Starting phenix.real_space_refine on Mon Mar 11 13:13:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwm_11488/03_2024/6zwm_11488_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwm_11488/03_2024/6zwm_11488.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwm_11488/03_2024/6zwm_11488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwm_11488/03_2024/6zwm_11488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwm_11488/03_2024/6zwm_11488_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zwm_11488/03_2024/6zwm_11488_neut_updated.pdb" } resolution = 3.2 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= -0.002 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 24 5.49 5 S 338 5.16 5 C 35984 2.51 5 N 10122 2.21 5 O 10477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 578": "OD1" <-> "OD2" Residue "A PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 614": "OE1" <-> "OE2" Residue "A GLU 617": "OE1" <-> "OE2" Residue "A GLU 709": "OE1" <-> "OE2" Residue "A PHE 729": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 785": "OD1" <-> "OD2" Residue "A GLU 819": "OE1" <-> "OE2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A GLU 856": "OE1" <-> "OE2" Residue "A GLU 866": "OE1" <-> "OE2" Residue "A ASP 928": "OD1" <-> "OD2" Residue "A TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 945": "OE1" <-> "OE2" Residue "A ASP 961": "OD1" <-> "OD2" Residue "A GLU 1033": "OE1" <-> "OE2" Residue "A ARG 1039": "NH1" <-> "NH2" Residue "A GLU 1057": "OE1" <-> "OE2" Residue "A GLU 1066": "OE1" <-> "OE2" Residue "A ASP 1085": "OD1" <-> "OD2" Residue "A ASP 1108": "OD1" <-> "OD2" Residue "A ASP 1109": "OD1" <-> "OD2" Residue "A GLU 1126": "OE1" <-> "OE2" Residue "A GLU 1137": "OE1" <-> "OE2" Residue "A ARG 1141": "NH1" <-> "NH2" Residue "A ASP 1147": "OD1" <-> "OD2" Residue "A ASP 1175": "OD1" <-> "OD2" Residue "A ASP 1210": "OD1" <-> "OD2" Residue "A ARG 1215": "NH1" <-> "NH2" Residue "A GLU 1225": "OE1" <-> "OE2" Residue "A ASP 1228": "OD1" <-> "OD2" Residue "A TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1238": "NH1" <-> "NH2" Residue "A ASP 1278": "OD1" <-> "OD2" Residue "A ASP 1279": "OD1" <-> "OD2" Residue "A ASP 1294": "OD1" <-> "OD2" Residue "A ASP 1316": "OD1" <-> "OD2" Residue "A GLU 1331": "OE1" <-> "OE2" Residue "A ASP 1332": "OD1" <-> "OD2" Residue "A ASP 1335": "OD1" <-> "OD2" Residue "A ASP 1376": "OD1" <-> "OD2" Residue "A ASP 1377": "OD1" <-> "OD2" Residue "A GLU 1401": "OE1" <-> "OE2" Residue "A PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1442": "OE1" <-> "OE2" Residue "A GLU 1451": "OE1" <-> "OE2" Residue "A GLU 1457": "OE1" <-> "OE2" Residue "A ASP 1464": "OD1" <-> "OD2" Residue "A ASP 1472": "OD1" <-> "OD2" Residue "A ASP 1506": "OD1" <-> "OD2" Residue "A GLU 1507": "OE1" <-> "OE2" Residue "A ASP 1527": "OD1" <-> "OD2" Residue "A GLU 1530": "OE1" <-> "OE2" Residue "A GLU 1531": "OE1" <-> "OE2" Residue "A ASP 1539": "OD1" <-> "OD2" Residue "A PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1555": "OD1" <-> "OD2" Residue "A ASP 1565": "OD1" <-> "OD2" Residue "A ASP 1569": "OD1" <-> "OD2" Residue "A GLU 1613": "OE1" <-> "OE2" Residue "A ASP 1649": "OD1" <-> "OD2" Residue "A ARG 1683": "NH1" <-> "NH2" Residue "A TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1712": "OD1" <-> "OD2" Residue "A GLU 1799": "OE1" <-> "OE2" Residue "A ARG 1905": "NH1" <-> "NH2" Residue "A ASP 1912": "OD1" <-> "OD2" Residue "A ASP 1918": "OD1" <-> "OD2" Residue "A ASP 1947": "OD1" <-> "OD2" Residue "A ARG 1955": "NH1" <-> "NH2" Residue "A ASP 1963": "OD1" <-> "OD2" Residue "A GLU 2014": "OE1" <-> "OE2" Residue "A GLU 2052": "OE1" <-> "OE2" Residue "A ARG 2086": "NH1" <-> "NH2" Residue "A ARG 2134": "NH1" <-> "NH2" Residue "A GLU 2137": "OE1" <-> "OE2" Residue "A GLU 2181": "OE1" <-> "OE2" Residue "A PHE 2182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2190": "OE1" <-> "OE2" Residue "A ASP 2195": "OD1" <-> "OD2" Residue "A ASP 2244": "OD1" <-> "OD2" Residue "A ASP 2252": "OD1" <-> "OD2" Residue "A ASP 2276": "OD1" <-> "OD2" Residue "A ASP 2297": "OD1" <-> "OD2" Residue "A GLU 2311": "OE1" <-> "OE2" Residue "A ASP 2315": "OD1" <-> "OD2" Residue "A ASP 2360": "OD1" <-> "OD2" Residue "A GLU 2369": "OE1" <-> "OE2" Residue "A ASP 2424": "OD1" <-> "OD2" Residue "A ASP 2433": "OD1" <-> "OD2" Residue "B GLU 617": "OE1" <-> "OE2" Residue "B GLU 621": "OE1" <-> "OE2" Residue "B ASP 654": "OD1" <-> "OD2" Residue "B ASP 666": "OD1" <-> "OD2" Residue "B ASP 668": "OD1" <-> "OD2" Residue "B ASP 684": "OD1" <-> "OD2" Residue "B GLU 691": "OE1" <-> "OE2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B GLU 804": "OE1" <-> "OE2" Residue "B GLU 812": "OE1" <-> "OE2" Residue "B GLU 866": "OE1" <-> "OE2" Residue "B ASP 928": "OD1" <-> "OD2" Residue "B TYR 929": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 944": "OD1" <-> "OD2" Residue "B ASP 961": "OD1" <-> "OD2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1005": "OD1" <-> "OD2" Residue "B GLU 1033": "OE1" <-> "OE2" Residue "B ARG 1039": "NH1" <-> "NH2" Residue "B GLU 1066": "OE1" <-> "OE2" Residue "B ASP 1108": "OD1" <-> "OD2" Residue "B ARG 1141": "NH1" <-> "NH2" Residue "B ASP 1147": "OD1" <-> "OD2" Residue "B ASP 1175": "OD1" <-> "OD2" Residue "B ARG 1215": "NH1" <-> "NH2" Residue "B TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1238": "NH1" <-> "NH2" Residue "B ASP 1279": "OD1" <-> "OD2" Residue "B GLU 1336": "OE1" <-> "OE2" Residue "B ASP 1349": "OD1" <-> "OD2" Residue "B GLU 1352": "OE1" <-> "OE2" Residue "B ASP 1376": "OD1" <-> "OD2" Residue "B ASP 1377": "OD1" <-> "OD2" Residue "B GLU 1401": "OE1" <-> "OE2" Residue "B PHE 1404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1442": "OE1" <-> "OE2" Residue "B GLU 1457": "OE1" <-> "OE2" Residue "B ASP 1464": "OD1" <-> "OD2" Residue "B ASP 1468": "OD1" <-> "OD2" Residue "B GLU 1489": "OE1" <-> "OE2" Residue "B GLU 1531": "OE1" <-> "OE2" Residue "B ASP 1539": "OD1" <-> "OD2" Residue "B ASP 1542": "OD1" <-> "OD2" Residue "B PHE 1545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1555": "OD1" <-> "OD2" Residue "B ASP 1569": "OD1" <-> "OD2" Residue "B GLU 1610": "OE1" <-> "OE2" Residue "B GLU 1613": "OE1" <-> "OE2" Residue "B GLU 1631": "OE1" <-> "OE2" Residue "B ARG 1683": "NH1" <-> "NH2" Residue "B TYR 1700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1742": "OE1" <-> "OE2" Residue "B GLU 1781": "OE1" <-> "OE2" Residue "B GLU 1799": "OE1" <-> "OE2" Residue "B ARG 1905": "NH1" <-> "NH2" Residue "B GLU 1921": "OE1" <-> "OE2" Residue "B GLU 1925": "OE1" <-> "OE2" Residue "B ASP 1947": "OD1" <-> "OD2" Residue "B ARG 1955": "NH1" <-> "NH2" Residue "B ASP 1963": "OD1" <-> "OD2" Residue "B GLU 2014": "OE1" <-> "OE2" Residue "B GLU 2049": "OE1" <-> "OE2" Residue "B GLU 2052": "OE1" <-> "OE2" Residue "B GLU 2080": "OE1" <-> "OE2" Residue "B ARG 2086": "NH1" <-> "NH2" Residue "B ASP 2102": "OD1" <-> "OD2" Residue "B GLU 2122": "OE1" <-> "OE2" Residue "B ARG 2134": "NH1" <-> "NH2" Residue "B GLU 2181": "OE1" <-> "OE2" Residue "B PHE 2182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 2184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2190": "OE1" <-> "OE2" Residue "B ASP 2195": "OD1" <-> "OD2" Residue "B ASP 2252": "OD1" <-> "OD2" Residue "B GLU 2311": "OE1" <-> "OE2" Residue "B ASP 2360": "OD1" <-> "OD2" Residue "B ASP 2433": "OD1" <-> "OD2" Residue "B ASP 2516": "OD1" <-> "OD2" Residue "B GLU 2526": "OE1" <-> "OE2" Residue "C PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C ASP 69": "OD1" <-> "OD2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ASP 106": "OD1" <-> "OD2" Residue "C ARG 115": "NH1" <-> "NH2" Residue "C PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 142": "OE1" <-> "OE2" Residue "C ASP 179": "OD1" <-> "OD2" Residue "C ASP 181": "OD1" <-> "OD2" Residue "C TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 231": "OD1" <-> "OD2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 21": "OD1" <-> "OD2" Residue "D PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 95": "OE1" <-> "OE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D ARG 115": "NH1" <-> "NH2" Residue "D PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 147": "OD1" <-> "OD2" Residue "D ASP 160": "OD1" <-> "OD2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 205": "OD1" <-> "OD2" Residue "D GLU 206": "OE1" <-> "OE2" Residue "D TYR 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 231": "OD1" <-> "OD2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "D GLU 307": "OE1" <-> "OE2" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 39": "NH1" <-> "NH2" Residue "E GLU 40": "OE1" <-> "OE2" Residue "E ARG 47": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E GLU 82": "OE1" <-> "OE2" Residue "E ASP 83": "OD1" <-> "OD2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "E ARG 105": "NH1" <-> "NH2" Residue "E ASP 134": "OD1" <-> "OD2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E GLU 193": "OE1" <-> "OE2" Residue "E ARG 205": "NH1" <-> "NH2" Residue "E ASP 247": "OD1" <-> "OD2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "E ASP 276": "OD1" <-> "OD2" Residue "E GLU 278": "OE1" <-> "OE2" Residue "E ASP 333": "OD1" <-> "OD2" Residue "E GLU 345": "OE1" <-> "OE2" Residue "E GLU 348": "OE1" <-> "OE2" Residue "E ASP 354": "OD1" <-> "OD2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ASP 360": "OD1" <-> "OD2" Residue "E ASP 389": "OD1" <-> "OD2" Residue "E PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 406": "OE1" <-> "OE2" Residue "E PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 481": "OE1" <-> "OE2" Residue "E ASP 495": "OD1" <-> "OD2" Residue "E ASP 509": "OD1" <-> "OD2" Residue "E ASP 523": "OD1" <-> "OD2" Residue "E GLU 525": "OE1" <-> "OE2" Residue "E ASP 534": "OD1" <-> "OD2" Residue "E GLU 542": "OE1" <-> "OE2" Residue "E ARG 563": "NH1" <-> "NH2" Residue "E ASP 567": "OD1" <-> "OD2" Residue "E ARG 576": "NH1" <-> "NH2" Residue "E GLU 610": "OE1" <-> "OE2" Residue "E GLU 614": "OE1" <-> "OE2" Residue "E GLU 624": "OE1" <-> "OE2" Residue "E ASP 695": "OD1" <-> "OD2" Residue "E ARG 709": "NH1" <-> "NH2" Residue "E ASP 710": "OD1" <-> "OD2" Residue "E ASP 726": "OD1" <-> "OD2" Residue "E ARG 737": "NH1" <-> "NH2" Residue "E GLU 745": "OE1" <-> "OE2" Residue "E PHE 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 772": "OD1" <-> "OD2" Residue "E ASP 775": "OD1" <-> "OD2" Residue "E GLU 779": "OE1" <-> "OE2" Residue "E ASP 780": "OD1" <-> "OD2" Residue "E PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 821": "NH1" <-> "NH2" Residue "E GLU 834": "OE1" <-> "OE2" Residue "E ASP 841": "OD1" <-> "OD2" Residue "E GLU 849": "OE1" <-> "OE2" Residue "E GLU 897": "OE1" <-> "OE2" Residue "E ASP 913": "OD1" <-> "OD2" Residue "E ASP 915": "OD1" <-> "OD2" Residue "E GLU 919": "OE1" <-> "OE2" Residue "E ASP 951": "OD1" <-> "OD2" Residue "E ASP 1432": "OD1" <-> "OD2" Residue "E ASP 1441": "OD1" <-> "OD2" Residue "E GLU 1491": "OE1" <-> "OE2" Residue "E GLU 1514": "OE1" <-> "OE2" Residue "E ASP 1517": "OD1" <-> "OD2" Residue "E ASP 1518": "OD1" <-> "OD2" Residue "E GLU 1527": "OE1" <-> "OE2" Residue "E GLU 1633": "OE1" <-> "OE2" Residue "E ASP 1648": "OD1" <-> "OD2" Residue "E PHE 1665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1666": "NH1" <-> "NH2" Residue "E GLU 1675": "OE1" <-> "OE2" Residue "E GLU 1687": "OE1" <-> "OE2" Residue "E GLU 1688": "OE1" <-> "OE2" Residue "E GLU 1690": "OE1" <-> "OE2" Residue "F ARG 39": "NH1" <-> "NH2" Residue "F GLU 40": "OE1" <-> "OE2" Residue "F ARG 47": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ASP 83": "OD1" <-> "OD2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "F ARG 105": "NH1" <-> "NH2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 175": "OD1" <-> "OD2" Residue "F GLU 200": "OE1" <-> "OE2" Residue "F ARG 205": "NH1" <-> "NH2" Residue "F ASP 247": "OD1" <-> "OD2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F GLU 278": "OE1" <-> "OE2" Residue "F GLU 345": "OE1" <-> "OE2" Residue "F ASP 354": "OD1" <-> "OD2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 406": "OE1" <-> "OE2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "F PHE 459": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F ASP 495": "OD1" <-> "OD2" Residue "F ASP 509": "OD1" <-> "OD2" Residue "F ASP 523": "OD1" <-> "OD2" Residue "F GLU 526": "OE1" <-> "OE2" Residue "F ASP 534": "OD1" <-> "OD2" Residue "F GLU 542": "OE1" <-> "OE2" Residue "F GLU 545": "OE1" <-> "OE2" Residue "F ARG 563": "NH1" <-> "NH2" Residue "F ASP 567": "OD1" <-> "OD2" Residue "F GLU 568": "OE1" <-> "OE2" Residue "F ARG 576": "NH1" <-> "NH2" Residue "F GLU 616": "OE1" <-> "OE2" Residue "F GLU 617": "OE1" <-> "OE2" Residue "F ASP 618": "OD1" <-> "OD2" Residue "F GLU 624": "OE1" <-> "OE2" Residue "F ASP 625": "OD1" <-> "OD2" Residue "F ARG 709": "NH1" <-> "NH2" Residue "F ASP 710": "OD1" <-> "OD2" Residue "F ARG 737": "NH1" <-> "NH2" Residue "F GLU 753": "OE1" <-> "OE2" Residue "F GLU 769": "OE1" <-> "OE2" Residue "F ASP 775": "OD1" <-> "OD2" Residue "F GLU 779": "OE1" <-> "OE2" Residue "F PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 820": "OE1" <-> "OE2" Residue "F ARG 821": "NH1" <-> "NH2" Residue "F ASP 841": "OD1" <-> "OD2" Residue "F GLU 897": "OE1" <-> "OE2" Residue "F GLU 919": "OE1" <-> "OE2" Residue "F ASP 951": "OD1" <-> "OD2" Residue "F GLU 1491": "OE1" <-> "OE2" Residue "F ASP 1517": "OD1" <-> "OD2" Residue "F ASP 1518": "OD1" <-> "OD2" Residue "F TYR 1522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 1527": "OE1" <-> "OE2" Residue "F GLU 1633": "OE1" <-> "OE2" Residue "F GLU 1641": "OE1" <-> "OE2" Residue "F ASP 1648": "OD1" <-> "OD2" Residue "F PHE 1665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 1666": "NH1" <-> "NH2" Residue "F ASP 1679": "OD1" <-> "OD2" Residue "F GLU 1687": "OE1" <-> "OE2" Residue "G ASP 5": "OD1" <-> "OD2" Residue "G ASP 23": "OD1" <-> "OD2" Residue "H ASP 23": "OD1" <-> "OD2" Residue "H ASP 35": "OD1" <-> "OD2" Residue "H GLU 91": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 56947 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 16337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2184, 16337 Classifications: {'peptide': 2184} Incomplete info: {'truncation_to_alanine': 359} Link IDs: {'PTRANS': 86, 'TRANS': 2097} Chain breaks: 20 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1316 Unresolved non-hydrogen angles: 1673 Unresolved non-hydrogen dihedrals: 1080 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 19, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 19, 'GLU:plan': 33, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 717 Chain: "B" Number of atoms: 16304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2185, 16304 Classifications: {'peptide': 2185} Incomplete info: {'truncation_to_alanine': 371} Link IDs: {'PTRANS': 86, 'TRANS': 2098} Chain breaks: 19 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 1358 Unresolved non-hydrogen angles: 1727 Unresolved non-hydrogen dihedrals: 1114 Unresolved non-hydrogen chiralities: 134 Planarities with less than four sites: {'GLN:plan1': 23, 'ASP:plan': 19, 'TYR:plan': 8, 'ASN:plan1': 10, 'TRP:plan': 4, 'HIS:plan': 9, 'PHE:plan': 21, 'GLU:plan': 34, 'ARG:plan': 32} Unresolved non-hydrogen planarities: 738 Chain: "C" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2465 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 13, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 8931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8931 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1079} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "F" Number of atoms: 8931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1117, 8931 Classifications: {'peptide': 1117} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 37, 'TRANS': 1079} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "G" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "H" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 655 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 142 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 119 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 63 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'AGS': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'AGS': 1, 'IHP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' ZN': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 3 Unusual residues: {'ACE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 45642 SG CYS E1520 42.632 96.945 25.790 1.00228.31 S ATOM 45668 SG CYS E1523 42.706 96.632 22.096 1.00232.67 S ATOM 46142 SG CYS E1651 42.642 100.005 23.588 1.00219.53 S ATOM 54573 SG CYS F1520 206.650 99.764 32.439 1.00149.03 S ATOM 54599 SG CYS F1523 207.028 99.803 28.749 1.00164.62 S ATOM 55073 SG CYS F1651 206.806 96.438 30.643 1.00125.45 S Time building chain proxies: 23.52, per 1000 atoms: 0.41 Number of scatterers: 56947 At special positions: 0 Unit cell: (248.64, 200.256, 158.592, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 338 16.00 P 24 15.00 O 10477 8.00 N 10122 7.00 C 35984 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 16.27 Conformation dependent library (CDL) restraints added in 7.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E4801 " pdb="ZN ZN E4801 " - pdb=" NE2 HIS E1515 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1651 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1523 " pdb="ZN ZN E4801 " - pdb=" SG CYS E1520 " pdb=" ZN F4801 " pdb="ZN ZN F4801 " - pdb=" NE2 HIS F1515 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1520 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1651 " pdb="ZN ZN F4801 " - pdb=" SG CYS F1523 " Number of angles added : 6 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 386 helices and 24 sheets defined 59.1% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 14.31 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 38 through 52 removed outlier: 3.661A pdb=" N LEU A 52 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.619A pdb=" N ASP A 65 " --> pdb=" O THR A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.650A pdb=" N ARG A 106 " --> pdb=" O THR A 102 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASN A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU A 114 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Proline residue: A 116 - end of helix Processing helix chain 'A' and resid 122 through 134 Processing helix chain 'A' and resid 139 through 155 removed outlier: 3.973A pdb=" N ALA A 142 " --> pdb=" O THR A 139 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 144 " --> pdb=" O THR A 141 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N VAL A 145 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU A 146 " --> pdb=" O GLU A 143 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE A 147 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL A 149 " --> pdb=" O GLU A 146 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS A 150 " --> pdb=" O PHE A 147 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG A 151 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU A 153 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP A 155 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 178 Processing helix chain 'A' and resid 188 through 197 removed outlier: 3.720A pdb=" N ASP A 192 " --> pdb=" O GLN A 188 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 222 removed outlier: 3.767A pdb=" N GLY A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 245 removed outlier: 3.529A pdb=" N PHE A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 275 removed outlier: 3.617A pdb=" N GLU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 271 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 275 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 286 removed outlier: 3.797A pdb=" N LEU A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 375 Processing helix chain 'A' and resid 387 through 402 Proline residue: A 397 - end of helix Processing helix chain 'A' and resid 411 through 425 removed outlier: 4.289A pdb=" N LYS A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 443 removed outlier: 3.520A pdb=" N GLN A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 463 removed outlier: 3.700A pdb=" N LEU A 452 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Proline residue: A 453 - end of helix removed outlier: 4.018A pdb=" N LEU A 456 " --> pdb=" O PRO A 453 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASP A 457 " --> pdb=" O ARG A 454 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE A 459 " --> pdb=" O LEU A 456 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ARG A 460 " --> pdb=" O ASP A 457 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ALA A 461 " --> pdb=" O ILE A 458 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU A 463 " --> pdb=" O ARG A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 490 removed outlier: 3.646A pdb=" N THR A 484 " --> pdb=" O ALA A 480 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA A 490 " --> pdb=" O ILE A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 511 removed outlier: 4.374A pdb=" N GLU A 506 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Proline residue: A 507 - end of helix Processing helix chain 'A' and resid 515 through 527 Processing helix chain 'A' and resid 533 through 548 removed outlier: 3.555A pdb=" N GLY A 538 " --> pdb=" O ASP A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 589 Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 609 through 612 No H-bonds generated for 'chain 'A' and resid 609 through 612' Processing helix chain 'A' and resid 616 through 631 removed outlier: 3.623A pdb=" N ARG A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR A 631 " --> pdb=" O SER A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 665 Processing helix chain 'A' and resid 669 through 678 Processing helix chain 'A' and resid 681 through 683 No H-bonds generated for 'chain 'A' and resid 681 through 683' Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.555A pdb=" N VAL A 698 " --> pdb=" O GLN A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 720 removed outlier: 5.113A pdb=" N SER A 720 " --> pdb=" O GLY A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 742 Proline residue: A 728 - end of helix Processing helix chain 'A' and resid 747 through 763 Processing helix chain 'A' and resid 765 through 768 No H-bonds generated for 'chain 'A' and resid 765 through 768' Processing helix chain 'A' and resid 772 through 783 Processing helix chain 'A' and resid 793 through 808 Processing helix chain 'A' and resid 817 through 828 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 856 through 860 Processing helix chain 'A' and resid 864 through 872 removed outlier: 3.799A pdb=" N PHE A 871 " --> pdb=" O VAL A 867 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N LEU A 872 " --> pdb=" O LEU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 891 Processing helix chain 'A' and resid 896 through 902 Processing helix chain 'A' and resid 929 through 935 Processing helix chain 'A' and resid 943 through 945 No H-bonds generated for 'chain 'A' and resid 943 through 945' Processing helix chain 'A' and resid 947 through 959 removed outlier: 3.773A pdb=" N ILE A 958 " --> pdb=" O ALA A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 982 Processing helix chain 'A' and resid 990 through 1003 Proline residue: A 995 - end of helix Processing helix chain 'A' and resid 1006 through 1022 removed outlier: 3.975A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N PHE A1013 " --> pdb=" O GLU A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1038 removed outlier: 5.391A pdb=" N ASP A1032 " --> pdb=" O PRO A1029 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N GLU A1033 " --> pdb=" O TYR A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1063 removed outlier: 3.667A pdb=" N LEU A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1069 No H-bonds generated for 'chain 'A' and resid 1067 through 1069' Processing helix chain 'A' and resid 1072 through 1083 Proline residue: A1076 - end of helix removed outlier: 4.344A pdb=" N MET A1083 " --> pdb=" O ARG A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1091 through 1102 removed outlier: 3.993A pdb=" N LEU A1102 " --> pdb=" O ALA A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1122 removed outlier: 3.643A pdb=" N LEU A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE A1122 " --> pdb=" O ILE A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1141 Processing helix chain 'A' and resid 1153 through 1163 removed outlier: 3.949A pdb=" N HIS A1157 " --> pdb=" O SER A1153 " (cutoff:3.500A) Proline residue: A1158 - end of helix Processing helix chain 'A' and resid 1170 through 1181 Processing helix chain 'A' and resid 1189 through 1201 removed outlier: 3.721A pdb=" N ILE A1192 " --> pdb=" O GLN A1189 " (cutoff:3.500A) Proline residue: A1193 - end of helix removed outlier: 3.698A pdb=" N ASN A1196 " --> pdb=" O PRO A1193 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A1197 " --> pdb=" O MET A1194 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1200 " --> pdb=" O LYS A1197 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG A1201 " --> pdb=" O VAL A1198 " (cutoff:3.500A) Processing helix chain 'A' and resid 1207 through 1217 Processing helix chain 'A' and resid 1229 through 1237 Processing helix chain 'A' and resid 1266 through 1269 No H-bonds generated for 'chain 'A' and resid 1266 through 1269' Processing helix chain 'A' and resid 1277 through 1293 Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 4.215A pdb=" N ALA A1305 " --> pdb=" O ARG A1301 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N LEU A1306 " --> pdb=" O SER A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1316 Processing helix chain 'A' and resid 1318 through 1326 Processing helix chain 'A' and resid 1331 through 1347 Processing helix chain 'A' and resid 1351 through 1365 Processing helix chain 'A' and resid 1377 through 1389 removed outlier: 6.000A pdb=" N VAL A1381 " --> pdb=" O ASN A1378 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU A1383 " --> pdb=" O ILE A1380 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY A1384 " --> pdb=" O VAL A1381 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ALA A1388 " --> pdb=" O GLU A1385 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS A1389 " --> pdb=" O ARG A1386 " (cutoff:3.500A) Processing helix chain 'A' and resid 1393 through 1406 removed outlier: 3.911A pdb=" N LYS A1406 " --> pdb=" O LEU A1402 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1422 removed outlier: 3.712A pdb=" N LYS A1422 " --> pdb=" O SER A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1426 through 1438 Processing helix chain 'A' and resid 1447 through 1452 Processing helix chain 'A' and resid 1456 through 1469 removed outlier: 4.293A pdb=" N THR A1469 " --> pdb=" O LYS A1465 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1487 Processing helix chain 'A' and resid 1490 through 1498 Processing helix chain 'A' and resid 1506 through 1523 removed outlier: 3.815A pdb=" N ALA A1510 " --> pdb=" O ASP A1506 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS A1511 " --> pdb=" O GLU A1507 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG A1514 " --> pdb=" O ALA A1510 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N MET A1515 " --> pdb=" O LYS A1511 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1535 removed outlier: 3.973A pdb=" N GLU A1531 " --> pdb=" O ASP A1527 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS A1534 " --> pdb=" O GLU A1530 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N MET A1535 " --> pdb=" O GLU A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1541 through 1553 Processing helix chain 'A' and resid 1559 through 1578 removed outlier: 3.796A pdb=" N ASP A1569 " --> pdb=" O ASP A1565 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLU A1574 " --> pdb=" O LEU A1570 " (cutoff:3.500A) Processing helix chain 'A' and resid 1583 through 1597 removed outlier: 4.968A pdb=" N GLY A1588 " --> pdb=" O SER A1584 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ALA A1589 " --> pdb=" O ARG A1585 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A1592 " --> pdb=" O GLY A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1607 Processing helix chain 'A' and resid 1612 through 1625 removed outlier: 4.099A pdb=" N TRP A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLY A1625 " --> pdb=" O GLU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1630 through 1642 removed outlier: 3.797A pdb=" N LYS A1635 " --> pdb=" O GLU A1631 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A1642 " --> pdb=" O MET A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1651 through 1662 removed outlier: 3.992A pdb=" N LYS A1655 " --> pdb=" O ARG A1651 " (cutoff:3.500A) Processing helix chain 'A' and resid 1666 through 1677 Processing helix chain 'A' and resid 1694 through 1707 Processing helix chain 'A' and resid 1712 through 1725 Processing helix chain 'A' and resid 1728 through 1730 No H-bonds generated for 'chain 'A' and resid 1728 through 1730' Processing helix chain 'A' and resid 1740 through 1762 Processing helix chain 'A' and resid 1769 through 1783 Processing helix chain 'A' and resid 1787 through 1807 Processing helix chain 'A' and resid 1876 through 1895 Proline residue: A1883 - end of helix removed outlier: 3.966A pdb=" N SER A1893 " --> pdb=" O PHE A1889 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A1894 " --> pdb=" O ARG A1890 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A1895 " --> pdb=" O SER A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1900 through 1913 Processing helix chain 'A' and resid 1919 through 1929 removed outlier: 3.667A pdb=" N LYS A1928 " --> pdb=" O VAL A1924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1933 through 1945 removed outlier: 4.333A pdb=" N GLN A1937 " --> pdb=" O THR A1934 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A1939 " --> pdb=" O LEU A1936 " (cutoff:3.500A) Proline residue: A1940 - end of helix removed outlier: 3.975A pdb=" N ALA A1944 " --> pdb=" O GLN A1941 " (cutoff:3.500A) Processing helix chain 'A' and resid 1951 through 1967 Processing helix chain 'A' and resid 1973 through 1980 Processing helix chain 'A' and resid 1985 through 1998 Processing helix chain 'A' and resid 2004 through 2016 Processing helix chain 'A' and resid 2023 through 2041 removed outlier: 3.592A pdb=" N ARG A2036 " --> pdb=" O GLU A2032 " (cutoff:3.500A) Processing helix chain 'A' and resid 2044 through 2058 Proline residue: A2053 - end of helix Processing helix chain 'A' and resid 2065 through 2090 removed outlier: 6.239A pdb=" N ARG A2076 " --> pdb=" O GLN A2072 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ASP A2077 " --> pdb=" O ALA A2073 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN A2082 " --> pdb=" O LEU A2078 " (cutoff:3.500A) Processing helix chain 'A' and resid 2094 through 2112 removed outlier: 4.450A pdb=" N GLN A2099 " --> pdb=" O LYS A2095 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ALA A2100 " --> pdb=" O ASP A2096 " (cutoff:3.500A) Processing helix chain 'A' and resid 2123 through 2126 No H-bonds generated for 'chain 'A' and resid 2123 through 2126' Processing helix chain 'A' and resid 2193 through 2210 removed outlier: 3.924A pdb=" N ARG A2197 " --> pdb=" O ARG A2193 " (cutoff:3.500A) Processing helix chain 'A' and resid 2213 through 2216 No H-bonds generated for 'chain 'A' and resid 2213 through 2216' Processing helix chain 'A' and resid 2247 through 2256 removed outlier: 4.242A pdb=" N ASP A2252 " --> pdb=" O ALA A2248 " (cutoff:3.500A) Processing helix chain 'A' and resid 2263 through 2271 Processing helix chain 'A' and resid 2275 through 2277 No H-bonds generated for 'chain 'A' and resid 2275 through 2277' Processing helix chain 'A' and resid 2280 through 2292 Processing helix chain 'A' and resid 2298 through 2305 Processing helix chain 'A' and resid 2310 through 2334 removed outlier: 4.164A pdb=" N VAL A2326 " --> pdb=" O ARG A2322 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET A2327 " --> pdb=" O SER A2323 " (cutoff:3.500A) Processing helix chain 'A' and resid 2381 through 2384 No H-bonds generated for 'chain 'A' and resid 2381 through 2384' Processing helix chain 'A' and resid 2395 through 2409 Processing helix chain 'A' and resid 2411 through 2422 Processing helix chain 'A' and resid 2493 through 2507 removed outlier: 3.956A pdb=" N LYS A2496 " --> pdb=" O LEU A2493 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ALA A2497 " --> pdb=" O ASN A2494 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN A2502 " --> pdb=" O GLN A2499 " (cutoff:3.500A) Processing helix chain 'A' and resid 2521 through 2532 Processing helix chain 'A' and resid 2535 through 2538 No H-bonds generated for 'chain 'A' and resid 2535 through 2538' Processing helix chain 'A' and resid 2543 through 2545 No H-bonds generated for 'chain 'A' and resid 2543 through 2545' Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.545A pdb=" N LEU B 52 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 73 Processing helix chain 'B' and resid 83 through 93 removed outlier: 3.816A pdb=" N LEU B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.785A pdb=" N ARG B 106 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ASN B 109 " --> pdb=" O GLY B 105 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR B 110 " --> pdb=" O ARG B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 134 Processing helix chain 'B' and resid 139 through 155 removed outlier: 4.187A pdb=" N ALA B 142 " --> pdb=" O THR B 139 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR B 144 " --> pdb=" O THR B 141 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL B 145 " --> pdb=" O ALA B 142 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU B 146 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N PHE B 147 " --> pdb=" O TYR B 144 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL B 149 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS B 150 " --> pdb=" O PHE B 147 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG B 151 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 153 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TRP B 155 " --> pdb=" O ALA B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 178 removed outlier: 3.645A pdb=" N VAL B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 removed outlier: 4.146A pdb=" N GLN B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 197 removed outlier: 3.587A pdb=" N ASP B 192 " --> pdb=" O GLN B 188 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 222 removed outlier: 3.983A pdb=" N GLY B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 245 Processing helix chain 'B' and resid 259 through 275 removed outlier: 4.597A pdb=" N GLY B 263 " --> pdb=" O ASP B 259 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA B 264 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU B 271 " --> pdb=" O ILE B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 286 removed outlier: 3.786A pdb=" N LEU B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG B 283 " --> pdb=" O GLY B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 375 Processing helix chain 'B' and resid 387 through 402 Proline residue: B 397 - end of helix Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 430 through 443 Processing helix chain 'B' and resid 448 through 463 removed outlier: 3.622A pdb=" N LEU B 452 " --> pdb=" O LYS B 449 " (cutoff:3.500A) Proline residue: B 453 - end of helix removed outlier: 4.099A pdb=" N LEU B 456 " --> pdb=" O PRO B 453 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP B 457 " --> pdb=" O ARG B 454 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE B 459 " --> pdb=" O LEU B 456 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 460 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA B 461 " --> pdb=" O ILE B 458 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 463 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 490 removed outlier: 3.978A pdb=" N THR B 484 " --> pdb=" O ALA B 480 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA B 490 " --> pdb=" O ILE B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 511 removed outlier: 4.377A pdb=" N GLU B 506 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Proline residue: B 507 - end of helix Processing helix chain 'B' and resid 515 through 527 Processing helix chain 'B' and resid 533 through 548 Processing helix chain 'B' and resid 580 through 591 Processing helix chain 'B' and resid 602 through 606 Processing helix chain 'B' and resid 609 through 612 No H-bonds generated for 'chain 'B' and resid 609 through 612' Processing helix chain 'B' and resid 616 through 631 removed outlier: 4.154A pdb=" N LEU B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N THR B 631 " --> pdb=" O SER B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 665 Processing helix chain 'B' and resid 669 through 677 Processing helix chain 'B' and resid 681 through 683 No H-bonds generated for 'chain 'B' and resid 681 through 683' Processing helix chain 'B' and resid 690 through 700 Processing helix chain 'B' and resid 705 through 717 Processing helix chain 'B' and resid 723 through 743 Proline residue: B 728 - end of helix Processing helix chain 'B' and resid 747 through 763 Processing helix chain 'B' and resid 765 through 768 No H-bonds generated for 'chain 'B' and resid 765 through 768' Processing helix chain 'B' and resid 772 through 783 Processing helix chain 'B' and resid 793 through 808 Processing helix chain 'B' and resid 817 through 828 Processing helix chain 'B' and resid 838 through 846 Processing helix chain 'B' and resid 856 through 860 Processing helix chain 'B' and resid 864 through 872 removed outlier: 3.606A pdb=" N PHE B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 872 " --> pdb=" O LEU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 891 Processing helix chain 'B' and resid 896 through 902 Processing helix chain 'B' and resid 930 through 935 Processing helix chain 'B' and resid 943 through 945 No H-bonds generated for 'chain 'B' and resid 943 through 945' Processing helix chain 'B' and resid 947 through 959 removed outlier: 3.641A pdb=" N ILE B 958 " --> pdb=" O ALA B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 982 Processing helix chain 'B' and resid 990 through 1003 Proline residue: B 995 - end of helix Processing helix chain 'B' and resid 1009 through 1022 removed outlier: 3.863A pdb=" N GLN B1014 " --> pdb=" O GLU B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1038 removed outlier: 5.304A pdb=" N ASP B1032 " --> pdb=" O PRO B1029 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU B1033 " --> pdb=" O TYR B1030 " (cutoff:3.500A) Processing helix chain 'B' and resid 1049 through 1063 removed outlier: 3.669A pdb=" N LEU B1054 " --> pdb=" O SER B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1067 through 1069 No H-bonds generated for 'chain 'B' and resid 1067 through 1069' Processing helix chain 'B' and resid 1072 through 1083 Proline residue: B1076 - end of helix removed outlier: 4.415A pdb=" N MET B1083 " --> pdb=" O ARG B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1091 through 1102 removed outlier: 4.041A pdb=" N LEU B1102 " --> pdb=" O ALA B1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1122 removed outlier: 3.531A pdb=" N LEU B1121 " --> pdb=" O PRO B1117 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE B1122 " --> pdb=" O ILE B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1129 through 1143 removed outlier: 4.015A pdb=" N THR B1143 " --> pdb=" O VAL B1139 " (cutoff:3.500A) Processing helix chain 'B' and resid 1153 through 1163 removed outlier: 4.024A pdb=" N HIS B1157 " --> pdb=" O SER B1153 " (cutoff:3.500A) Proline residue: B1158 - end of helix Processing helix chain 'B' and resid 1170 through 1183 removed outlier: 4.105A pdb=" N GLN B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) Processing helix chain 'B' and resid 1186 through 1188 No H-bonds generated for 'chain 'B' and resid 1186 through 1188' Processing helix chain 'B' and resid 1192 through 1201 removed outlier: 3.942A pdb=" N LYS B1197 " --> pdb=" O PRO B1193 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL B1198 " --> pdb=" O MET B1194 " (cutoff:3.500A) Processing helix chain 'B' and resid 1207 through 1217 Processing helix chain 'B' and resid 1229 through 1237 Processing helix chain 'B' and resid 1266 through 1269 No H-bonds generated for 'chain 'B' and resid 1266 through 1269' Processing helix chain 'B' and resid 1277 through 1293 Processing helix chain 'B' and resid 1298 through 1307 removed outlier: 4.233A pdb=" N ALA B1305 " --> pdb=" O ARG B1301 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU B1306 " --> pdb=" O SER B1302 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1316 Processing helix chain 'B' and resid 1318 through 1326 Processing helix chain 'B' and resid 1331 through 1347 Processing helix chain 'B' and resid 1351 through 1365 Processing helix chain 'B' and resid 1377 through 1388 removed outlier: 3.553A pdb=" N ILE B1380 " --> pdb=" O ASP B1377 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N VAL B1381 " --> pdb=" O ASN B1378 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LEU B1383 " --> pdb=" O ILE B1380 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B1384 " --> pdb=" O VAL B1381 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ALA B1388 " --> pdb=" O GLU B1385 " (cutoff:3.500A) Processing helix chain 'B' and resid 1393 through 1406 removed outlier: 4.080A pdb=" N LYS B1406 " --> pdb=" O LEU B1402 " (cutoff:3.500A) Processing helix chain 'B' and resid 1410 through 1422 removed outlier: 3.658A pdb=" N LYS B1422 " --> pdb=" O SER B1418 " (cutoff:3.500A) Processing helix chain 'B' and resid 1426 through 1438 Processing helix chain 'B' and resid 1447 through 1452 Processing helix chain 'B' and resid 1456 through 1467 Processing helix chain 'B' and resid 1477 through 1487 Processing helix chain 'B' and resid 1490 through 1498 Processing helix chain 'B' and resid 1506 through 1523 removed outlier: 4.841A pdb=" N LYS B1511 " --> pdb=" O GLU B1507 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG B1514 " --> pdb=" O ALA B1510 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N MET B1515 " --> pdb=" O LYS B1511 " (cutoff:3.500A) Processing helix chain 'B' and resid 1526 through 1535 removed outlier: 3.794A pdb=" N GLU B1531 " --> pdb=" O ASP B1527 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS B1534 " --> pdb=" O GLU B1530 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N MET B1535 " --> pdb=" O GLU B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1541 through 1553 Processing helix chain 'B' and resid 1559 through 1578 removed outlier: 3.676A pdb=" N ASP B1569 " --> pdb=" O ASP B1565 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU B1574 " --> pdb=" O LEU B1570 " (cutoff:3.500A) Processing helix chain 'B' and resid 1583 through 1597 removed outlier: 4.980A pdb=" N GLY B1588 " --> pdb=" O SER B1584 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N ALA B1589 " --> pdb=" O ARG B1585 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N SER B1592 " --> pdb=" O GLY B1588 " (cutoff:3.500A) Processing helix chain 'B' and resid 1599 through 1607 Processing helix chain 'B' and resid 1612 through 1625 removed outlier: 3.565A pdb=" N ARG B1616 " --> pdb=" O ARG B1612 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TRP B1620 " --> pdb=" O ARG B1616 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N GLY B1625 " --> pdb=" O GLU B1621 " (cutoff:3.500A) Processing helix chain 'B' and resid 1630 through 1640 removed outlier: 3.701A pdb=" N LYS B1635 " --> pdb=" O GLU B1631 " (cutoff:3.500A) Processing helix chain 'B' and resid 1651 through 1662 removed outlier: 3.957A pdb=" N LYS B1655 " --> pdb=" O ARG B1651 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR B1656 " --> pdb=" O THR B1652 " (cutoff:3.500A) Processing helix chain 'B' and resid 1666 through 1677 Processing helix chain 'B' and resid 1694 through 1707 Processing helix chain 'B' and resid 1712 through 1725 Processing helix chain 'B' and resid 1728 through 1730 No H-bonds generated for 'chain 'B' and resid 1728 through 1730' Processing helix chain 'B' and resid 1740 through 1762 Processing helix chain 'B' and resid 1769 through 1783 Processing helix chain 'B' and resid 1787 through 1808 removed outlier: 3.563A pdb=" N ASN B1808 " --> pdb=" O TYR B1804 " (cutoff:3.500A) Processing helix chain 'B' and resid 1874 through 1895 Proline residue: B1883 - end of helix removed outlier: 3.810A pdb=" N SER B1893 " --> pdb=" O PHE B1889 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B1894 " --> pdb=" O ARG B1890 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER B1895 " --> pdb=" O SER B1891 " (cutoff:3.500A) Processing helix chain 'B' and resid 1900 through 1913 Processing helix chain 'B' and resid 1917 through 1929 removed outlier: 3.901A pdb=" N GLU B1921 " --> pdb=" O PRO B1917 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA B1922 " --> pdb=" O ASP B1918 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS B1928 " --> pdb=" O VAL B1924 " (cutoff:3.500A) Processing helix chain 'B' and resid 1933 through 1935 No H-bonds generated for 'chain 'B' and resid 1933 through 1935' Processing helix chain 'B' and resid 1939 through 1945 removed outlier: 4.024A pdb=" N ARG B1945 " --> pdb=" O GLN B1941 " (cutoff:3.500A) Processing helix chain 'B' and resid 1951 through 1967 Processing helix chain 'B' and resid 1973 through 1981 removed outlier: 3.852A pdb=" N LYS B1981 " --> pdb=" O THR B1977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1985 through 2000 removed outlier: 4.493A pdb=" N GLU B2000 " --> pdb=" O LYS B1996 " (cutoff:3.500A) Processing helix chain 'B' and resid 2004 through 2016 Processing helix chain 'B' and resid 2023 through 2041 removed outlier: 3.599A pdb=" N ARG B2036 " --> pdb=" O GLU B2032 " (cutoff:3.500A) Processing helix chain 'B' and resid 2044 through 2058 removed outlier: 3.877A pdb=" N GLU B2049 " --> pdb=" O LYS B2045 " (cutoff:3.500A) Proline residue: B2053 - end of helix Processing helix chain 'B' and resid 2065 through 2090 removed outlier: 6.078A pdb=" N ARG B2076 " --> pdb=" O GLN B2072 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N ASP B2077 " --> pdb=" O ALA B2073 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN B2082 " --> pdb=" O LEU B2078 " (cutoff:3.500A) Processing helix chain 'B' and resid 2094 through 2112 removed outlier: 4.340A pdb=" N GLN B2099 " --> pdb=" O LYS B2095 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA B2100 " --> pdb=" O ASP B2096 " (cutoff:3.500A) Processing helix chain 'B' and resid 2123 through 2126 No H-bonds generated for 'chain 'B' and resid 2123 through 2126' Processing helix chain 'B' and resid 2193 through 2210 removed outlier: 3.838A pdb=" N ARG B2197 " --> pdb=" O ARG B2193 " (cutoff:3.500A) Processing helix chain 'B' and resid 2213 through 2216 No H-bonds generated for 'chain 'B' and resid 2213 through 2216' Processing helix chain 'B' and resid 2247 through 2256 removed outlier: 4.271A pdb=" N ASP B2252 " --> pdb=" O ALA B2248 " (cutoff:3.500A) Processing helix chain 'B' and resid 2263 through 2271 Processing helix chain 'B' and resid 2275 through 2277 No H-bonds generated for 'chain 'B' and resid 2275 through 2277' Processing helix chain 'B' and resid 2280 through 2292 Processing helix chain 'B' and resid 2298 through 2305 Processing helix chain 'B' and resid 2310 through 2334 removed outlier: 4.190A pdb=" N VAL B2326 " --> pdb=" O ARG B2322 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET B2327 " --> pdb=" O SER B2323 " (cutoff:3.500A) Processing helix chain 'B' and resid 2381 through 2384 No H-bonds generated for 'chain 'B' and resid 2381 through 2384' Processing helix chain 'B' and resid 2395 through 2409 Processing helix chain 'B' and resid 2411 through 2422 Processing helix chain 'B' and resid 2495 through 2507 removed outlier: 3.628A pdb=" N ARG B2503 " --> pdb=" O GLN B2499 " (cutoff:3.500A) Processing helix chain 'B' and resid 2521 through 2532 Processing helix chain 'B' and resid 2535 through 2538 No H-bonds generated for 'chain 'B' and resid 2535 through 2538' Processing helix chain 'B' and resid 2543 through 2545 No H-bonds generated for 'chain 'B' and resid 2543 through 2545' Processing helix chain 'E' and resid 33 through 48 removed outlier: 6.288A pdb=" N ARG E 47 " --> pdb=" O GLN E 43 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 48 " --> pdb=" O ASN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 69 Processing helix chain 'E' and resid 74 through 77 No H-bonds generated for 'chain 'E' and resid 74 through 77' Processing helix chain 'E' and resid 81 through 89 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 114 through 122 Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 142 through 156 removed outlier: 3.781A pdb=" N ALA E 146 " --> pdb=" O GLU E 142 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU E 147 " --> pdb=" O ARG E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 174 Processing helix chain 'E' and resid 184 through 197 removed outlier: 4.036A pdb=" N ILE E 190 " --> pdb=" O ALA E 186 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU E 196 " --> pdb=" O CYS E 192 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLN E 197 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing helix chain 'E' and resid 199 through 204 Processing helix chain 'E' and resid 208 through 214 Processing helix chain 'E' and resid 221 through 234 removed outlier: 4.291A pdb=" N THR E 230 " --> pdb=" O ALA E 226 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE E 231 " --> pdb=" O LEU E 227 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 243 removed outlier: 4.993A pdb=" N TYR E 243 " --> pdb=" O LYS E 239 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 252 No H-bonds generated for 'chain 'E' and resid 250 through 252' Processing helix chain 'E' and resid 255 through 258 No H-bonds generated for 'chain 'E' and resid 255 through 258' Processing helix chain 'E' and resid 274 through 291 Processing helix chain 'E' and resid 295 through 301 removed outlier: 3.667A pdb=" N ASN E 300 " --> pdb=" O ALA E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 314 Processing helix chain 'E' and resid 323 through 334 removed outlier: 3.646A pdb=" N LEU E 328 " --> pdb=" O ARG E 324 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU E 329 " --> pdb=" O ARG E 325 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL E 330 " --> pdb=" O GLY E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 352 removed outlier: 3.843A pdb=" N LEU E 351 " --> pdb=" O ILE E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 370 through 376 removed outlier: 3.701A pdb=" N THR E 375 " --> pdb=" O ALA E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 404 through 413 Processing helix chain 'E' and resid 417 through 437 removed outlier: 4.039A pdb=" N ARG E 422 " --> pdb=" O HIS E 418 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN E 435 " --> pdb=" O LEU E 431 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR E 436 " --> pdb=" O HIS E 432 " (cutoff:3.500A) Processing helix chain 'E' and resid 440 through 443 No H-bonds generated for 'chain 'E' and resid 440 through 443' Processing helix chain 'E' and resid 450 through 456 removed outlier: 3.779A pdb=" N MET E 455 " --> pdb=" O THR E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 485 Processing helix chain 'E' and resid 492 through 508 Processing helix chain 'E' and resid 526 through 534 Processing helix chain 'E' and resid 548 through 556 Processing helix chain 'E' and resid 568 through 581 Processing helix chain 'E' and resid 588 through 590 No H-bonds generated for 'chain 'E' and resid 588 through 590' Processing helix chain 'E' and resid 599 through 611 Processing helix chain 'E' and resid 623 through 638 Processing helix chain 'E' and resid 648 through 651 No H-bonds generated for 'chain 'E' and resid 648 through 651' Processing helix chain 'E' and resid 655 through 667 removed outlier: 3.641A pdb=" N TYR E 659 " --> pdb=" O SER E 656 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE E 660 " --> pdb=" O GLN E 657 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE E 662 " --> pdb=" O TYR E 659 " (cutoff:3.500A) Processing helix chain 'E' and resid 670 through 678 removed outlier: 3.903A pdb=" N LYS E 674 " --> pdb=" O PRO E 670 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET E 675 " --> pdb=" O HIS E 671 " (cutoff:3.500A) Processing helix chain 'E' and resid 682 through 688 Processing helix chain 'E' and resid 696 through 702 Processing helix chain 'E' and resid 712 through 722 removed outlier: 4.156A pdb=" N ILE E 716 " --> pdb=" O LEU E 712 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU E 717 " --> pdb=" O ALA E 713 " (cutoff:3.500A) Processing helix chain 'E' and resid 726 through 734 Processing helix chain 'E' and resid 738 through 741 No H-bonds generated for 'chain 'E' and resid 738 through 741' Processing helix chain 'E' and resid 747 through 759 removed outlier: 4.602A pdb=" N ILE E 752 " --> pdb=" O ASN E 748 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU E 753 " --> pdb=" O ASN E 749 " (cutoff:3.500A) Processing helix chain 'E' and resid 764 through 779 removed outlier: 4.129A pdb=" N GLU E 779 " --> pdb=" O ASP E 775 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 789 removed outlier: 3.578A pdb=" N ALA E 786 " --> pdb=" O ALA E 782 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN E 789 " --> pdb=" O HIS E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 799 through 810 removed outlier: 4.138A pdb=" N PHE E 808 " --> pdb=" O LEU E 804 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU E 809 " --> pdb=" O LEU E 805 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N SER E 810 " --> pdb=" O LEU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 812 through 820 removed outlier: 6.268A pdb=" N TYR E 817 " --> pdb=" O LYS E 813 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU E 820 " --> pdb=" O SER E 816 " (cutoff:3.500A) Processing helix chain 'E' and resid 824 through 833 removed outlier: 4.114A pdb=" N GLU E 829 " --> pdb=" O ALA E 825 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS E 830 " --> pdb=" O LYS E 826 " (cutoff:3.500A) Processing helix chain 'E' and resid 835 through 851 removed outlier: 4.148A pdb=" N VAL E 840 " --> pdb=" O ASN E 836 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASP E 841 " --> pdb=" O SER E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 882 through 886 Processing helix chain 'E' and resid 892 through 899 removed outlier: 4.095A pdb=" N GLN E 899 " --> pdb=" O LEU E 895 " (cutoff:3.500A) Processing helix chain 'E' and resid 902 through 910 Processing helix chain 'E' and resid 917 through 935 removed outlier: 4.244A pdb=" N SER E 935 " --> pdb=" O GLY E 931 " (cutoff:3.500A) Processing helix chain 'E' and resid 937 through 944 removed outlier: 3.840A pdb=" N ASN E 941 " --> pdb=" O ASN E 937 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E 942 " --> pdb=" O TRP E 938 " (cutoff:3.500A) Processing helix chain 'E' and resid 949 through 958 removed outlier: 3.945A pdb=" N LYS E 957 " --> pdb=" O LEU E 953 " (cutoff:3.500A) Processing helix chain 'E' and resid 962 through 976 removed outlier: 3.573A pdb=" N VAL E 969 " --> pdb=" O ARG E 965 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA E 976 " --> pdb=" O LEU E 972 " (cutoff:3.500A) Processing helix chain 'E' and resid 979 through 987 removed outlier: 3.772A pdb=" N CYS E 987 " --> pdb=" O ASP E 983 " (cutoff:3.500A) Processing helix chain 'E' and resid 1433 through 1435 No H-bonds generated for 'chain 'E' and resid 1433 through 1435' Processing helix chain 'E' and resid 1480 through 1483 No H-bonds generated for 'chain 'E' and resid 1480 through 1483' Processing helix chain 'E' and resid 1489 through 1493 removed outlier: 3.882A pdb=" N MET E1493 " --> pdb=" O LEU E1489 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1489 through 1493' Processing helix chain 'E' and resid 1525 through 1529 Processing helix chain 'E' and resid 1610 through 1624 Processing helix chain 'E' and resid 1629 through 1642 Processing helix chain 'E' and resid 1650 through 1660 removed outlier: 3.693A pdb=" N GLU E1655 " --> pdb=" O CYS E1651 " (cutoff:3.500A) Processing helix chain 'E' and resid 1667 through 1676 Processing helix chain 'E' and resid 1683 through 1693 Processing helix chain 'F' and resid 33 through 48 removed outlier: 6.163A pdb=" N ARG F 47 " --> pdb=" O GLN F 43 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LEU F 48 " --> pdb=" O ASN F 44 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 69 Processing helix chain 'F' and resid 81 through 89 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 142 through 156 removed outlier: 3.747A pdb=" N ALA F 146 " --> pdb=" O GLU F 142 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 147 " --> pdb=" O ARG F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 160 No H-bonds generated for 'chain 'F' and resid 158 through 160' Processing helix chain 'F' and resid 163 through 174 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.697A pdb=" N ILE F 190 " --> pdb=" O ALA F 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 204 Processing helix chain 'F' and resid 207 through 214 Processing helix chain 'F' and resid 221 through 234 removed outlier: 3.986A pdb=" N THR F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ILE F 231 " --> pdb=" O LEU F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 243 removed outlier: 5.098A pdb=" N TYR F 243 " --> pdb=" O LYS F 239 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 252 No H-bonds generated for 'chain 'F' and resid 250 through 252' Processing helix chain 'F' and resid 255 through 258 No H-bonds generated for 'chain 'F' and resid 255 through 258' Processing helix chain 'F' and resid 274 through 291 Processing helix chain 'F' and resid 295 through 301 removed outlier: 3.621A pdb=" N ASN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 314 Processing helix chain 'F' and resid 324 through 334 removed outlier: 3.682A pdb=" N LEU F 328 " --> pdb=" O ARG F 324 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU F 329 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL F 330 " --> pdb=" O GLY F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 352 removed outlier: 3.894A pdb=" N LEU F 351 " --> pdb=" O ILE F 347 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER F 352 " --> pdb=" O GLU F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 364 through 367 No H-bonds generated for 'chain 'F' and resid 364 through 367' Processing helix chain 'F' and resid 370 through 376 removed outlier: 3.543A pdb=" N THR F 375 " --> pdb=" O ALA F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 401 Processing helix chain 'F' and resid 404 through 413 Processing helix chain 'F' and resid 417 through 437 removed outlier: 3.955A pdb=" N ARG F 422 " --> pdb=" O HIS F 418 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN F 435 " --> pdb=" O LEU F 431 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 436 " --> pdb=" O HIS F 432 " (cutoff:3.500A) Processing helix chain 'F' and resid 440 through 443 No H-bonds generated for 'chain 'F' and resid 440 through 443' Processing helix chain 'F' and resid 450 through 456 removed outlier: 3.808A pdb=" N MET F 455 " --> pdb=" O THR F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 485 Processing helix chain 'F' and resid 493 through 508 Processing helix chain 'F' and resid 526 through 534 Processing helix chain 'F' and resid 548 through 556 Processing helix chain 'F' and resid 568 through 581 Processing helix chain 'F' and resid 599 through 614 removed outlier: 3.729A pdb=" N LEU F 613 " --> pdb=" O THR F 609 " (cutoff:3.500A) Processing helix chain 'F' and resid 623 through 638 Processing helix chain 'F' and resid 648 through 651 No H-bonds generated for 'chain 'F' and resid 648 through 651' Processing helix chain 'F' and resid 655 through 667 removed outlier: 3.802A pdb=" N TYR F 659 " --> pdb=" O SER F 656 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE F 660 " --> pdb=" O GLN F 657 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE F 662 " --> pdb=" O TYR F 659 " (cutoff:3.500A) Processing helix chain 'F' and resid 670 through 678 removed outlier: 3.961A pdb=" N LYS F 674 " --> pdb=" O PRO F 670 " (cutoff:3.500A) Processing helix chain 'F' and resid 682 through 690 removed outlier: 4.130A pdb=" N SER F 690 " --> pdb=" O LEU F 686 " (cutoff:3.500A) Processing helix chain 'F' and resid 696 through 702 Processing helix chain 'F' and resid 712 through 722 removed outlier: 3.623A pdb=" N ILE F 716 " --> pdb=" O LEU F 712 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU F 717 " --> pdb=" O ALA F 713 " (cutoff:3.500A) Processing helix chain 'F' and resid 726 through 740 removed outlier: 4.184A pdb=" N LEU F 736 " --> pdb=" O ALA F 732 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ARG F 737 " --> pdb=" O THR F 733 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N VAL F 738 " --> pdb=" O LYS F 734 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU F 739 " --> pdb=" O HIS F 735 " (cutoff:3.500A) Processing helix chain 'F' and resid 747 through 760 removed outlier: 4.589A pdb=" N ILE F 752 " --> pdb=" O ASN F 748 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLU F 753 " --> pdb=" O ASN F 749 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N HIS F 760 " --> pdb=" O VAL F 756 " (cutoff:3.500A) Processing helix chain 'F' and resid 764 through 779 removed outlier: 4.512A pdb=" N GLU F 779 " --> pdb=" O ASP F 775 " (cutoff:3.500A) Processing helix chain 'F' and resid 781 through 789 Processing helix chain 'F' and resid 799 through 810 removed outlier: 3.792A pdb=" N ARG F 807 " --> pdb=" O LEU F 803 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N PHE F 808 " --> pdb=" O LEU F 804 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU F 809 " --> pdb=" O LEU F 805 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER F 810 " --> pdb=" O LEU F 806 " (cutoff:3.500A) Processing helix chain 'F' and resid 812 through 820 removed outlier: 6.245A pdb=" N TYR F 817 " --> pdb=" O LYS F 813 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLU F 820 " --> pdb=" O SER F 816 " (cutoff:3.500A) Processing helix chain 'F' and resid 824 through 833 removed outlier: 3.843A pdb=" N GLU F 829 " --> pdb=" O ALA F 825 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS F 830 " --> pdb=" O LYS F 826 " (cutoff:3.500A) Processing helix chain 'F' and resid 836 through 851 removed outlier: 3.975A pdb=" N VAL F 840 " --> pdb=" O ASN F 836 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ASP F 841 " --> pdb=" O SER F 837 " (cutoff:3.500A) Processing helix chain 'F' and resid 882 through 886 Processing helix chain 'F' and resid 891 through 897 Processing helix chain 'F' and resid 902 through 910 Processing helix chain 'F' and resid 918 through 935 removed outlier: 3.882A pdb=" N SER F 935 " --> pdb=" O GLY F 931 " (cutoff:3.500A) Processing helix chain 'F' and resid 937 through 943 removed outlier: 3.677A pdb=" N ASN F 941 " --> pdb=" O ASN F 937 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU F 942 " --> pdb=" O TRP F 938 " (cutoff:3.500A) Processing helix chain 'F' and resid 949 through 958 removed outlier: 3.855A pdb=" N LYS F 957 " --> pdb=" O LEU F 953 " (cutoff:3.500A) Processing helix chain 'F' and resid 962 through 977 removed outlier: 3.647A pdb=" N VAL F 969 " --> pdb=" O ARG F 965 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA F 976 " --> pdb=" O LEU F 972 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LYS F 977 " --> pdb=" O GLY F 973 " (cutoff:3.500A) Processing helix chain 'F' and resid 979 through 987 removed outlier: 3.763A pdb=" N CYS F 987 " --> pdb=" O ASP F 983 " (cutoff:3.500A) Processing helix chain 'F' and resid 1433 through 1435 No H-bonds generated for 'chain 'F' and resid 1433 through 1435' Processing helix chain 'F' and resid 1480 through 1483 No H-bonds generated for 'chain 'F' and resid 1480 through 1483' Processing helix chain 'F' and resid 1489 through 1492 No H-bonds generated for 'chain 'F' and resid 1489 through 1492' Processing helix chain 'F' and resid 1525 through 1528 No H-bonds generated for 'chain 'F' and resid 1525 through 1528' Processing helix chain 'F' and resid 1610 through 1624 removed outlier: 4.073A pdb=" N SER F1624 " --> pdb=" O VAL F1620 " (cutoff:3.500A) Processing helix chain 'F' and resid 1629 through 1642 Processing helix chain 'F' and resid 1650 through 1662 removed outlier: 3.750A pdb=" N GLU F1655 " --> pdb=" O CYS F1651 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS F1662 " --> pdb=" O HIS F1658 " (cutoff:3.500A) Processing helix chain 'F' and resid 1667 through 1676 Processing helix chain 'F' and resid 1683 through 1693 Processing helix chain 'G' and resid 7 through 20 Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 85 through 100 removed outlier: 3.670A pdb=" N ASN G 99 " --> pdb=" O LYS G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 117 through 123 removed outlier: 4.021A pdb=" N SER G 122 " --> pdb=" O GLN G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 145 Processing helix chain 'H' and resid 7 through 20 Processing helix chain 'H' and resid 26 through 30 Processing helix chain 'H' and resid 85 through 100 removed outlier: 3.552A pdb=" N ASN H 99 " --> pdb=" O LYS H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 123 removed outlier: 4.027A pdb=" N SER H 122 " --> pdb=" O GLN H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 145 Processing sheet with id= A, first strand: chain 'A' and resid 2120 through 2122 Processing sheet with id= B, first strand: chain 'A' and resid 2181 through 2183 Processing sheet with id= C, first strand: chain 'A' and resid 2184 through 2188 Processing sheet with id= D, first strand: chain 'A' and resid 2243 through 2245 Processing sheet with id= E, first strand: chain 'B' and resid 2120 through 2122 Processing sheet with id= F, first strand: chain 'B' and resid 2181 through 2183 Processing sheet with id= G, first strand: chain 'B' and resid 2184 through 2188 Processing sheet with id= H, first strand: chain 'B' and resid 2243 through 2245 Processing sheet with id= I, first strand: chain 'C' and resid 315 through 321 removed outlier: 7.117A pdb=" N ALA C 18 " --> pdb=" O VAL C 316 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU C 318 " --> pdb=" O ALA C 16 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA C 16 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N PHE C 320 " --> pdb=" O ILE C 14 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE C 14 " --> pdb=" O PHE C 320 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY C 19 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N THR C 23 " --> pdb=" O GLY C 19 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG C 36 " --> pdb=" O PHE C 26 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 47 through 50 Processing sheet with id= K, first strand: chain 'C' and resid 124 through 126 removed outlier: 4.572A pdb=" N THR C 108 " --> pdb=" O GLY C 104 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 90 " --> pdb=" O GLY C 103 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 162 through 166 removed outlier: 4.670A pdb=" N ALA C 151 " --> pdb=" O ASP C 147 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP C 147 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 173 through 177 removed outlier: 7.008A pdb=" N VAL C 188 " --> pdb=" O THR C 174 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA C 176 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ALA C 186 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN C 193 " --> pdb=" O ASN C 189 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS C 194 " --> pdb=" O ILE C 216 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ASN C 198 " --> pdb=" O PRO C 212 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 223 through 228 removed outlier: 6.894A pdb=" N CYS C 238 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N CYS C 226 " --> pdb=" O ALA C 236 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N ALA C 236 " --> pdb=" O CYS C 226 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE C 228 " --> pdb=" O LEU C 234 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU C 234 " --> pdb=" O PHE C 228 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ARG C 248 " --> pdb=" O LEU C 254 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LEU C 254 " --> pdb=" O ARG C 248 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 273 through 277 removed outlier: 6.824A pdb=" N ALA C 288 " --> pdb=" O TRP C 274 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N CYS C 276 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL C 286 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER C 289 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU C 293 " --> pdb=" O SER C 289 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N CYS C 298 " --> pdb=" O ILE C 304 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE C 304 " --> pdb=" O CYS C 298 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 315 through 321 removed outlier: 7.134A pdb=" N ALA D 18 " --> pdb=" O VAL D 316 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU D 318 " --> pdb=" O ALA D 16 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ALA D 16 " --> pdb=" O LEU D 318 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE D 320 " --> pdb=" O ILE D 14 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 14 " --> pdb=" O PHE D 320 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU D 15 " --> pdb=" O TRP D 27 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY D 19 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N THR D 23 " --> pdb=" O GLY D 19 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 36 " --> pdb=" O PHE D 26 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 47 through 50 removed outlier: 4.100A pdb=" N ILE D 79 " --> pdb=" O MET D 67 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 124 through 126 removed outlier: 4.434A pdb=" N THR D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N SER D 90 " --> pdb=" O GLY D 103 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 162 through 166 removed outlier: 4.629A pdb=" N ALA D 151 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP D 147 " --> pdb=" O ALA D 151 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 173 through 178 removed outlier: 7.083A pdb=" N VAL D 188 " --> pdb=" O THR D 174 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA D 176 " --> pdb=" O ALA D 186 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ALA D 186 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N ASN D 193 " --> pdb=" O ASN D 189 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N CYS D 194 " --> pdb=" O ILE D 216 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN D 198 " --> pdb=" O PRO D 212 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 223 through 228 removed outlier: 6.938A pdb=" N CYS D 238 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N CYS D 226 " --> pdb=" O ALA D 236 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ALA D 236 " --> pdb=" O CYS D 226 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE D 228 " --> pdb=" O LEU D 234 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 234 " --> pdb=" O PHE D 228 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ARG D 248 " --> pdb=" O LEU D 254 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU D 254 " --> pdb=" O ARG D 248 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 273 through 277 removed outlier: 6.849A pdb=" N ALA D 288 " --> pdb=" O TRP D 274 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N CYS D 276 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL D 286 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N CYS D 298 " --> pdb=" O ILE D 304 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE D 304 " --> pdb=" O CYS D 298 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 990 through 992 Processing sheet with id= X, first strand: chain 'F' and resid 990 through 992 2674 hydrogen bonds defined for protein. 7740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 25.67 Time building geometry restraints manager: 17.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 19454 1.36 - 1.51: 14432 1.51 - 1.65: 23576 1.65 - 1.79: 143 1.79 - 1.93: 383 Bond restraints: 57988 Sorted by residual: bond pdb=" C5 AGS B2601 " pdb=" C6 AGS B2601 " ideal model delta sigma weight residual 1.409 1.329 0.080 1.00e-02 1.00e+04 6.45e+01 bond pdb=" C5 AGS A2601 " pdb=" C6 AGS A2601 " ideal model delta sigma weight residual 1.409 1.330 0.079 1.00e-02 1.00e+04 6.23e+01 bond pdb=" C5 AGS F4802 " pdb=" C6 AGS F4802 " ideal model delta sigma weight residual 1.409 1.332 0.077 1.00e-02 1.00e+04 5.98e+01 bond pdb=" C5 AGS E4802 " pdb=" C6 AGS E4802 " ideal model delta sigma weight residual 1.409 1.333 0.076 1.00e-02 1.00e+04 5.83e+01 bond pdb=" C2 AGS E4802 " pdb=" N3 AGS E4802 " ideal model delta sigma weight residual 1.335 1.398 -0.063 1.00e-02 1.00e+04 3.98e+01 ... (remaining 57983 not shown) Histogram of bond angle deviations from ideal: 96.20 - 104.05: 771 104.05 - 111.91: 27233 111.91 - 119.76: 23349 119.76 - 127.61: 26727 127.61 - 135.46: 671 Bond angle restraints: 78751 Sorted by residual: angle pdb=" N1 AGS A2601 " pdb=" C2 AGS A2601 " pdb=" N3 AGS A2601 " ideal model delta sigma weight residual 128.80 117.85 10.95 8.41e-01 1.41e+00 1.70e+02 angle pdb=" N1 AGS F4802 " pdb=" C2 AGS F4802 " pdb=" N3 AGS F4802 " ideal model delta sigma weight residual 128.80 117.86 10.94 8.41e-01 1.41e+00 1.69e+02 angle pdb=" N1 AGS B2601 " pdb=" C2 AGS B2601 " pdb=" N3 AGS B2601 " ideal model delta sigma weight residual 128.80 117.87 10.93 8.41e-01 1.41e+00 1.69e+02 angle pdb=" N1 AGS E4802 " pdb=" C2 AGS E4802 " pdb=" N3 AGS E4802 " ideal model delta sigma weight residual 128.80 117.93 10.87 8.41e-01 1.41e+00 1.67e+02 angle pdb=" C5 AGS E4802 " pdb=" N7 AGS E4802 " pdb=" C8 AGS E4802 " ideal model delta sigma weight residual 103.67 108.11 -4.44 4.26e-01 5.51e+00 1.09e+02 ... (remaining 78746 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.62: 33794 30.62 - 61.25: 1201 61.25 - 91.87: 90 91.87 - 122.50: 3 122.50 - 153.12: 3 Dihedral angle restraints: 35091 sinusoidal: 13319 harmonic: 21772 Sorted by residual: dihedral pdb=" CA GLY E 367 " pdb=" C GLY E 367 " pdb=" N PHE E 368 " pdb=" CA PHE E 368 " ideal model delta harmonic sigma weight residual -180.00 -145.09 -34.91 0 5.00e+00 4.00e-02 4.88e+01 dihedral pdb=" CA GLY F 367 " pdb=" C GLY F 367 " pdb=" N PHE F 368 " pdb=" CA PHE F 368 " ideal model delta harmonic sigma weight residual 180.00 -153.44 -26.56 0 5.00e+00 4.00e-02 2.82e+01 dihedral pdb=" CA LEU B 891 " pdb=" C LEU B 891 " pdb=" N GLY B 892 " pdb=" CA GLY B 892 " ideal model delta harmonic sigma weight residual 180.00 154.31 25.69 0 5.00e+00 4.00e-02 2.64e+01 ... (remaining 35088 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 7548 0.062 - 0.125: 1402 0.125 - 0.187: 166 0.187 - 0.250: 21 0.250 - 0.312: 3 Chirality restraints: 9140 Sorted by residual: chirality pdb=" CB ILE C 216 " pdb=" CA ILE C 216 " pdb=" CG1 ILE C 216 " pdb=" CG2 ILE C 216 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" CA ASN F1519 " pdb=" N ASN F1519 " pdb=" C ASN F1519 " pdb=" CB ASN F1519 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA ASN E1519 " pdb=" N ASN E1519 " pdb=" C ASN E1519 " pdb=" CB ASN E1519 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 9137 not shown) Planarity restraints: 10082 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1157 " 0.045 5.00e-02 4.00e+02 6.73e-02 7.25e+00 pdb=" N PRO A1158 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO A1158 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A1158 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 769 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.96e+00 pdb=" N PRO B 770 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO B 770 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 770 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 769 " -0.041 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 770 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 770 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 770 " -0.034 5.00e-02 4.00e+02 ... (remaining 10079 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 10412 2.77 - 3.31: 51833 3.31 - 3.84: 92545 3.84 - 4.37: 107063 4.37 - 4.90: 186329 Nonbonded interactions: 448182 Sorted by model distance: nonbonded pdb=" O GLY E 650 " pdb=" OG1 THR E 654 " model vdw 2.242 2.440 nonbonded pdb=" O LEU B1343 " pdb=" OG SER B1347 " model vdw 2.272 2.440 nonbonded pdb=" OG SER C 239 " pdb=" OD1 ASP C 241 " model vdw 2.296 2.440 nonbonded pdb=" O GLU F 225 " pdb=" OG1 THR F 229 " model vdw 2.309 2.440 nonbonded pdb=" O SER F 138 " pdb=" OG SER F 138 " model vdw 2.310 2.440 ... (remaining 448177 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 17 through 580 or (resid 581 through 589 and (name N or na \ me CA or name C or name O or name CB )) or resid 590 or (resid 591 through 595 a \ nd (name N or name CA or name C or name O or name CB )) or resid 599 through 254 \ 9 or resid 2601 through 2602)) selection = (chain 'B' and (resid 17 through 578 or resid 580 through 2549 or resid 2601 thr \ ough 2602)) } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 8.980 Check model and map are aligned: 0.640 Set scattering table: 0.390 Process input model: 128.850 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.340 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:2.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 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 : 0.005 0.087 57988 Z= 0.307 Angle : 0.848 14.524 78751 Z= 0.487 Chirality : 0.049 0.312 9140 Planarity : 0.006 0.067 10082 Dihedral : 15.307 153.119 20881 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.68 % Favored : 96.30 % Rotamer: Outliers : 1.57 % Allowed : 11.66 % Favored : 86.76 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.08), residues: 7316 helix: -2.33 (0.06), residues: 4594 sheet: -1.91 (0.26), residues: 302 loop : -2.53 (0.11), residues: 2420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 297 HIS 0.014 0.001 HIS A1988 PHE 0.021 0.002 PHE B1122 TYR 0.024 0.002 TYR E1522 ARG 0.014 0.001 ARG E 533 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1051 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 961 time to evaluate : 5.178 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 676 LEU cc_start: 0.9231 (mm) cc_final: 0.8979 (mm) REVERT: A 934 MET cc_start: 0.8464 (mmm) cc_final: 0.8059 (mmm) REVERT: A 970 MET cc_start: 0.8975 (ptp) cc_final: 0.8539 (ptm) REVERT: A 1174 MET cc_start: 0.8739 (mmm) cc_final: 0.8442 (mmm) REVERT: A 1269 TRP cc_start: 0.6552 (m100) cc_final: 0.5965 (m100) REVERT: A 1282 GLU cc_start: 0.9195 (tt0) cc_final: 0.8927 (pp20) REVERT: A 1458 ASP cc_start: 0.8301 (m-30) cc_final: 0.7748 (t0) REVERT: A 1542 ASP cc_start: 0.7273 (m-30) cc_final: 0.7040 (m-30) REVERT: A 1704 MET cc_start: 0.9081 (ttm) cc_final: 0.8832 (ttt) REVERT: A 1802 LEU cc_start: 0.9529 (mt) cc_final: 0.9319 (mm) REVERT: A 2415 MET cc_start: 0.8356 (tpp) cc_final: 0.8100 (tpp) REVERT: B 721 MET cc_start: 0.7824 (mmm) cc_final: 0.7571 (mtp) REVERT: B 795 ILE cc_start: 0.5449 (mm) cc_final: 0.5036 (mm) REVERT: B 1030 TYR cc_start: 0.7603 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: B 1122 PHE cc_start: 0.7187 (p90) cc_final: 0.6984 (p90) REVERT: B 1289 LEU cc_start: 0.7842 (mp) cc_final: 0.7632 (mm) REVERT: B 1443 LEU cc_start: 0.8385 (mt) cc_final: 0.8156 (pp) REVERT: B 1512 MET cc_start: 0.8609 (ptm) cc_final: 0.8171 (ptm) REVERT: B 1701 MET cc_start: 0.8597 (mtm) cc_final: 0.8004 (mtp) REVERT: B 1952 LEU cc_start: 0.6852 (mt) cc_final: 0.6123 (mp) REVERT: B 2199 MET cc_start: 0.8024 (mmt) cc_final: 0.7463 (mmm) REVERT: C 67 MET cc_start: 0.7065 (mmm) cc_final: 0.6814 (mmm) REVERT: C 125 PHE cc_start: 0.6754 (t80) cc_final: 0.6529 (t80) REVERT: C 128 ASN cc_start: 0.8434 (p0) cc_final: 0.8147 (m110) REVERT: C 273 MET cc_start: 0.8167 (mmm) cc_final: 0.6671 (tpp) REVERT: D 81 TYR cc_start: 0.7603 (m-80) cc_final: 0.6872 (m-80) REVERT: D 86 LYS cc_start: 0.7798 (mmtp) cc_final: 0.7144 (mmmt) REVERT: D 112 TRP cc_start: 0.8187 (m100) cc_final: 0.6604 (m100) REVERT: D 158 LYS cc_start: 0.8193 (mmmt) cc_final: 0.7689 (mmtt) REVERT: D 185 MET cc_start: 0.8495 (tmm) cc_final: 0.7764 (tmm) REVERT: D 224 LEU cc_start: 0.8432 (mt) cc_final: 0.8128 (mp) REVERT: D 306 ARG cc_start: 0.6743 (OUTLIER) cc_final: 0.6298 (mmm-85) REVERT: E 160 LEU cc_start: 0.8953 (mt) cc_final: 0.8750 (mp) REVERT: E 183 MET cc_start: 0.7665 (mtp) cc_final: 0.7412 (tmm) REVERT: E 198 ASN cc_start: 0.7765 (t0) cc_final: 0.7310 (t0) REVERT: E 237 HIS cc_start: 0.5467 (t70) cc_final: 0.5265 (t70) REVERT: E 254 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.6742 (pp) REVERT: E 259 ASP cc_start: 0.7360 (t0) cc_final: 0.7005 (t0) REVERT: E 388 MET cc_start: 0.7321 (tpt) cc_final: 0.6858 (ttp) REVERT: E 669 HIS cc_start: 0.7775 (m90) cc_final: 0.7336 (t70) REVERT: E 691 LEU cc_start: 0.5349 (OUTLIER) cc_final: 0.5031 (pp) REVERT: E 886 LEU cc_start: 0.7127 (tp) cc_final: 0.6825 (tp) REVERT: E 900 ASN cc_start: 0.7800 (m110) cc_final: 0.7196 (p0) REVERT: E 945 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8597 (pm20) REVERT: E 1532 GLN cc_start: 0.8941 (mm-40) cc_final: 0.8605 (tp40) REVERT: F 79 PHE cc_start: 0.7858 (m-80) cc_final: 0.7512 (m-80) REVERT: F 87 CYS cc_start: 0.8359 (m) cc_final: 0.7750 (t) REVERT: F 128 LEU cc_start: 0.8909 (mt) cc_final: 0.8692 (mt) REVERT: F 388 MET cc_start: 0.8474 (tpt) cc_final: 0.8240 (tpt) REVERT: F 453 MET cc_start: 0.8256 (mmm) cc_final: 0.7996 (mmm) REVERT: F 534 ASP cc_start: 0.8652 (t70) cc_final: 0.8403 (m-30) REVERT: F 696 HIS cc_start: 0.7026 (m170) cc_final: 0.6607 (m-70) REVERT: F 717 LEU cc_start: 0.9002 (tp) cc_final: 0.8788 (tp) REVERT: F 1518 ASP cc_start: 0.8918 (p0) cc_final: 0.8536 (t0) REVERT: F 1521 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8545 (mt) REVERT: F 1683 LEU cc_start: 0.7906 (tt) cc_final: 0.7486 (tt) REVERT: H 28 GLU cc_start: 0.8623 (pm20) cc_final: 0.8335 (pm20) REVERT: H 107 GLN cc_start: 0.8896 (mp10) cc_final: 0.8671 (mm-40) outliers start: 90 outliers final: 19 residues processed: 1041 average time/residue: 0.5820 time to fit residues: 991.0323 Evaluate side-chains 586 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 561 time to evaluate : 5.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 725 PHE Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1953 VAL Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1697 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2426 LEU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 214 THR Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 334 ILE Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1521 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 35 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 623 optimal weight: 0.8980 chunk 559 optimal weight: 20.0000 chunk 310 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 377 optimal weight: 3.9990 chunk 298 optimal weight: 0.0040 chunk 578 optimal weight: 9.9990 chunk 223 optimal weight: 9.9990 chunk 351 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 chunk 670 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS A 612 ASN A 743 HIS A 791 ASN A 797 ASN A1077 HIS A1112 HIS A1183 GLN A1333 GLN A1495 GLN A1670 HIS A1715 GLN ** A1722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1726 GLN A1898 ASN A2106 HIS A2340 HIS A2385 ASN A2401 HIS B 646 GLN B 838 GLN B 967 HIS B1014 GLN B1045 ASN B1077 HIS B1106 ASN B1112 HIS B1525 GLN B1670 HIS B1715 GLN B1722 GLN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 GLN ** C 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 118 ASN E 49 GLN E 112 GLN E 219 GLN E 237 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 379 HIS E 432 HIS E 447 HIS E 505 HIS E 531 ASN E 540 HIS E 547 ASN E 564 ASN E 749 ASN E 848 ASN E 894 HIS E 900 ASN E 958 GLN E1674 GLN F 94 ASN F 145 GLN F 214 ASN F 219 GLN F 264 HIS F 359 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 418 HIS F 447 HIS F 505 HIS F 539 GLN F 549 ASN F 846 GLN F 848 ASN F 881 HIS F 908 ASN F 958 GLN F1535 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 57988 Z= 0.177 Angle : 0.558 11.390 78751 Z= 0.279 Chirality : 0.040 0.181 9140 Planarity : 0.004 0.049 10082 Dihedral : 6.286 156.255 8154 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.32 % Allowed : 16.20 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.09), residues: 7316 helix: -0.79 (0.07), residues: 4635 sheet: -1.49 (0.27), residues: 324 loop : -2.22 (0.12), residues: 2357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 99 HIS 0.008 0.001 HIS B2410 PHE 0.022 0.001 PHE B 725 TYR 0.023 0.001 TYR A1220 ARG 0.008 0.000 ARG A1955 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 606 time to evaluate : 5.033 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 970 MET cc_start: 0.8916 (ptp) cc_final: 0.8701 (ptm) REVERT: A 1033 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7953 (pm20) REVERT: A 1174 MET cc_start: 0.8764 (mmm) cc_final: 0.8511 (tmm) REVERT: A 1269 TRP cc_start: 0.6468 (m100) cc_final: 0.5836 (m100) REVERT: A 1282 GLU cc_start: 0.9240 (tt0) cc_final: 0.9017 (pp20) REVERT: A 1458 ASP cc_start: 0.8334 (m-30) cc_final: 0.7803 (t0) REVERT: A 1467 MET cc_start: 0.7589 (mtt) cc_final: 0.7259 (mtt) REVERT: A 1484 LEU cc_start: 0.8095 (tp) cc_final: 0.7857 (tp) REVERT: A 1894 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 1899 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.7120 (p0) REVERT: A 2415 MET cc_start: 0.8365 (tpp) cc_final: 0.8140 (tpp) REVERT: B 1030 TYR cc_start: 0.8047 (OUTLIER) cc_final: 0.7838 (m-80) REVERT: B 1477 MET cc_start: 0.7103 (pmm) cc_final: 0.6720 (ptt) REVERT: B 1512 MET cc_start: 0.8362 (ptm) cc_final: 0.7858 (ptm) REVERT: B 2143 THR cc_start: 0.8784 (OUTLIER) cc_final: 0.8474 (p) REVERT: C 68 TYR cc_start: 0.6562 (m-80) cc_final: 0.6094 (m-80) REVERT: C 81 TYR cc_start: 0.7218 (m-10) cc_final: 0.6798 (m-80) REVERT: C 128 ASN cc_start: 0.8401 (p0) cc_final: 0.8175 (m110) REVERT: C 273 MET cc_start: 0.8259 (mmm) cc_final: 0.6285 (tpp) REVERT: D 86 LYS cc_start: 0.7791 (mmtp) cc_final: 0.7373 (mmmt) REVERT: D 112 TRP cc_start: 0.8135 (m100) cc_final: 0.7817 (m100) REVERT: D 158 LYS cc_start: 0.8085 (mmmt) cc_final: 0.7604 (mmtt) REVERT: D 185 MET cc_start: 0.8307 (tmm) cc_final: 0.7455 (tmm) REVERT: D 224 LEU cc_start: 0.8425 (mt) cc_final: 0.8118 (mp) REVERT: E 198 ASN cc_start: 0.7817 (t0) cc_final: 0.7404 (t0) REVERT: E 388 MET cc_start: 0.7323 (tpt) cc_final: 0.7078 (ttp) REVERT: E 532 LEU cc_start: 0.8222 (pp) cc_final: 0.7912 (pp) REVERT: E 588 TYR cc_start: 0.7568 (t80) cc_final: 0.6755 (t80) REVERT: E 669 HIS cc_start: 0.7775 (m90) cc_final: 0.7339 (t-90) REVERT: E 787 LEU cc_start: 0.9212 (tt) cc_final: 0.8867 (pp) REVERT: E 927 LEU cc_start: 0.8039 (mt) cc_final: 0.7574 (mt) REVERT: E 930 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8344 (mp) REVERT: E 1510 THR cc_start: 0.5606 (OUTLIER) cc_final: 0.5326 (t) REVERT: E 1532 GLN cc_start: 0.8979 (mm-40) cc_final: 0.8708 (tp40) REVERT: F 79 PHE cc_start: 0.7757 (m-80) cc_final: 0.7369 (m-80) REVERT: F 87 CYS cc_start: 0.8359 (m) cc_final: 0.7908 (t) REVERT: F 453 MET cc_start: 0.8308 (mmm) cc_final: 0.8029 (mmm) REVERT: F 534 ASP cc_start: 0.8780 (t70) cc_final: 0.8363 (t0) REVERT: F 696 HIS cc_start: 0.7097 (m170) cc_final: 0.6818 (m-70) REVERT: G 92 ARG cc_start: 0.7974 (mtm-85) cc_final: 0.7773 (mtm-85) REVERT: H 28 GLU cc_start: 0.8622 (pm20) cc_final: 0.8344 (pm20) REVERT: H 88 GLN cc_start: 0.8864 (mm-40) cc_final: 0.8656 (mp10) REVERT: H 96 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8076 (tp30) REVERT: H 107 GLN cc_start: 0.8907 (mp10) cc_final: 0.8679 (mm-40) outliers start: 133 outliers final: 60 residues processed: 706 average time/residue: 0.5253 time to fit residues: 632.2267 Evaluate side-chains 593 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 525 time to evaluate : 5.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1109 ASP Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1899 ASN Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1953 VAL Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2338 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain B residue 664 ILE Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1030 TYR Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1508 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1898 ASN Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2260 LEU Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain C residue 27 TRP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 308 TYR Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 129 ILE Chi-restraints excluded: chain E residue 753 GLU Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 96 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 372 optimal weight: 0.9980 chunk 207 optimal weight: 1.9990 chunk 557 optimal weight: 5.9990 chunk 456 optimal weight: 20.0000 chunk 184 optimal weight: 1.9990 chunk 671 optimal weight: 0.9990 chunk 725 optimal weight: 9.9990 chunk 597 optimal weight: 8.9990 chunk 665 optimal weight: 0.5980 chunk 228 optimal weight: 7.9990 chunk 538 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1722 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1898 ASN B1202 HIS B1492 GLN B1693 HIS B1744 HIS ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2385 ASN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN E 264 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 418 HIS E 440 HIS ** E 531 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 632 GLN E 881 HIS E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 390 ASN F 543 ASN F 995 HIS H 13 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 57988 Z= 0.200 Angle : 0.544 9.709 78751 Z= 0.270 Chirality : 0.040 0.165 9140 Planarity : 0.004 0.048 10082 Dihedral : 6.051 161.190 8129 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.57 % Allowed : 17.67 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.10), residues: 7316 helix: -0.05 (0.08), residues: 4631 sheet: -1.25 (0.27), residues: 324 loop : -2.00 (0.12), residues: 2361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 99 HIS 0.013 0.001 HIS F 505 PHE 0.023 0.001 PHE B1122 TYR 0.022 0.001 TYR B2542 ARG 0.006 0.000 ARG B1709 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 553 time to evaluate : 5.133 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 820 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 838 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.8017 (tp40) REVERT: A 1018 MET cc_start: 0.8284 (mtm) cc_final: 0.8076 (mpp) REVERT: A 1033 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: A 1174 MET cc_start: 0.8832 (mmm) cc_final: 0.8534 (tmm) REVERT: A 1282 GLU cc_start: 0.9247 (tt0) cc_final: 0.9015 (pp20) REVERT: A 1458 ASP cc_start: 0.8285 (m-30) cc_final: 0.7845 (t70) REVERT: A 1484 LEU cc_start: 0.8120 (tp) cc_final: 0.7812 (tp) REVERT: A 1701 MET cc_start: 0.8207 (mtm) cc_final: 0.8007 (ttp) REVERT: A 1747 MET cc_start: 0.8595 (ptp) cc_final: 0.8367 (ptp) REVERT: A 1894 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8650 (mp) REVERT: A 2047 MET cc_start: 0.7563 (ppp) cc_final: 0.7296 (ppp) REVERT: A 2415 MET cc_start: 0.8348 (tpp) cc_final: 0.8109 (tpp) REVERT: B 710 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8181 (tp) REVERT: B 721 MET cc_start: 0.7917 (mmm) cc_final: 0.6806 (mtp) REVERT: B 1238 ARG cc_start: 0.5575 (mmt-90) cc_final: 0.5211 (mmt-90) REVERT: B 1477 MET cc_start: 0.7142 (pmm) cc_final: 0.6806 (ttp) REVERT: B 1701 MET cc_start: 0.8080 (mtp) cc_final: 0.7685 (mtp) REVERT: B 2143 THR cc_start: 0.8854 (OUTLIER) cc_final: 0.8569 (p) REVERT: B 2404 MET cc_start: 0.7923 (tpt) cc_final: 0.7508 (tpt) REVERT: C 68 TYR cc_start: 0.6741 (m-80) cc_final: 0.6474 (m-80) REVERT: C 81 TYR cc_start: 0.7362 (m-10) cc_final: 0.6802 (m-10) REVERT: C 128 ASN cc_start: 0.8485 (p0) cc_final: 0.8160 (m110) REVERT: C 273 MET cc_start: 0.8221 (mmm) cc_final: 0.7251 (mtt) REVERT: D 81 TYR cc_start: 0.6948 (m-80) cc_final: 0.6623 (m-80) REVERT: D 86 LYS cc_start: 0.8027 (mmtp) cc_final: 0.7372 (mmmt) REVERT: D 112 TRP cc_start: 0.8008 (m100) cc_final: 0.6420 (m100) REVERT: D 158 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7589 (mmtt) REVERT: D 185 MET cc_start: 0.8412 (tmm) cc_final: 0.7519 (tmm) REVERT: D 224 LEU cc_start: 0.8431 (mt) cc_final: 0.8104 (mp) REVERT: D 243 THR cc_start: 0.8323 (OUTLIER) cc_final: 0.7913 (p) REVERT: E 198 ASN cc_start: 0.7840 (t0) cc_final: 0.7381 (t0) REVERT: E 588 TYR cc_start: 0.7648 (t80) cc_final: 0.6903 (t80) REVERT: E 669 HIS cc_start: 0.7519 (m90) cc_final: 0.7290 (t-90) REVERT: E 787 LEU cc_start: 0.9191 (tt) cc_final: 0.8887 (pp) REVERT: E 927 LEU cc_start: 0.8048 (mt) cc_final: 0.7561 (mt) REVERT: E 930 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8340 (mp) REVERT: E 983 ASP cc_start: 0.8777 (m-30) cc_final: 0.8411 (m-30) REVERT: E 1510 THR cc_start: 0.5444 (OUTLIER) cc_final: 0.5157 (t) REVERT: E 1532 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8773 (tp40) REVERT: F 79 PHE cc_start: 0.7886 (m-80) cc_final: 0.7469 (m-80) REVERT: F 453 MET cc_start: 0.8365 (mmm) cc_final: 0.7980 (mmm) REVERT: F 534 ASP cc_start: 0.8781 (t70) cc_final: 0.8470 (m-30) REVERT: F 696 HIS cc_start: 0.7158 (m170) cc_final: 0.6865 (m-70) REVERT: F 1611 LEU cc_start: 0.7867 (tt) cc_final: 0.7648 (tt) REVERT: F 1643 TYR cc_start: 0.7933 (m-10) cc_final: 0.7653 (m-10) REVERT: F 1646 THR cc_start: 0.8175 (t) cc_final: 0.7956 (t) REVERT: H 28 GLU cc_start: 0.8714 (pm20) cc_final: 0.8415 (pm20) REVERT: H 88 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8526 (mp10) REVERT: H 107 GLN cc_start: 0.8876 (mp10) cc_final: 0.8656 (mm-40) outliers start: 147 outliers final: 75 residues processed: 673 average time/residue: 0.5259 time to fit residues: 607.6498 Evaluate side-chains 601 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 517 time to evaluate : 5.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 710 LEU Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1508 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1898 ASN Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2058 MET Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain C residue 27 TRP Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 632 GLN Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 467 LEU Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 663 optimal weight: 3.9990 chunk 504 optimal weight: 3.9990 chunk 348 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 320 optimal weight: 6.9990 chunk 450 optimal weight: 10.0000 chunk 673 optimal weight: 0.9980 chunk 713 optimal weight: 7.9990 chunk 352 optimal weight: 2.9990 chunk 638 optimal weight: 0.0270 chunk 192 optimal weight: 2.9990 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A1106 ASN A1439 HIS A1687 HIS A1898 ASN A2093 ASN B1045 ASN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN E 846 GLN E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 57988 Z= 0.223 Angle : 0.546 9.910 78751 Z= 0.271 Chirality : 0.040 0.241 9140 Planarity : 0.003 0.046 10082 Dihedral : 5.955 164.290 8122 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.62 % Allowed : 18.70 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.10), residues: 7316 helix: 0.33 (0.08), residues: 4637 sheet: -1.03 (0.27), residues: 332 loop : -1.93 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1269 HIS 0.007 0.001 HIS E 418 PHE 0.021 0.001 PHE E 682 TYR 0.022 0.001 TYR B2542 ARG 0.015 0.000 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 545 time to evaluate : 5.056 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 609 HIS cc_start: 0.5582 (OUTLIER) cc_final: 0.5263 (t-90) REVERT: A 727 MET cc_start: 0.8044 (mmm) cc_final: 0.7795 (tpp) REVERT: A 820 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8563 (mp) REVERT: A 838 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7972 (tp40) REVERT: A 1033 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: A 1269 TRP cc_start: 0.7297 (m100) cc_final: 0.6510 (m100) REVERT: A 1304 TRP cc_start: 0.8449 (OUTLIER) cc_final: 0.8094 (t60) REVERT: A 1458 ASP cc_start: 0.8309 (m-30) cc_final: 0.7784 (t0) REVERT: A 1484 LEU cc_start: 0.8120 (tp) cc_final: 0.7843 (tp) REVERT: A 1894 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8666 (mp) REVERT: A 2047 MET cc_start: 0.7608 (ppp) cc_final: 0.7366 (ppp) REVERT: A 2415 MET cc_start: 0.8390 (tpp) cc_final: 0.8132 (tpp) REVERT: A 2430 ARG cc_start: 0.7311 (mtm180) cc_final: 0.6945 (ttp-170) REVERT: B 710 LEU cc_start: 0.8158 (tt) cc_final: 0.7948 (tp) REVERT: B 721 MET cc_start: 0.7962 (mmm) cc_final: 0.6801 (mtp) REVERT: B 865 LEU cc_start: 0.8416 (tp) cc_final: 0.8161 (mp) REVERT: B 1701 MET cc_start: 0.8105 (mtp) cc_final: 0.7876 (mtp) REVERT: B 2143 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8620 (p) REVERT: C 68 TYR cc_start: 0.6783 (m-80) cc_final: 0.6571 (m-80) REVERT: C 81 TYR cc_start: 0.7205 (m-10) cc_final: 0.6692 (m-80) REVERT: C 170 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: C 273 MET cc_start: 0.8272 (mmm) cc_final: 0.7401 (mtt) REVERT: D 81 TYR cc_start: 0.7088 (m-80) cc_final: 0.6480 (m-80) REVERT: D 86 LYS cc_start: 0.8088 (mmtp) cc_final: 0.7446 (mmmt) REVERT: D 112 TRP cc_start: 0.8109 (m100) cc_final: 0.6674 (m100) REVERT: D 158 LYS cc_start: 0.8096 (mmmt) cc_final: 0.7707 (mmtt) REVERT: D 185 MET cc_start: 0.8437 (tmm) cc_final: 0.7464 (tmm) REVERT: D 224 LEU cc_start: 0.8447 (mt) cc_final: 0.8118 (mp) REVERT: D 243 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.7932 (p) REVERT: E 198 ASN cc_start: 0.7870 (t0) cc_final: 0.7382 (t0) REVERT: E 258 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8106 (p) REVERT: E 588 TYR cc_start: 0.7674 (t80) cc_final: 0.6907 (t80) REVERT: E 669 HIS cc_start: 0.7489 (m90) cc_final: 0.7201 (t-90) REVERT: E 691 LEU cc_start: 0.5139 (OUTLIER) cc_final: 0.4844 (pp) REVERT: E 927 LEU cc_start: 0.8085 (mt) cc_final: 0.7617 (mt) REVERT: E 930 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8364 (mp) REVERT: E 983 ASP cc_start: 0.8779 (m-30) cc_final: 0.8415 (m-30) REVERT: E 1487 MET cc_start: 0.6403 (tmm) cc_final: 0.6037 (tmm) REVERT: E 1532 GLN cc_start: 0.8999 (mm-40) cc_final: 0.8730 (tp40) REVERT: F 79 PHE cc_start: 0.7982 (m-80) cc_final: 0.7562 (m-80) REVERT: F 534 ASP cc_start: 0.8607 (t70) cc_final: 0.8364 (m-30) REVERT: F 696 HIS cc_start: 0.7230 (m170) cc_final: 0.6943 (m-70) REVERT: F 1611 LEU cc_start: 0.7912 (tt) cc_final: 0.7697 (tt) REVERT: F 1643 TYR cc_start: 0.8027 (m-80) cc_final: 0.7710 (m-10) REVERT: F 1646 THR cc_start: 0.8204 (t) cc_final: 0.7975 (t) REVERT: G 9 ILE cc_start: 0.8629 (mt) cc_final: 0.8404 (tp) REVERT: G 93 LEU cc_start: 0.7625 (tt) cc_final: 0.7424 (tt) REVERT: H 28 GLU cc_start: 0.8706 (pm20) cc_final: 0.8475 (pm20) REVERT: H 88 GLN cc_start: 0.8802 (mm-40) cc_final: 0.8458 (mp10) outliers start: 150 outliers final: 96 residues processed: 667 average time/residue: 0.5314 time to fit residues: 610.3075 Evaluate side-chains 616 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 508 time to evaluate : 5.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1304 TRP Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1953 VAL Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2189 HIS Chi-restraints excluded: chain A residue 2237 ILE Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 629 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1508 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1768 THR Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2058 MET Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2382 MET Chi-restraints excluded: chain C residue 27 TRP Chi-restraints excluded: chain C residue 37 THR Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 594 optimal weight: 6.9990 chunk 404 optimal weight: 0.9980 chunk 10 optimal weight: 0.0770 chunk 531 optimal weight: 0.8980 chunk 294 optimal weight: 0.9980 chunk 608 optimal weight: 8.9990 chunk 493 optimal weight: 0.7980 chunk 0 optimal weight: 60.0000 chunk 364 optimal weight: 0.4980 chunk 640 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A1202 HIS A1670 HIS A1898 ASN A2093 ASN B1045 ASN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN E 214 ASN E 237 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 57988 Z= 0.143 Angle : 0.518 10.704 78751 Z= 0.254 Chirality : 0.039 0.182 9140 Planarity : 0.003 0.040 10082 Dihedral : 5.856 166.218 8122 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.46 % Allowed : 19.47 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 7316 helix: 0.63 (0.08), residues: 4635 sheet: -0.91 (0.28), residues: 330 loop : -1.78 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1269 HIS 0.006 0.001 HIS E 418 PHE 0.019 0.001 PHE B1122 TYR 0.022 0.001 TYR B2542 ARG 0.006 0.000 ARG B1709 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 548 time to evaluate : 5.165 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 609 HIS cc_start: 0.5473 (OUTLIER) cc_final: 0.5119 (t-90) REVERT: A 821 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.7930 (t80) REVERT: A 970 MET cc_start: 0.8610 (ptm) cc_final: 0.8091 (ptm) REVERT: A 1033 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: A 1174 MET cc_start: 0.8879 (tpp) cc_final: 0.8535 (tpp) REVERT: A 1269 TRP cc_start: 0.7064 (m100) cc_final: 0.6458 (m100) REVERT: A 1458 ASP cc_start: 0.8290 (m-30) cc_final: 0.7776 (t0) REVERT: A 1685 LEU cc_start: 0.8731 (mt) cc_final: 0.8389 (tt) REVERT: A 2047 MET cc_start: 0.7579 (ppp) cc_final: 0.7341 (ppp) REVERT: A 2404 MET cc_start: 0.8478 (tpt) cc_final: 0.7996 (tpt) REVERT: A 2415 MET cc_start: 0.8293 (tpp) cc_final: 0.8072 (tpp) REVERT: A 2430 ARG cc_start: 0.7280 (mtm180) cc_final: 0.6935 (ttp-170) REVERT: B 707 ILE cc_start: 0.7796 (mt) cc_final: 0.7579 (tp) REVERT: B 721 MET cc_start: 0.7895 (mmm) cc_final: 0.6771 (mtp) REVERT: B 821 PHE cc_start: 0.8374 (OUTLIER) cc_final: 0.7729 (m-80) REVERT: B 1377 ASP cc_start: 0.6955 (t0) cc_final: 0.6697 (t0) REVERT: B 1955 ARG cc_start: 0.7854 (mtm180) cc_final: 0.7583 (mtm-85) REVERT: B 2143 THR cc_start: 0.8831 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 2404 MET cc_start: 0.7935 (tpt) cc_final: 0.7454 (tpt) REVERT: C 81 TYR cc_start: 0.7025 (m-10) cc_final: 0.6568 (m-80) REVERT: C 170 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6713 (tm-30) REVERT: C 273 MET cc_start: 0.8203 (mmm) cc_final: 0.7467 (mtt) REVERT: D 81 TYR cc_start: 0.7075 (m-80) cc_final: 0.6705 (m-80) REVERT: D 86 LYS cc_start: 0.8057 (mmtp) cc_final: 0.7419 (mmmt) REVERT: D 90 SER cc_start: 0.8993 (m) cc_final: 0.8713 (p) REVERT: D 112 TRP cc_start: 0.7958 (m100) cc_final: 0.6493 (m100) REVERT: D 158 LYS cc_start: 0.8128 (mmmt) cc_final: 0.7719 (mmtt) REVERT: D 185 MET cc_start: 0.8407 (tmm) cc_final: 0.7324 (tmm) REVERT: D 224 LEU cc_start: 0.8399 (mt) cc_final: 0.8051 (mp) REVERT: D 243 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.7943 (p) REVERT: E 198 ASN cc_start: 0.7866 (t0) cc_final: 0.7344 (t0) REVERT: E 588 TYR cc_start: 0.7755 (t80) cc_final: 0.7101 (t80) REVERT: E 669 HIS cc_start: 0.7472 (m90) cc_final: 0.7248 (t-90) REVERT: E 691 LEU cc_start: 0.5162 (OUTLIER) cc_final: 0.4872 (pp) REVERT: E 787 LEU cc_start: 0.9143 (tt) cc_final: 0.8787 (pp) REVERT: E 927 LEU cc_start: 0.8103 (mt) cc_final: 0.7646 (mt) REVERT: E 930 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8423 (mp) REVERT: E 945 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8607 (pp20) REVERT: E 983 ASP cc_start: 0.8769 (m-30) cc_final: 0.8400 (m-30) REVERT: E 1675 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7222 (mm-30) REVERT: F 79 PHE cc_start: 0.7986 (m-80) cc_final: 0.7545 (m-80) REVERT: F 453 MET cc_start: 0.8427 (mmm) cc_final: 0.8108 (mmm) REVERT: F 696 HIS cc_start: 0.7182 (m170) cc_final: 0.6886 (m-70) REVERT: F 712 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8519 (tt) REVERT: F 1611 LEU cc_start: 0.7899 (tt) cc_final: 0.7698 (tt) REVERT: F 1643 TYR cc_start: 0.8071 (m-80) cc_final: 0.7732 (m-10) REVERT: F 1646 THR cc_start: 0.8196 (t) cc_final: 0.7964 (t) REVERT: G 9 ILE cc_start: 0.8711 (mt) cc_final: 0.8510 (tp) REVERT: G 26 MET cc_start: 0.7430 (mpp) cc_final: 0.7140 (mpp) REVERT: H 88 GLN cc_start: 0.8778 (mm-40) cc_final: 0.8419 (mp10) outliers start: 141 outliers final: 88 residues processed: 660 average time/residue: 0.5252 time to fit residues: 597.8858 Evaluate side-chains 612 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 512 time to evaluate : 5.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1898 ASN Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1907 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1953 VAL Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2189 HIS Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2338 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1037 LEU Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1508 THR Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1898 ASN Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2382 MET Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 270 ARG Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 746 PHE Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1675 GLU Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 712 LEU Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 240 optimal weight: 20.0000 chunk 642 optimal weight: 4.9990 chunk 141 optimal weight: 0.6980 chunk 418 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 714 optimal weight: 0.8980 chunk 592 optimal weight: 7.9990 chunk 330 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 236 optimal weight: 40.0000 chunk 374 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A1670 HIS ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 GLN D 44 GLN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 57988 Z= 0.191 Angle : 0.533 10.772 78751 Z= 0.262 Chirality : 0.040 0.229 9140 Planarity : 0.004 0.153 10082 Dihedral : 5.811 167.717 8121 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.93 % Allowed : 19.75 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7316 helix: 0.81 (0.08), residues: 4654 sheet: -0.81 (0.28), residues: 330 loop : -1.68 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1501 HIS 0.006 0.001 HIS A1202 PHE 0.020 0.001 PHE B1122 TYR 0.022 0.001 TYR B2542 ARG 0.011 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 528 time to evaluate : 5.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 609 HIS cc_start: 0.5585 (OUTLIER) cc_final: 0.5134 (t-90) REVERT: A 666 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: A 821 PHE cc_start: 0.8976 (OUTLIER) cc_final: 0.7867 (t80) REVERT: A 838 GLN cc_start: 0.8305 (OUTLIER) cc_final: 0.7941 (tp40) REVERT: A 1033 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: A 1174 MET cc_start: 0.8999 (tpp) cc_final: 0.8672 (tpp) REVERT: A 1269 TRP cc_start: 0.7037 (m100) cc_final: 0.6487 (m100) REVERT: A 1458 ASP cc_start: 0.8313 (m-30) cc_final: 0.7770 (t0) REVERT: A 1565 ASP cc_start: 0.7379 (t70) cc_final: 0.7122 (m-30) REVERT: A 1685 LEU cc_start: 0.8725 (mt) cc_final: 0.8391 (tt) REVERT: A 1894 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8691 (mp) REVERT: A 2047 MET cc_start: 0.7617 (ppp) cc_final: 0.6994 (ppp) REVERT: A 2404 MET cc_start: 0.8498 (tpt) cc_final: 0.8015 (tpt) REVERT: A 2415 MET cc_start: 0.8284 (tpp) cc_final: 0.8030 (tpp) REVERT: A 2430 ARG cc_start: 0.7184 (mtm180) cc_final: 0.6888 (ttp-170) REVERT: B 821 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 1377 ASP cc_start: 0.6960 (t0) cc_final: 0.6696 (t0) REVERT: B 1955 ARG cc_start: 0.7878 (mtm180) cc_final: 0.7591 (mtm-85) REVERT: B 2143 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8685 (p) REVERT: C 68 TYR cc_start: 0.5716 (m-80) cc_final: 0.5371 (m-80) REVERT: C 81 TYR cc_start: 0.6987 (m-10) cc_final: 0.6522 (m-80) REVERT: C 170 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6725 (tm-30) REVERT: C 273 MET cc_start: 0.8173 (mmm) cc_final: 0.7567 (mtt) REVERT: D 15 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.5194 (pt) REVERT: D 81 TYR cc_start: 0.7191 (m-80) cc_final: 0.6635 (m-80) REVERT: D 86 LYS cc_start: 0.7871 (mmtp) cc_final: 0.7300 (mmmt) REVERT: D 90 SER cc_start: 0.8983 (m) cc_final: 0.8711 (p) REVERT: D 112 TRP cc_start: 0.8026 (m100) cc_final: 0.6651 (m100) REVERT: D 158 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7745 (mmtt) REVERT: D 185 MET cc_start: 0.8423 (tmm) cc_final: 0.7537 (tmm) REVERT: D 243 THR cc_start: 0.8351 (OUTLIER) cc_final: 0.7944 (p) REVERT: E 198 ASN cc_start: 0.7898 (t0) cc_final: 0.7361 (t0) REVERT: E 588 TYR cc_start: 0.7766 (t80) cc_final: 0.7147 (t80) REVERT: E 669 HIS cc_start: 0.7333 (m90) cc_final: 0.7063 (t-90) REVERT: E 691 LEU cc_start: 0.5238 (OUTLIER) cc_final: 0.4954 (pp) REVERT: E 734 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8582 (tptp) REVERT: E 927 LEU cc_start: 0.8181 (mt) cc_final: 0.7704 (mt) REVERT: E 930 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8561 (mp) REVERT: E 945 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8637 (pp20) REVERT: E 983 ASP cc_start: 0.8769 (m-30) cc_final: 0.8399 (m-30) REVERT: E 1675 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7283 (mm-30) REVERT: F 79 PHE cc_start: 0.8033 (m-80) cc_final: 0.7569 (m-80) REVERT: F 453 MET cc_start: 0.8433 (mmm) cc_final: 0.8113 (mmm) REVERT: F 696 HIS cc_start: 0.7287 (m170) cc_final: 0.6956 (m-70) REVERT: F 790 MET cc_start: 0.8124 (ptp) cc_final: 0.7881 (ptp) REVERT: F 1611 LEU cc_start: 0.7946 (tt) cc_final: 0.7745 (tt) REVERT: F 1643 TYR cc_start: 0.8052 (m-80) cc_final: 0.7717 (m-10) REVERT: F 1646 THR cc_start: 0.8236 (t) cc_final: 0.8001 (t) REVERT: G 9 ILE cc_start: 0.8715 (mt) cc_final: 0.8514 (tp) REVERT: H 88 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8432 (mp10) outliers start: 168 outliers final: 110 residues processed: 660 average time/residue: 0.5148 time to fit residues: 591.2355 Evaluate side-chains 623 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 497 time to evaluate : 5.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 853 TYR Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1572 ASP Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 1953 VAL Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2189 HIS Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2338 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 579 VAL Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1508 THR Chi-restraints excluded: chain B residue 1539 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1597 SER Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1768 THR Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2382 MET Chi-restraints excluded: chain B residue 2426 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 237 HIS Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 734 LYS Chi-restraints excluded: chain E residue 746 PHE Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1675 GLU Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain F residue 1531 PHE Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 90 LEU Chi-restraints excluded: chain H residue 105 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 688 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 406 optimal weight: 3.9990 chunk 521 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 601 optimal weight: 0.9990 chunk 398 optimal weight: 0.6980 chunk 711 optimal weight: 8.9990 chunk 445 optimal weight: 30.0000 chunk 433 optimal weight: 2.9990 chunk 328 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A1670 HIS A1693 HIS B1045 ASN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN D 64 HIS ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 390 ASN E 932 ASN E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 540 HIS ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 18 HIS H 107 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 57988 Z= 0.234 Angle : 0.559 11.219 78751 Z= 0.274 Chirality : 0.040 0.153 9140 Planarity : 0.003 0.058 10082 Dihedral : 5.830 170.174 8121 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.13 % Allowed : 19.92 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.10), residues: 7316 helix: 0.92 (0.08), residues: 4648 sheet: -0.77 (0.29), residues: 328 loop : -1.62 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 297 HIS 0.006 0.001 HIS F1686 PHE 0.017 0.001 PHE E 573 TYR 0.023 0.001 TYR B2542 ARG 0.013 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 509 time to evaluate : 5.173 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 609 HIS cc_start: 0.5720 (OUTLIER) cc_final: 0.5127 (t-90) REVERT: A 666 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: A 821 PHE cc_start: 0.9062 (OUTLIER) cc_final: 0.7876 (t80) REVERT: A 838 GLN cc_start: 0.8308 (OUTLIER) cc_final: 0.7918 (tp40) REVERT: A 952 MET cc_start: 0.9343 (tpp) cc_final: 0.9060 (mmm) REVERT: A 1033 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: A 1174 MET cc_start: 0.9069 (tpp) cc_final: 0.8613 (tpp) REVERT: A 1269 TRP cc_start: 0.7014 (m100) cc_final: 0.6374 (m100) REVERT: A 1458 ASP cc_start: 0.8337 (m-30) cc_final: 0.7783 (t0) REVERT: A 1565 ASP cc_start: 0.7394 (t70) cc_final: 0.7110 (m-30) REVERT: A 1595 MET cc_start: 0.8483 (ttp) cc_final: 0.8239 (ttm) REVERT: A 1685 LEU cc_start: 0.8758 (mt) cc_final: 0.8307 (tt) REVERT: A 1894 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8726 (mp) REVERT: A 2415 MET cc_start: 0.8296 (tpp) cc_final: 0.8015 (tpp) REVERT: B 721 MET cc_start: 0.7751 (mmm) cc_final: 0.6595 (mtp) REVERT: B 821 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7679 (m-80) REVERT: B 952 MET cc_start: 0.8312 (tpp) cc_final: 0.7844 (tpp) REVERT: B 956 MET cc_start: 0.8627 (tpp) cc_final: 0.8309 (mmm) REVERT: B 1377 ASP cc_start: 0.6979 (t0) cc_final: 0.6706 (t0) REVERT: B 1747 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7761 (mmm) REVERT: B 1904 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 2143 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8735 (p) REVERT: C 81 TYR cc_start: 0.7142 (m-10) cc_final: 0.6625 (m-10) REVERT: C 170 GLU cc_start: 0.7300 (OUTLIER) cc_final: 0.6786 (tm-30) REVERT: C 273 MET cc_start: 0.8139 (mmm) cc_final: 0.7538 (mtt) REVERT: D 15 LEU cc_start: 0.5682 (OUTLIER) cc_final: 0.5454 (pt) REVERT: D 86 LYS cc_start: 0.7970 (mmtp) cc_final: 0.7356 (mmmt) REVERT: D 90 SER cc_start: 0.8955 (m) cc_final: 0.8698 (p) REVERT: D 101 TYR cc_start: 0.9125 (p90) cc_final: 0.8624 (p90) REVERT: D 158 LYS cc_start: 0.8225 (mmmt) cc_final: 0.7798 (mmtt) REVERT: D 185 MET cc_start: 0.8435 (tmm) cc_final: 0.7717 (tmm) REVERT: D 213 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8784 (mtpt) REVERT: D 243 THR cc_start: 0.8335 (OUTLIER) cc_final: 0.7945 (p) REVERT: E 198 ASN cc_start: 0.8027 (t0) cc_final: 0.7470 (t0) REVERT: E 254 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7341 (pp) REVERT: E 258 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8180 (p) REVERT: E 588 TYR cc_start: 0.7798 (t80) cc_final: 0.7159 (t80) REVERT: E 669 HIS cc_start: 0.7278 (m90) cc_final: 0.6962 (t70) REVERT: E 691 LEU cc_start: 0.5277 (OUTLIER) cc_final: 0.4975 (pp) REVERT: E 734 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8673 (tptp) REVERT: E 927 LEU cc_start: 0.8229 (mt) cc_final: 0.7767 (mt) REVERT: E 930 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8579 (mp) REVERT: E 932 ASN cc_start: 0.9013 (OUTLIER) cc_final: 0.8656 (t0) REVERT: E 945 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8627 (pp20) REVERT: E 983 ASP cc_start: 0.8765 (m-30) cc_final: 0.8394 (m-30) REVERT: E 1675 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7304 (mm-30) REVERT: F 79 PHE cc_start: 0.8122 (m-80) cc_final: 0.7628 (m-80) REVERT: F 696 HIS cc_start: 0.7286 (m170) cc_final: 0.6955 (m-70) REVERT: F 1643 TYR cc_start: 0.8117 (m-80) cc_final: 0.7909 (m-80) REVERT: F 1646 THR cc_start: 0.8307 (t) cc_final: 0.8082 (t) REVERT: G 27 CYS cc_start: 0.7907 (m) cc_final: 0.7706 (p) outliers start: 179 outliers final: 109 residues processed: 652 average time/residue: 0.5222 time to fit residues: 591.2750 Evaluate side-chains 634 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 503 time to evaluate : 5.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 715 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 839 VAL Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 885 ILE Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1527 ASP Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1572 ASP Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2189 HIS Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2338 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1000 VAL Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1162 THR Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1319 ASN Chi-restraints excluded: chain B residue 1508 THR Chi-restraints excluded: chain B residue 1539 ASP Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1597 SER Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1747 MET Chi-restraints excluded: chain B residue 1768 THR Chi-restraints excluded: chain B residue 1898 ASN Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1953 VAL Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2143 THR Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2406 VAL Chi-restraints excluded: chain B residue 2426 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 54 MET Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 237 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 734 LYS Chi-restraints excluded: chain E residue 746 PHE Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 932 ASN Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1675 GLU Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain F residue 59 HIS Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 433 MET Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain F residue 1649 ASP Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 105 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 440 optimal weight: 20.0000 chunk 284 optimal weight: 3.9990 chunk 424 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 137 optimal weight: 0.5980 chunk 452 optimal weight: 0.0270 chunk 484 optimal weight: 9.9990 chunk 351 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 559 optimal weight: 7.9990 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 609 HIS A 791 ASN A1670 HIS ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 932 ASN E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 57988 Z= 0.160 Angle : 0.535 11.995 78751 Z= 0.261 Chirality : 0.039 0.213 9140 Planarity : 0.003 0.046 10082 Dihedral : 5.749 171.895 8121 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.44 % Allowed : 20.71 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.10), residues: 7316 helix: 1.06 (0.08), residues: 4646 sheet: -0.66 (0.28), residues: 338 loop : -1.58 (0.13), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B1501 HIS 0.006 0.001 HIS F1686 PHE 0.018 0.001 PHE E1672 TYR 0.021 0.001 TYR B2542 ARG 0.012 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 520 time to evaluate : 5.212 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: A 609 HIS cc_start: 0.5639 (OUTLIER) cc_final: 0.5010 (t-170) REVERT: A 666 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7247 (m-30) REVERT: A 821 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.7983 (t80) REVERT: A 838 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7894 (tp40) REVERT: A 970 MET cc_start: 0.8538 (ptm) cc_final: 0.8147 (ptm) REVERT: A 1033 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: A 1174 MET cc_start: 0.9046 (tpp) cc_final: 0.8596 (tpp) REVERT: A 1269 TRP cc_start: 0.6980 (m100) cc_final: 0.6356 (m100) REVERT: A 1458 ASP cc_start: 0.8321 (m-30) cc_final: 0.7784 (t0) REVERT: A 1565 ASP cc_start: 0.7324 (t70) cc_final: 0.7045 (m-30) REVERT: A 1595 MET cc_start: 0.8459 (ttp) cc_final: 0.8232 (ttm) REVERT: A 1685 LEU cc_start: 0.8734 (mt) cc_final: 0.8284 (tt) REVERT: A 1894 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8723 (mp) REVERT: A 2382 MET cc_start: 0.8052 (mtt) cc_final: 0.7796 (mmt) REVERT: A 2404 MET cc_start: 0.8485 (tpt) cc_final: 0.8018 (tpt) REVERT: A 2415 MET cc_start: 0.8233 (tpp) cc_final: 0.7931 (tpp) REVERT: A 2430 ARG cc_start: 0.7382 (mtm180) cc_final: 0.6967 (ttp-170) REVERT: B 721 MET cc_start: 0.7814 (mmm) cc_final: 0.6710 (mtp) REVERT: B 821 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.7636 (m-80) REVERT: B 956 MET cc_start: 0.8583 (tpp) cc_final: 0.8281 (mmm) REVERT: B 1377 ASP cc_start: 0.6804 (t0) cc_final: 0.6579 (t0) REVERT: B 1389 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7939 (pttm) REVERT: B 1904 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7915 (mm) REVERT: C 68 TYR cc_start: 0.5210 (m-80) cc_final: 0.4957 (m-80) REVERT: C 81 TYR cc_start: 0.6991 (m-10) cc_final: 0.6429 (m-10) REVERT: C 128 ASN cc_start: 0.8368 (OUTLIER) cc_final: 0.8160 (p0) REVERT: C 170 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6775 (tm-30) REVERT: C 273 MET cc_start: 0.8059 (mmm) cc_final: 0.7572 (mtt) REVERT: D 15 LEU cc_start: 0.5651 (OUTLIER) cc_final: 0.5415 (pt) REVERT: D 81 TYR cc_start: 0.7031 (m-80) cc_final: 0.6749 (m-80) REVERT: D 86 LYS cc_start: 0.7939 (mmtp) cc_final: 0.7334 (mmmt) REVERT: D 90 SER cc_start: 0.9015 (m) cc_final: 0.8736 (p) REVERT: D 112 TRP cc_start: 0.8036 (m100) cc_final: 0.6710 (m100) REVERT: D 184 TYR cc_start: 0.7835 (m-80) cc_final: 0.7627 (m-80) REVERT: D 185 MET cc_start: 0.8422 (tmm) cc_final: 0.7741 (tmm) REVERT: D 213 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8819 (tttt) REVERT: D 243 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7991 (p) REVERT: E 198 ASN cc_start: 0.8016 (t0) cc_final: 0.7456 (t0) REVERT: E 254 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7407 (pp) REVERT: E 258 THR cc_start: 0.8412 (OUTLIER) cc_final: 0.8182 (p) REVERT: E 368 PHE cc_start: 0.7951 (t80) cc_final: 0.7566 (t80) REVERT: E 588 TYR cc_start: 0.7798 (t80) cc_final: 0.7155 (t80) REVERT: E 669 HIS cc_start: 0.7267 (m90) cc_final: 0.6966 (t70) REVERT: E 691 LEU cc_start: 0.5037 (OUTLIER) cc_final: 0.4710 (pp) REVERT: E 734 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8677 (tptp) REVERT: E 927 LEU cc_start: 0.8241 (mt) cc_final: 0.7753 (mt) REVERT: E 930 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8470 (mp) REVERT: E 945 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.8673 (pp20) REVERT: E 983 ASP cc_start: 0.8757 (m-30) cc_final: 0.8386 (m-30) REVERT: E 1675 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7379 (mm-30) REVERT: F 79 PHE cc_start: 0.8162 (m-80) cc_final: 0.7697 (m-80) REVERT: F 696 HIS cc_start: 0.7213 (m170) cc_final: 0.6930 (m-70) REVERT: F 1646 THR cc_start: 0.8297 (t) cc_final: 0.8075 (t) REVERT: G 27 CYS cc_start: 0.7920 (m) cc_final: 0.7718 (p) REVERT: G 104 LYS cc_start: 0.7835 (tmmt) cc_final: 0.7193 (ttmm) REVERT: H 88 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8821 (mp10) outliers start: 140 outliers final: 92 residues processed: 633 average time/residue: 0.5235 time to fit residues: 572.6330 Evaluate side-chains 612 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 499 time to evaluate : 5.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1572 ASP Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1904 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2189 HIS Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2338 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 811 LEU Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 863 THR Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1389 LYS Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1597 SER Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2244 ASP Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2426 LEU Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 237 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 734 LYS Chi-restraints excluded: chain E residue 746 PHE Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 851 LEU Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1675 GLU Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 647 optimal weight: 0.6980 chunk 681 optimal weight: 0.7980 chunk 621 optimal weight: 4.9990 chunk 662 optimal weight: 1.9990 chunk 398 optimal weight: 0.9990 chunk 288 optimal weight: 4.9990 chunk 520 optimal weight: 0.0040 chunk 203 optimal weight: 0.8980 chunk 598 optimal weight: 0.7980 chunk 626 optimal weight: 0.7980 chunk 660 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN A1670 HIS B1045 ASN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 57988 Z= 0.143 Angle : 0.535 12.686 78751 Z= 0.259 Chirality : 0.039 0.152 9140 Planarity : 0.003 0.038 10082 Dihedral : 5.684 172.335 8121 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.43 % Allowed : 20.87 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.10), residues: 7316 helix: 1.18 (0.08), residues: 4625 sheet: -0.60 (0.28), residues: 338 loop : -1.53 (0.13), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B1501 HIS 0.012 0.001 HIS A 609 PHE 0.031 0.001 PHE B1122 TYR 0.024 0.001 TYR B2542 ARG 0.013 0.000 ARG G 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 522 time to evaluate : 5.054 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: A 609 HIS cc_start: 0.6096 (OUTLIER) cc_final: 0.4963 (t-90) REVERT: A 666 ASP cc_start: 0.7890 (OUTLIER) cc_final: 0.7216 (m-30) REVERT: A 821 PHE cc_start: 0.8988 (OUTLIER) cc_final: 0.7923 (t80) REVERT: A 838 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7893 (tp40) REVERT: A 970 MET cc_start: 0.8502 (ptm) cc_final: 0.8130 (ptm) REVERT: A 1033 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.7672 (pm20) REVERT: A 1174 MET cc_start: 0.9110 (tpp) cc_final: 0.8828 (tpp) REVERT: A 1269 TRP cc_start: 0.6700 (m100) cc_final: 0.6214 (m100) REVERT: A 1458 ASP cc_start: 0.8317 (m-30) cc_final: 0.7785 (t0) REVERT: A 1565 ASP cc_start: 0.7293 (t70) cc_final: 0.7009 (m-30) REVERT: A 1595 MET cc_start: 0.8439 (ttp) cc_final: 0.8228 (ttm) REVERT: A 1685 LEU cc_start: 0.8694 (mt) cc_final: 0.8253 (tt) REVERT: A 1894 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8765 (mp) REVERT: A 2382 MET cc_start: 0.8045 (mtt) cc_final: 0.7791 (mmt) REVERT: A 2404 MET cc_start: 0.8489 (tpt) cc_final: 0.8040 (tpt) REVERT: A 2415 MET cc_start: 0.8207 (tpp) cc_final: 0.7913 (tpp) REVERT: A 2430 ARG cc_start: 0.7327 (mtm180) cc_final: 0.6976 (ttp-170) REVERT: B 721 MET cc_start: 0.7799 (mmm) cc_final: 0.6691 (mtp) REVERT: B 821 PHE cc_start: 0.8503 (OUTLIER) cc_final: 0.7669 (m-80) REVERT: B 956 MET cc_start: 0.8556 (tpp) cc_final: 0.8277 (mmm) REVERT: B 1377 ASP cc_start: 0.6854 (t0) cc_final: 0.6591 (t0) REVERT: B 1389 LYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7922 (pttm) REVERT: B 1904 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7919 (mm) REVERT: B 1955 ARG cc_start: 0.7847 (mtm180) cc_final: 0.7515 (mtm-85) REVERT: C 68 TYR cc_start: 0.5226 (m-80) cc_final: 0.4981 (m-80) REVERT: C 81 TYR cc_start: 0.6991 (m-10) cc_final: 0.6421 (m-10) REVERT: C 170 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: C 273 MET cc_start: 0.7990 (mmm) cc_final: 0.7490 (mtt) REVERT: D 15 LEU cc_start: 0.5639 (OUTLIER) cc_final: 0.5396 (pt) REVERT: D 81 TYR cc_start: 0.6900 (m-80) cc_final: 0.6340 (m-80) REVERT: D 86 LYS cc_start: 0.7940 (mmtp) cc_final: 0.7325 (mmmt) REVERT: D 90 SER cc_start: 0.9009 (m) cc_final: 0.8724 (p) REVERT: D 101 TYR cc_start: 0.9071 (p90) cc_final: 0.8568 (p90) REVERT: D 112 TRP cc_start: 0.8026 (m100) cc_final: 0.6701 (m100) REVERT: D 184 TYR cc_start: 0.7799 (m-80) cc_final: 0.7598 (m-80) REVERT: D 185 MET cc_start: 0.8414 (tmm) cc_final: 0.7727 (tmm) REVERT: D 213 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8805 (tttt) REVERT: D 243 THR cc_start: 0.8321 (OUTLIER) cc_final: 0.7957 (p) REVERT: E 198 ASN cc_start: 0.8002 (t0) cc_final: 0.7436 (t0) REVERT: E 254 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7397 (pp) REVERT: E 258 THR cc_start: 0.8400 (OUTLIER) cc_final: 0.8171 (p) REVERT: E 368 PHE cc_start: 0.7943 (t80) cc_final: 0.7549 (t80) REVERT: E 588 TYR cc_start: 0.7800 (t80) cc_final: 0.7164 (t80) REVERT: E 669 HIS cc_start: 0.7251 (m90) cc_final: 0.6931 (t70) REVERT: E 691 LEU cc_start: 0.5064 (OUTLIER) cc_final: 0.4734 (pp) REVERT: E 734 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8675 (tptp) REVERT: E 927 LEU cc_start: 0.8154 (mt) cc_final: 0.7691 (mt) REVERT: E 930 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8549 (mp) REVERT: E 945 GLU cc_start: 0.8990 (OUTLIER) cc_final: 0.8672 (pp20) REVERT: E 983 ASP cc_start: 0.8751 (m-30) cc_final: 0.8432 (m-30) REVERT: E 1675 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7374 (mm-30) REVERT: F 79 PHE cc_start: 0.8180 (m-80) cc_final: 0.7807 (m-80) REVERT: F 696 HIS cc_start: 0.7270 (m170) cc_final: 0.6977 (m-70) REVERT: F 1646 THR cc_start: 0.8263 (t) cc_final: 0.8049 (t) REVERT: G 28 GLU cc_start: 0.8810 (pm20) cc_final: 0.8592 (pm20) REVERT: G 104 LYS cc_start: 0.7868 (tmmt) cc_final: 0.7237 (ttmm) outliers start: 139 outliers final: 94 residues processed: 632 average time/residue: 0.5293 time to fit residues: 579.3338 Evaluate side-chains 618 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 504 time to evaluate : 5.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 609 HIS Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1337 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1439 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1572 ASP Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1746 LEU Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2189 HIS Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2338 ASP Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 659 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1075 ILE Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1300 LEU Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1389 LYS Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2426 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 48 LEU Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 237 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 734 LYS Chi-restraints excluded: chain E residue 746 PHE Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 945 GLU Chi-restraints excluded: chain E residue 969 VAL Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1675 GLU Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain E residue 1684 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 975 ILE Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1510 THR Chi-restraints excluded: chain F residue 1649 ASP Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 435 optimal weight: 4.9990 chunk 700 optimal weight: 0.9990 chunk 427 optimal weight: 1.9990 chunk 332 optimal weight: 4.9990 chunk 487 optimal weight: 8.9990 chunk 735 optimal weight: 30.0000 chunk 676 optimal weight: 0.0170 chunk 585 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 452 optimal weight: 8.9990 chunk 358 optimal weight: 0.0470 overall best weight: 0.5320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 ASN ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 57988 Z= 0.136 Angle : 0.536 13.578 78751 Z= 0.258 Chirality : 0.039 0.181 9140 Planarity : 0.003 0.051 10082 Dihedral : 5.607 172.801 8121 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 21.48 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.10), residues: 7316 helix: 1.30 (0.08), residues: 4609 sheet: -0.56 (0.28), residues: 338 loop : -1.47 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B1280 HIS 0.010 0.000 HIS A 759 PHE 0.027 0.001 PHE B1122 TYR 0.023 0.001 TYR B2542 ARG 0.015 0.000 ARG B1784 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14632 Ramachandran restraints generated. 7316 Oldfield, 0 Emsley, 7316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 531 time to evaluate : 5.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 666 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7205 (m-30) REVERT: A 821 PHE cc_start: 0.8967 (OUTLIER) cc_final: 0.7975 (t80) REVERT: A 838 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7858 (tp40) REVERT: A 970 MET cc_start: 0.8487 (ptm) cc_final: 0.8108 (ptm) REVERT: A 1033 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7629 (pm20) REVERT: A 1174 MET cc_start: 0.9123 (tpp) cc_final: 0.8566 (tpp) REVERT: A 1269 TRP cc_start: 0.6668 (m100) cc_final: 0.6199 (m100) REVERT: A 1458 ASP cc_start: 0.8354 (m-30) cc_final: 0.7867 (t0) REVERT: A 1565 ASP cc_start: 0.7263 (t70) cc_final: 0.6968 (m-30) REVERT: A 1595 MET cc_start: 0.8427 (ttp) cc_final: 0.8220 (ttm) REVERT: A 1685 LEU cc_start: 0.8671 (mt) cc_final: 0.8237 (tt) REVERT: A 1704 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8876 (ttt) REVERT: A 1894 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 2404 MET cc_start: 0.8492 (tpt) cc_final: 0.8096 (tpt) REVERT: B 721 MET cc_start: 0.7774 (mmm) cc_final: 0.6656 (mtp) REVERT: B 821 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: B 956 MET cc_start: 0.8513 (tpp) cc_final: 0.8254 (mmm) REVERT: B 1377 ASP cc_start: 0.6735 (t0) cc_final: 0.6517 (t0) REVERT: B 1389 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7885 (pttm) REVERT: B 1904 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7924 (mm) REVERT: B 1955 ARG cc_start: 0.7816 (mtm180) cc_final: 0.7504 (mtm-85) REVERT: C 68 TYR cc_start: 0.5224 (m-80) cc_final: 0.4973 (m-80) REVERT: C 81 TYR cc_start: 0.6981 (m-10) cc_final: 0.6426 (m-10) REVERT: C 170 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: C 185 MET cc_start: 0.8225 (tpt) cc_final: 0.7581 (ptt) REVERT: C 273 MET cc_start: 0.7935 (mmm) cc_final: 0.7610 (mtt) REVERT: D 15 LEU cc_start: 0.5628 (OUTLIER) cc_final: 0.5383 (pt) REVERT: D 81 TYR cc_start: 0.7367 (m-80) cc_final: 0.6811 (m-80) REVERT: D 86 LYS cc_start: 0.7951 (mmtp) cc_final: 0.7373 (mmmt) REVERT: D 90 SER cc_start: 0.8995 (m) cc_final: 0.8717 (p) REVERT: D 101 TYR cc_start: 0.9021 (p90) cc_final: 0.8591 (p90) REVERT: D 112 TRP cc_start: 0.7879 (m100) cc_final: 0.6633 (m100) REVERT: D 185 MET cc_start: 0.8497 (tmm) cc_final: 0.7868 (tmm) REVERT: D 213 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8879 (tttt) REVERT: D 215 LYS cc_start: 0.7283 (tmtt) cc_final: 0.6970 (tttp) REVERT: D 243 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7817 (p) REVERT: E 198 ASN cc_start: 0.8001 (t0) cc_final: 0.7436 (t0) REVERT: E 254 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7372 (pp) REVERT: E 258 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8151 (p) REVERT: E 332 TYR cc_start: 0.8242 (m-80) cc_final: 0.7973 (m-80) REVERT: E 368 PHE cc_start: 0.7928 (t80) cc_final: 0.7543 (t80) REVERT: E 455 MET cc_start: 0.8714 (ttm) cc_final: 0.8442 (ttm) REVERT: E 588 TYR cc_start: 0.7817 (t80) cc_final: 0.7184 (t80) REVERT: E 669 HIS cc_start: 0.7235 (m90) cc_final: 0.6905 (t70) REVERT: E 691 LEU cc_start: 0.5312 (OUTLIER) cc_final: 0.4995 (pp) REVERT: E 734 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8599 (tptp) REVERT: E 927 LEU cc_start: 0.8144 (mt) cc_final: 0.7606 (mt) REVERT: E 930 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8619 (mp) REVERT: E 983 ASP cc_start: 0.8744 (m-30) cc_final: 0.8421 (m-30) REVERT: E 1674 GLN cc_start: 0.7740 (OUTLIER) cc_final: 0.7463 (tp40) REVERT: F 79 PHE cc_start: 0.8182 (m-80) cc_final: 0.7821 (m-80) REVERT: F 254 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8435 (pp) REVERT: F 696 HIS cc_start: 0.7181 (m170) cc_final: 0.6938 (m-70) REVERT: F 1611 LEU cc_start: 0.7948 (mm) cc_final: 0.7533 (tt) REVERT: F 1646 THR cc_start: 0.8246 (t) cc_final: 0.8028 (t) REVERT: G 104 LYS cc_start: 0.7883 (tmmt) cc_final: 0.7255 (ttmm) outliers start: 116 outliers final: 84 residues processed: 626 average time/residue: 0.5277 time to fit residues: 573.6783 Evaluate side-chains 615 residues out of total 6577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 511 time to evaluate : 5.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 666 ASP Chi-restraints excluded: chain A residue 791 ASN Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 821 PHE Chi-restraints excluded: chain A residue 838 GLN Chi-restraints excluded: chain A residue 858 TYR Chi-restraints excluded: chain A residue 969 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1030 TYR Chi-restraints excluded: chain A residue 1033 GLU Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1074 LEU Chi-restraints excluded: chain A residue 1306 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 HIS Chi-restraints excluded: chain A residue 1439 HIS Chi-restraints excluded: chain A residue 1552 LEU Chi-restraints excluded: chain A residue 1572 ASP Chi-restraints excluded: chain A residue 1634 GLN Chi-restraints excluded: chain A residue 1704 MET Chi-restraints excluded: chain A residue 1876 THR Chi-restraints excluded: chain A residue 1894 LEU Chi-restraints excluded: chain A residue 1932 ILE Chi-restraints excluded: chain A residue 1952 LEU Chi-restraints excluded: chain A residue 2021 ILE Chi-restraints excluded: chain A residue 2093 ASN Chi-restraints excluded: chain A residue 2173 THR Chi-restraints excluded: chain A residue 2326 VAL Chi-restraints excluded: chain A residue 2349 LEU Chi-restraints excluded: chain A residue 2405 GLU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 693 LEU Chi-restraints excluded: chain B residue 694 GLN Chi-restraints excluded: chain B residue 709 GLU Chi-restraints excluded: chain B residue 795 ILE Chi-restraints excluded: chain B residue 821 PHE Chi-restraints excluded: chain B residue 853 TYR Chi-restraints excluded: chain B residue 854 VAL Chi-restraints excluded: chain B residue 890 LEU Chi-restraints excluded: chain B residue 966 HIS Chi-restraints excluded: chain B residue 1074 LEU Chi-restraints excluded: chain B residue 1100 ILE Chi-restraints excluded: chain B residue 1109 ASP Chi-restraints excluded: chain B residue 1313 MET Chi-restraints excluded: chain B residue 1389 LYS Chi-restraints excluded: chain B residue 1593 CYS Chi-restraints excluded: chain B residue 1679 VAL Chi-restraints excluded: chain B residue 1739 HIS Chi-restraints excluded: chain B residue 1898 ASN Chi-restraints excluded: chain B residue 1899 ASN Chi-restraints excluded: chain B residue 1904 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 2004 THR Chi-restraints excluded: chain B residue 2044 VAL Chi-restraints excluded: chain B residue 2050 VAL Chi-restraints excluded: chain B residue 2131 LEU Chi-restraints excluded: chain B residue 2173 THR Chi-restraints excluded: chain B residue 2276 ASP Chi-restraints excluded: chain B residue 2354 LEU Chi-restraints excluded: chain B residue 2426 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 197 TRP Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain D residue 15 LEU Chi-restraints excluded: chain D residue 27 TRP Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 147 ASP Chi-restraints excluded: chain D residue 213 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 301 THR Chi-restraints excluded: chain E residue 69 ASP Chi-restraints excluded: chain E residue 225 GLU Chi-restraints excluded: chain E residue 237 HIS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 258 THR Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 544 LEU Chi-restraints excluded: chain E residue 691 LEU Chi-restraints excluded: chain E residue 734 LYS Chi-restraints excluded: chain E residue 746 PHE Chi-restraints excluded: chain E residue 799 ASP Chi-restraints excluded: chain E residue 930 LEU Chi-restraints excluded: chain E residue 1510 THR Chi-restraints excluded: chain E residue 1674 GLN Chi-restraints excluded: chain E residue 1675 GLU Chi-restraints excluded: chain E residue 1680 VAL Chi-restraints excluded: chain E residue 1684 GLN Chi-restraints excluded: chain F residue 88 LEU Chi-restraints excluded: chain F residue 111 ILE Chi-restraints excluded: chain F residue 221 SER Chi-restraints excluded: chain F residue 254 LEU Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 441 SER Chi-restraints excluded: chain F residue 505 HIS Chi-restraints excluded: chain F residue 765 THR Chi-restraints excluded: chain F residue 852 THR Chi-restraints excluded: chain F residue 876 VAL Chi-restraints excluded: chain F residue 1003 VAL Chi-restraints excluded: chain F residue 1649 ASP Chi-restraints excluded: chain G residue 6 ASN Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 36 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 738 random chunks: chunk 465 optimal weight: 0.9990 chunk 623 optimal weight: 0.7980 chunk 179 optimal weight: 0.8980 chunk 539 optimal weight: 0.6980 chunk 86 optimal weight: 0.0670 chunk 162 optimal weight: 0.6980 chunk 586 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 602 optimal weight: 8.9990 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 0.0980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 GLN ** E 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1674 GLN ** F 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.147082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.090369 restraints weight = 108967.646| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.50 r_work: 0.3146 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.230 57988 Z= 0.191 Angle : 0.662 59.197 78751 Z= 0.351 Chirality : 0.040 0.704 9140 Planarity : 0.003 0.055 10082 Dihedral : 5.489 172.803 8118 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.97 % Allowed : 21.56 % Favored : 76.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.10), residues: 7316 helix: 1.30 (0.08), residues: 4609 sheet: -0.55 (0.28), residues: 338 loop : -1.47 (0.13), residues: 2369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B1280 HIS 0.009 0.000 HIS A 759 PHE 0.024 0.001 PHE B1122 TYR 0.022 0.001 TYR B2542 ARG 0.007 0.000 ARG G 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12964.86 seconds wall clock time: 228 minutes 3.70 seconds (13683.70 seconds total)