.049 0.430 7770 Planarity : 0.005 0.109 8639 Dihedral : 13.144 179.747 7427 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.56 % Favored : 90.39 % Rotamer: Outliers : 3.55 % Allowed : 22.70 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.11 % Cis-general : 0.03 % Twisted Proline : 1.17 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 5943 helix: -0.56 (0.11), residues: 2123 sheet: -1.61 (0.18), residues: 794 loop : -2.07 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP P 365 HIS 0.012 0.001 HIS B1038 PHE 0.039 0.002 PHE R 438 TYR 0.028 0.002 TYR O 445 ARG 0.008 0.001 ARG B 560 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 435 time to evaluate : 4.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8393 (t80) cc_final: 0.7923 (t80) REVERT: A 462 LYS cc_start: 0.8593 (pttm) cc_final: 0.8315 (pttp) REVERT: A 574 ASN cc_start: 0.9025 (OUTLIER) cc_final: 0.8808 (p0) REVERT: A 808 LYS cc_start: 0.7981 (tptt) cc_final: 0.7261 (tptt) REVERT: A 928 MET cc_start: 0.8812 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: A 1074 TYR cc_start: 0.8257 (m-80) cc_final: 0.8010 (m-80) REVERT: B 217 ILE cc_start: 0.8926 (mm) cc_final: 0.8618 (tt) REVERT: B 287 GLU cc_start: 0.8007 (mt-10) cc_final: 0.7691 (mt-10) REVERT: B 461 MET cc_start: 0.8836 (mmm) cc_final: 0.8041 (mmm) REVERT: B 941 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8889 (p) REVERT: C 94 ASP cc_start: 0.8757 (OUTLIER) cc_final: 0.8336 (m-30) REVERT: E 25 ASP cc_start: 0.8342 (m-30) cc_final: 0.8085 (m-30) REVERT: E 58 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8538 (ttm) REVERT: E 93 MET cc_start: 0.8305 (tpp) cc_final: 0.7945 (tpt) REVERT: I 27 ASN cc_start: 0.6417 (m-40) cc_final: 0.6118 (t0) REVERT: K 81 MET cc_start: 0.8784 (mmm) cc_final: 0.8410 (mmt) REVERT: M 18 GLN cc_start: 0.7857 (mm110) cc_final: 0.7648 (mm110) REVERT: M 81 PHE cc_start: 0.6084 (t80) cc_final: 0.5755 (t80) REVERT: N 82 ILE cc_start: 0.6799 (mt) cc_final: 0.6593 (mt) REVERT: O 328 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8056 (mm) REVERT: O 396 MET cc_start: 0.7871 (mmt) cc_final: 0.7572 (mmt) REVERT: O 467 MET cc_start: 0.7097 (mmt) cc_final: 0.6784 (mpp) REVERT: P 195 ASN cc_start: 0.7662 (OUTLIER) cc_final: 0.7095 (p0) REVERT: P 201 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.5057 (mp0) REVERT: P 419 ARG cc_start: 0.6348 (tmt170) cc_final: 0.4290 (ttp80) REVERT: P 471 MET cc_start: 0.7884 (mtt) cc_final: 0.7559 (ptp) REVERT: P 681 GLN cc_start: 0.7605 (tp-100) cc_final: 0.6871 (tm-30) REVERT: P 693 PHE cc_start: 0.5856 (m-80) cc_final: 0.5451 (m-80) REVERT: Q 360 LYS cc_start: 0.8825 (mttt) cc_final: 0.8322 (mptt) REVERT: Q 385 PHE cc_start: 0.7721 (OUTLIER) cc_final: 0.6872 (m-80) REVERT: R 227 HIS cc_start: 0.7336 (m90) cc_final: 0.7021 (m90) outliers start: 193 outliers final: 165 residues processed: 595 average time/residue: 0.5055 time to fit residues: 523.6150 Evaluate side-chains 599 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 425 time to evaluate : 5.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 199 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 634 ASN Chi-restraints excluded: chain A residue 652 ASN Chi-restraints excluded: chain A residue 655 SER Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 968 SER Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1090 ASP Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain A residue 1622 LEU Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain B residue 466 SER Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 604 ILE Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 749 THR Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 989 ASP Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1052 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1136 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1175 THR Chi-restraints excluded: chain B residue 1176 VAL Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 154 ASN Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain K residue 86 VAL Chi-restraints excluded: chain M residue 21 VAL Chi-restraints excluded: chain M residue 62 TYR Chi-restraints excluded: chain M residue 73 SER Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 611 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 201 GLU Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 427 SER Chi-restraints excluded: chain P residue 439 LYS Chi-restraints excluded: chain P residue 443 ASP Chi-restraints excluded: chain P residue 464 LEU Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 579 ASN Chi-restraints excluded: chain P residue 598 LEU Chi-restraints excluded: chain P residue 637 LEU Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 667 ASP Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain P residue 778 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 10 CYS Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 23 ILE Chi-restraints excluded: chain Q residue 29 CYS Chi-restraints excluded: chain Q residue 165 LEU Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 198 ILE Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 385 PHE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain Q residue 439 ILE Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain Q residue 513 MET Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 215 THR Chi-restraints excluded: chain R residue 245 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 352 TRP Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 355 optimal weight: 3.9990 chunk 571 optimal weight: 8.9990 chunk 348 optimal weight: 8.9990 chunk 271 optimal weight: 0.8980 chunk 397 optimal weight: 4.9990 chunk 599 optimal weight: 10.0000 chunk 551 optimal weight: 0.9980 chunk 477 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 368 optimal weight: 0.2980 chunk 292 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 ASN ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 51242 Z= 0.169 Angle : 0.565 12.681 69565 Z= 0.295 Chirality : 0.043 0.242 7770 Planarity : 0.004 0.112 8639 Dihedral : 12.846 178.491 7427 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.47 % Favored : 94.48 % Rotamer: Outliers : 2.61 % Allowed : 23.72 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.11), residues: 5943 helix: -0.18 (0.11), residues: 2135 sheet: -1.43 (0.18), residues: 818 loop : -1.88 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP O 125 HIS 0.009 0.001 HIS P 58 PHE 0.039 0.001 PHE R 438 TYR 0.029 0.001 TYR E 112 ARG 0.008 0.000 ARG B 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11886 Ramachandran restraints generated. 5943 Oldfield, 0 Emsley, 5943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 451 time to evaluate : 4.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 TYR cc_start: 0.8257 (t80) cc_final: 0.7788 (t80) REVERT: A 574 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8828 (p0) REVERT: A 808 LYS cc_start: 0.7867 (tptt) cc_final: 0.7174 (tptt) REVERT: A 928 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8688 (mtp) REVERT: B 217 ILE cc_start: 0.8875 (mm) cc_final: 0.8595 (tt) REVERT: B 287 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7645 (mt-10) REVERT: B 461 MET cc_start: 0.8743 (mmm) cc_final: 0.8351 (mmt) REVERT: B 941 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8822 (p) REVERT: D 91 ARG cc_start: 0.8589 (mtm110) cc_final: 0.8059 (mtp180) REVERT: E 25 ASP cc_start: 0.8273 (m-30) cc_final: 0.8042 (m-30) REVERT: E 93 MET cc_start: 0.8363 (tpp) cc_final: 0.7975 (tpt) REVERT: G 71 MET cc_start: 0.8645 (mmm) cc_final: 0.8410 (mmt) REVERT: G 151 ASP cc_start: 0.6606 (t0) cc_final: 0.6404 (t0) REVERT: K 81 MET cc_start: 0.8757 (mmm) cc_final: 0.8507 (mmt) REVERT: M 18 GLN cc_start: 0.7777 (mm110) cc_final: 0.7572 (mm110) REVERT: O 182 MET cc_start: 0.7675 (mmm) cc_final: 0.7198 (mmm) REVERT: O 328 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.7984 (mm) REVERT: O 396 MET cc_start: 0.7879 (mmt) cc_final: 0.7512 (mmt) REVERT: O 467 MET cc_start: 0.6965 (mmt) cc_final: 0.6610 (mpp) REVERT: P 195 ASN cc_start: 0.7622 (OUTLIER) cc_final: 0.6666 (p0) REVERT: P 419 ARG cc_start: 0.6174 (tmt170) cc_final: 0.4322 (ttp80) REVERT: P 471 MET cc_start: 0.7873 (mtt) cc_final: 0.7480 (ptp) REVERT: P 693 PHE cc_start: 0.5790 (m-80) cc_final: 0.5369 (m-80) REVERT: Q 360 LYS cc_start: 0.8737 (mttt) cc_final: 0.8207 (mptt) REVERT: Q 385 PHE cc_start: 0.7570 (OUTLIER) cc_final: 0.6637 (m-80) REVERT: R 227 HIS cc_start: 0.7171 (m90) cc_final: 0.6810 (m90) outliers start: 142 outliers final: 125 residues processed: 565 average time/residue: 0.4693 time to fit residues: 456.2636 Evaluate side-chains 571 residues out of total 5438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 440 time to evaluate : 4.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 574 ASN Chi-restraints excluded: chain A residue 594 THR Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 832 ASP Chi-restraints excluded: chain A residue 868 THR Chi-restraints excluded: chain A residue 928 MET Chi-restraints excluded: chain A residue 990 ILE Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1190 SER Chi-restraints excluded: chain A residue 1240 LEU Chi-restraints excluded: chain A residue 1275 THR Chi-restraints excluded: chain A residue 1329 ILE Chi-restraints excluded: chain A residue 1450 ILE Chi-restraints excluded: chain A residue 1470 CYS Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1538 VAL Chi-restraints excluded: chain A residue 1594 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 117 VAL Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 268 GLU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 498 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 672 MET Chi-restraints excluded: chain B residue 731 VAL Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 752 VAL Chi-restraints excluded: chain B residue 763 ASP Chi-restraints excluded: chain B residue 785 ASP Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 873 THR Chi-restraints excluded: chain B residue 900 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 926 VAL Chi-restraints excluded: chain B residue 941 THR Chi-restraints excluded: chain B residue 964 VAL Chi-restraints excluded: chain B residue 1025 ASP Chi-restraints excluded: chain B residue 1046 VAL Chi-restraints excluded: chain B residue 1097 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1173 THR Chi-restraints excluded: chain B residue 1200 VAL Chi-restraints excluded: chain C residue 55 ASP Chi-restraints excluded: chain C residue 94 ASP Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 224 THR Chi-restraints excluded: chain C residue 308 MET Chi-restraints excluded: chain C residue 309 THR Chi-restraints excluded: chain C residue 334 THR Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain G residue 110 ASP Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 242 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 38 LEU Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 58 THR Chi-restraints excluded: chain H residue 108 SER Chi-restraints excluded: chain H residue 129 TYR Chi-restraints excluded: chain I residue 11 LEU Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 14 VAL Chi-restraints excluded: chain J residue 67 GLU Chi-restraints excluded: chain K residue 79 VAL Chi-restraints excluded: chain M residue 84 GLU Chi-restraints excluded: chain N residue 38 PHE Chi-restraints excluded: chain N residue 53 VAL Chi-restraints excluded: chain N residue 111 VAL Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 159 ASP Chi-restraints excluded: chain O residue 63 LEU Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 88 ILE Chi-restraints excluded: chain O residue 328 LEU Chi-restraints excluded: chain O residue 332 LEU Chi-restraints excluded: chain O residue 372 VAL Chi-restraints excluded: chain O residue 373 LEU Chi-restraints excluded: chain O residue 506 PHE Chi-restraints excluded: chain O residue 524 VAL Chi-restraints excluded: chain O residue 611 ILE Chi-restraints excluded: chain P residue 178 VAL Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain P residue 224 THR Chi-restraints excluded: chain P residue 245 ILE Chi-restraints excluded: chain P residue 332 ASN Chi-restraints excluded: chain P residue 417 THR Chi-restraints excluded: chain P residue 427 SER Chi-restraints excluded: chain P residue 439 LYS Chi-restraints excluded: chain P residue 468 VAL Chi-restraints excluded: chain P residue 579 ASN Chi-restraints excluded: chain P residue 659 LEU Chi-restraints excluded: chain P residue 726 SER Chi-restraints excluded: chain P residue 778 ASP Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 17 SER Chi-restraints excluded: chain Q residue 182 ILE Chi-restraints excluded: chain Q residue 214 ILE Chi-restraints excluded: chain Q residue 245 SER Chi-restraints excluded: chain Q residue 247 ILE Chi-restraints excluded: chain Q residue 283 ASN Chi-restraints excluded: chain Q residue 338 LEU Chi-restraints excluded: chain Q residue 356 VAL Chi-restraints excluded: chain Q residue 385 PHE Chi-restraints excluded: chain Q residue 405 ASP Chi-restraints excluded: chain Q residue 450 THR Chi-restraints excluded: chain R residue 10 ASN Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain R residue 205 VAL Chi-restraints excluded: chain R residue 285 VAL Chi-restraints excluded: chain R residue 289 ASN Chi-restraints excluded: chain R residue 294 VAL Chi-restraints excluded: chain R residue 304 HIS Chi-restraints excluded: chain R residue 305 THR Chi-restraints excluded: chain R residue 384 VAL Chi-restraints excluded: chain R residue 402 ASN Chi-restraints excluded: chain R residue 418 CYS Chi-restraints excluded: chain R residue 431 ILE Chi-restraints excluded: chain R residue 438 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 602 random chunks: chunk 379 optimal weight: 4.9990 chunk 508 optimal weight: 8.9990 chunk 146 optimal weight: 0.0010 chunk 440 optimal weight: 9.9990 chunk 70 optimal weight: 0.0670 chunk 132 optimal weight: 0.0050 chunk 478 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 chunk 491 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 overall best weight: 1.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 656 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1203 ASN ** A1319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 893 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 ASN ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 298 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.093946 restraints weight = 98589.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.093574 restraints weight = 65118.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.093493 restraints weight = 80916.133| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 51242 Z= 0.197 Angle : 0.560 12.571 69565 Z= 0.292 Chirality : 0.043 0.243 7770 Planarity : 0.004 0.111 8639 Dihedral : 12.767 178.775 7427 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.07 % Rotamer: Outliers : 2.80 % Allowed : 23.53 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.03 % Twisted Proline : 0.78 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5943 helix: -0.08 (0.11), residues: 2141 sheet: -1.38 (0.18), residues: 829 loop : -1.79 (0.11), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP O 125 HIS 0.007 0.001 HIS P 58 PHE 0.042 0.001 PHE R 438 TYR 0.027 0.001 TYR O 445 ARG 0.008 0.000 ARG B 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9102.73 seconds wall clock time: 162 minutes 28.43 seconds (9748.43 seconds total)