Starting phenix.real_space_refine on Mon Mar 25 13:45:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/03_2024/8i4y_35188_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/03_2024/8i4y_35188.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/03_2024/8i4y_35188.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/03_2024/8i4y_35188.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/03_2024/8i4y_35188_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4y_35188/03_2024/8i4y_35188_trim_updated.pdb" } resolution = 3.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians S 46 5.16 5 C 15374 2.51 5 N 4566 2.21 5 O 4682 1.98 5 H 24348 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 359": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 390": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 430": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 480": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 485": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 487": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 506": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 510": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 520": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 541": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 565": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 573": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 576": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 579": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 605": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 609": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 635": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 643": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 678": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 682": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 741": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 745": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 751": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 754": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 770": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 779": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 800": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 810": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 814": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 820": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 821": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 823": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 845": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 855": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 896": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 899": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 900": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 912": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 984": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 998": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1017": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1025": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1027": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1039": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1043": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1054": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1059": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1079": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1080": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1083": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1093": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1096": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1097": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1194": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1296": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1328": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1331": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1422": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1430": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1440": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1443": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1447": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1486": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1502": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1518": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1527": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1569": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1570": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1595": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1613": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1616": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1681": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1686": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1703": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 1718": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 127": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 136": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 139": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 179": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 238": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 239": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 247": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 271": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 276": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 277": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 287": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 310": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 313": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 320": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 355": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 359": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 390": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 393": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 396": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 415": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 424": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 428": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 430": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 459": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 465": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 480": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 485": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 487": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 506": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 510": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 512": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 520": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 534": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 541": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 545": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 565": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 573": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 576": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 585": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 605": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 609": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 635": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 640": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 643": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 678": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 682": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 694": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 701": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 735": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 741": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 745": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 751": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 754": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 770": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 779": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 800": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 810": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 814": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 820": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 821": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 823": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 829": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 845": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 855": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 867": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 896": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 899": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 900": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 912": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 975": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 984": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 998": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1017": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1025": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1027": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1039": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1043": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1054": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1059": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1079": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1080": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1083": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1093": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1096": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1097": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1143": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1150": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1164": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1166": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1192": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1194": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1199": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1211": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1224": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1244": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1270": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1294": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1296": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1312": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1327": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1328": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1331": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1337": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1349": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1412": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1418": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1422": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1425": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1430": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1433": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1434": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1440": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1443": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1447": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1460": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1472": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1475": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1486": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1493": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1502": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1518": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1527": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1531": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1552": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1562": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1569": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1570": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1595": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1613": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1616": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1681": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1686": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1693": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1703": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 1718": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 49016 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 24479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 24479 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 122, 'TRANS': 1564} Chain: "B" Number of atoms: 24479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 24479 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 122, 'TRANS': 1564} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'3HA': 1, 'ONF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ONF:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {'3HA': 1, 'ONF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ONF:plan-3': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 18.70, per 1000 atoms: 0.38 Number of scatterers: 49016 At special positions: 0 Unit cell: (195.8, 172.66, 121.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 46 16.00 O 4682 8.00 N 4566 7.00 C 15374 6.00 H 24348 1.00 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: 37.61 Conformation dependent library (CDL) restraints added in 5.0 seconds 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5896 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 132 helices and 15 sheets defined 38.6% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.82 Creating SS restraints... Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 79 through 81 No H-bonds generated for 'chain 'A' and resid 79 through 81' Processing helix chain 'A' and resid 97 through 100 No H-bonds generated for 'chain 'A' and resid 97 through 100' Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 112 through 128 Processing helix chain 'A' and resid 151 through 154 Processing helix chain 'A' and resid 163 through 171 removed outlier: 5.150A pdb=" N GLY A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 183 removed outlier: 4.128A pdb=" N SER A 177 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 4.528A pdb=" N SER A 200 " --> pdb=" O CYS A 197 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 238 removed outlier: 3.792A pdb=" N ASP A 235 " --> pdb=" O VAL A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 3.949A pdb=" N ARG A 277 " --> pdb=" O SER A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 318 removed outlier: 3.622A pdb=" N ILE A 312 " --> pdb=" O GLN A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 339 through 349 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.908A pdb=" N ILE A 370 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 removed outlier: 5.415A pdb=" N ALA A 378 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 380 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL A 386 " --> pdb=" O VAL A 383 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ASN A 391 " --> pdb=" O ALA A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 411 No H-bonds generated for 'chain 'A' and resid 409 through 411' Processing helix chain 'A' and resid 476 through 490 removed outlier: 3.555A pdb=" N ARG A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N THR A 489 " --> pdb=" O ARG A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 502 Processing helix chain 'A' and resid 520 through 532 Processing helix chain 'A' and resid 558 through 561 Processing helix chain 'A' and resid 565 through 581 Proline residue: A 572 - end of helix removed outlier: 4.183A pdb=" N GLY A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU A 578 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLU A 580 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 removed outlier: 3.525A pdb=" N GLU A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N HIS A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLY A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.504A pdb=" N VAL A 608 " --> pdb=" O ARG A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 616 Processing helix chain 'A' and resid 620 through 639 Processing helix chain 'A' and resid 651 through 660 removed outlier: 4.129A pdb=" N VAL A 655 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 660 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 685 removed outlier: 3.513A pdb=" N VAL A 673 " --> pdb=" O GLY A 669 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 674 " --> pdb=" O ALA A 670 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA A 675 " --> pdb=" O ALA A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 705 removed outlier: 4.094A pdb=" N ALA A 702 " --> pdb=" O ASP A 698 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA A 703 " --> pdb=" O GLU A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 730 through 743 removed outlier: 3.572A pdb=" N TRP A 740 " --> pdb=" O VAL A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 775 removed outlier: 4.001A pdb=" N ALA A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 774 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLY A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 No H-bonds generated for 'chain 'A' and resid 796 through 799' Processing helix chain 'A' and resid 802 through 810 removed outlier: 4.259A pdb=" N HIS A 808 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N LEU A 809 " --> pdb=" O TRP A 805 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG A 810 " --> pdb=" O LEU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 824 Processing helix chain 'A' and resid 839 through 847 Processing helix chain 'A' and resid 869 through 883 removed outlier: 4.226A pdb=" N LEU A 873 " --> pdb=" O PRO A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 893 Processing helix chain 'A' and resid 953 through 959 removed outlier: 3.826A pdb=" N ALA A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 984 Processing helix chain 'A' and resid 1062 through 1068 Proline residue: A1066 - end of helix Processing helix chain 'A' and resid 1074 through 1084 removed outlier: 3.817A pdb=" N GLN A1084 " --> pdb=" O ARG A1080 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1092 No H-bonds generated for 'chain 'A' and resid 1090 through 1092' Processing helix chain 'A' and resid 1122 through 1137 removed outlier: 3.719A pdb=" N LEU A1128 " --> pdb=" O ALA A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1194 through 1196 No H-bonds generated for 'chain 'A' and resid 1194 through 1196' Processing helix chain 'A' and resid 1201 through 1203 No H-bonds generated for 'chain 'A' and resid 1201 through 1203' Processing helix chain 'A' and resid 1242 through 1254 Processing helix chain 'A' and resid 1283 through 1295 removed outlier: 3.977A pdb=" N GLU A1292 " --> pdb=" O LYS A1288 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU A1293 " --> pdb=" O THR A1289 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A1294 " --> pdb=" O PHE A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1312 removed outlier: 4.094A pdb=" N ARG A1312 " --> pdb=" O GLY A1309 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1309 through 1312' Processing helix chain 'A' and resid 1321 through 1346 removed outlier: 3.613A pdb=" N GLY A1330 " --> pdb=" O CYS A1326 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLN A1346 " --> pdb=" O GLU A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1368 through 1383 Proline residue: A1372 - end of helix removed outlier: 3.629A pdb=" N VAL A1381 " --> pdb=" O THR A1378 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU A1383 " --> pdb=" O LEU A1380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1412 Processing helix chain 'A' and resid 1438 through 1443 Processing helix chain 'A' and resid 1459 through 1471 removed outlier: 4.078A pdb=" N GLU A1467 " --> pdb=" O ALA A1463 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP A1468 " --> pdb=" O ALA A1464 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1496 Processing helix chain 'A' and resid 1513 through 1523 Processing helix chain 'A' and resid 1545 through 1547 No H-bonds generated for 'chain 'A' and resid 1545 through 1547' Processing helix chain 'A' and resid 1550 through 1573 removed outlier: 4.332A pdb=" N GLY A1554 " --> pdb=" O GLY A1550 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ALA A1555 " --> pdb=" O ALA A1551 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N GLY A1563 " --> pdb=" O GLY A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix removed outlier: 3.501A pdb=" N THR A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1589 through 1593 Proline residue: A1593 - end of helix Processing helix chain 'A' and resid 1599 through 1618 removed outlier: 3.593A pdb=" N HIS A1615 " --> pdb=" O LEU A1611 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA A1618 " --> pdb=" O HIS A1614 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1633 No H-bonds generated for 'chain 'A' and resid 1631 through 1633' Processing helix chain 'A' and resid 1639 through 1647 Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1665 through 1668 No H-bonds generated for 'chain 'A' and resid 1665 through 1668' Processing helix chain 'A' and resid 1684 through 1691 Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 79 through 81 No H-bonds generated for 'chain 'B' and resid 79 through 81' Processing helix chain 'B' and resid 97 through 100 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 112 through 128 Processing helix chain 'B' and resid 151 through 154 Processing helix chain 'B' and resid 161 through 171 removed outlier: 3.981A pdb=" N HIS B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLY B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 183 removed outlier: 4.120A pdb=" N ARG B 179 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.399A pdb=" N SER B 200 " --> pdb=" O CYS B 197 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 206 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 237 Processing helix chain 'B' and resid 272 through 278 Processing helix chain 'B' and resid 299 through 301 No H-bonds generated for 'chain 'B' and resid 299 through 301' Processing helix chain 'B' and resid 303 through 319 removed outlier: 3.609A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 removed outlier: 3.715A pdb=" N GLU B 343 " --> pdb=" O GLY B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 353 No H-bonds generated for 'chain 'B' and resid 351 through 353' Processing helix chain 'B' and resid 366 through 370 removed outlier: 4.199A pdb=" N ILE B 370 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 removed outlier: 5.073A pdb=" N ALA B 378 " --> pdb=" O THR B 375 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA B 380 " --> pdb=" O GLY B 377 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 383 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 409 through 411 No H-bonds generated for 'chain 'B' and resid 409 through 411' Processing helix chain 'B' and resid 476 through 490 removed outlier: 3.656A pdb=" N ARG B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 removed outlier: 3.763A pdb=" N HIS B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N THR B 504 " --> pdb=" O HIS B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 565 through 581 removed outlier: 4.325A pdb=" N GLU B 570 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLY B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Proline residue: B 572 - end of helix removed outlier: 4.014A pdb=" N GLY B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 599 removed outlier: 3.513A pdb=" N GLU B 587 " --> pdb=" O PRO B 583 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY B 598 " --> pdb=" O GLU B 594 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 609 removed outlier: 4.232A pdb=" N ALA B 606 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG B 609 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.554A pdb=" N ALA B 660 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 removed outlier: 3.802A pdb=" N ARG B 678 " --> pdb=" O THR B 674 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG B 682 " --> pdb=" O ARG B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.710A pdb=" N ALA B 702 " --> pdb=" O ASP B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 711 No H-bonds generated for 'chain 'B' and resid 709 through 711' Processing helix chain 'B' and resid 730 through 742 removed outlier: 3.555A pdb=" N ALA B 738 " --> pdb=" O ALA B 734 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG B 741 " --> pdb=" O ALA B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 775 removed outlier: 4.360A pdb=" N ALA B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE B 772 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA B 774 " --> pdb=" O ARG B 770 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLY B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 799 No H-bonds generated for 'chain 'B' and resid 796 through 799' Processing helix chain 'B' and resid 802 through 808 removed outlier: 4.089A pdb=" N HIS B 808 " --> pdb=" O HIS B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 839 through 847 Processing helix chain 'B' and resid 869 through 883 removed outlier: 4.261A pdb=" N LEU B 873 " --> pdb=" O PRO B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 889 through 893 Processing helix chain 'B' and resid 953 through 959 removed outlier: 4.580A pdb=" N ALA B 957 " --> pdb=" O PRO B 953 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N GLY B 958 " --> pdb=" O GLY B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 972 through 983 Processing helix chain 'B' and resid 1062 through 1064 No H-bonds generated for 'chain 'B' and resid 1062 through 1064' Processing helix chain 'B' and resid 1066 through 1068 No H-bonds generated for 'chain 'B' and resid 1066 through 1068' Processing helix chain 'B' and resid 1074 through 1084 removed outlier: 3.790A pdb=" N GLN B1084 " --> pdb=" O ARG B1080 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1092 No H-bonds generated for 'chain 'B' and resid 1090 through 1092' Processing helix chain 'B' and resid 1121 through 1137 removed outlier: 3.795A pdb=" N LEU B1128 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B1134 " --> pdb=" O ALA B1131 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1196 No H-bonds generated for 'chain 'B' and resid 1194 through 1196' Processing helix chain 'B' and resid 1242 through 1255 removed outlier: 3.993A pdb=" N PHE B1255 " --> pdb=" O GLU B1251 " (cutoff:3.500A) Processing helix chain 'B' and resid 1283 through 1296 removed outlier: 3.879A pdb=" N GLU B1292 " --> pdb=" O LYS B1288 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU B1293 " --> pdb=" O THR B1289 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B1294 " --> pdb=" O PHE B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1309 through 1316 removed outlier: 4.110A pdb=" N ARG B1312 " --> pdb=" O GLY B1309 " (cutoff:3.500A) Proline residue: B1314 - end of helix Processing helix chain 'B' and resid 1321 through 1346 removed outlier: 3.939A pdb=" N ARG B1328 " --> pdb=" O ALA B1324 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLY B1330 " --> pdb=" O CYS B1326 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG B1331 " --> pdb=" O ARG B1327 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU B1345 " --> pdb=" O GLN B1341 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N GLN B1346 " --> pdb=" O GLU B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1368 through 1383 Proline residue: B1372 - end of helix removed outlier: 3.560A pdb=" N ALA B1375 " --> pdb=" O PRO B1372 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER B1379 " --> pdb=" O LEU B1376 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TRP B1382 " --> pdb=" O SER B1379 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1411 Processing helix chain 'B' and resid 1438 through 1443 Processing helix chain 'B' and resid 1459 through 1472 removed outlier: 3.799A pdb=" N ALA B1464 " --> pdb=" O ARG B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1482 through 1485 removed outlier: 3.535A pdb=" N GLU B1485 " --> pdb=" O ALA B1482 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1482 through 1485' Processing helix chain 'B' and resid 1490 through 1497 Processing helix chain 'B' and resid 1513 through 1523 removed outlier: 3.574A pdb=" N ALA B1520 " --> pdb=" O VAL B1516 " (cutoff:3.500A) Processing helix chain 'B' and resid 1550 through 1573 removed outlier: 3.872A pdb=" N ALA B1558 " --> pdb=" O GLY B1554 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY B1563 " --> pdb=" O GLY B1559 " (cutoff:3.500A) Proline residue: B1564 - end of helix removed outlier: 3.501A pdb=" N THR B1572 " --> pdb=" O THR B1568 " (cutoff:3.500A) Processing helix chain 'B' and resid 1589 through 1593 Proline residue: B1593 - end of helix Processing helix chain 'B' and resid 1599 through 1617 removed outlier: 3.619A pdb=" N HIS B1615 " --> pdb=" O LEU B1611 " (cutoff:3.500A) Processing helix chain 'B' and resid 1631 through 1633 No H-bonds generated for 'chain 'B' and resid 1631 through 1633' Processing helix chain 'B' and resid 1639 through 1648 Processing helix chain 'B' and resid 1655 through 1663 Processing helix chain 'B' and resid 1684 through 1689 Processing helix chain 'B' and resid 1716 through 1718 No H-bonds generated for 'chain 'B' and resid 1716 through 1718' Processing sheet with id= A, first strand: chain 'A' and resid 190 through 193 removed outlier: 8.695A pdb=" N VAL A 191 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N VAL A 142 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL A 193 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N LEU A 218 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N TYR A 143 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N LEU A 220 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLY A 145 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N GLY A 222 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY A 40 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLU A 270 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N VAL A 38 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA A 284 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE A 447 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N THR A 289 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N HIS A 445 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ILE A 291 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ASN A 443 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA A 328 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N THR A 435 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N GLU A 330 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU A 362 " --> pdb=" O VAL A 329 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 467 through 473 removed outlier: 3.825A pdb=" N GLY A 517 " --> pdb=" O VAL A 467 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 784 through 787 removed outlier: 3.668A pdb=" N GLY A 649 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 646 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ARG A 829 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU A 553 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 831 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N GLY A 555 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU A 858 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N GLY A 832 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA A 860 " --> pdb=" O GLY A 832 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 689 through 693 removed outlier: 3.517A pdb=" N ALA A 717 " --> pdb=" O VAL A 725 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER A 727 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL A 715 " --> pdb=" O SER A 727 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 946 through 951 removed outlier: 5.869A pdb=" N GLY A1032 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N GLU A1042 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU A1185 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL A1177 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ALA A1187 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ALA A1175 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A1161 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1097 " --> pdb=" O LEU A1108 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A1098 " --> pdb=" O LEU A1072 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1676 through 1680 removed outlier: 3.895A pdb=" N GLU A1676 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ARG A1418 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 11.052A pdb=" N LEU A1431 " --> pdb=" O ALA A1416 " (cutoff:3.500A) removed outlier: 15.484A pdb=" N ALA A1416 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N CYS A1389 " --> pdb=" O GLY A1417 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A1419 " --> pdb=" O CYS A1389 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLN A1391 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL A1421 " --> pdb=" O GLN A1391 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ASP A1393 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ILE A1350 " --> pdb=" O ALA A1390 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL A1392 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU A1352 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N LEU A1394 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N SER A1354 " --> pdb=" O LEU A1394 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N SER A1234 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N LEU A1303 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU A1236 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A1305 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N PHE A1238 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER A1239 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLY A1264 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLU A1274 " --> pdb=" O ALA A1263 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1502 through 1505 removed outlier: 7.768A pdb=" N LEU A1453 " --> pdb=" O ARG A1531 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A1533 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA A1455 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LEU A1535 " --> pdb=" O ALA A1455 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N PHE A1582 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N LEU A1535 " --> pdb=" O PHE A1582 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A1584 " --> pdb=" O LEU A1535 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 190 through 193 removed outlier: 8.816A pdb=" N VAL B 191 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL B 142 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU B 218 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N TYR B 143 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 220 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY B 145 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLY B 222 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY B 40 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU B 270 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N VAL B 38 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 284 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE B 447 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR B 289 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS B 445 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ILE B 291 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ASN B 443 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ALA B 328 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR B 435 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU B 330 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N LEU B 437 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 362 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 467 through 473 removed outlier: 3.684A pdb=" N GLY B 517 " --> pdb=" O VAL B 467 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 784 through 787 removed outlier: 3.987A pdb=" N GLY B 649 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA B 646 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ARG B 829 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N LEU B 553 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 831 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N GLY B 555 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU B 858 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 832 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA B 860 " --> pdb=" O GLY B 832 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 689 through 693 removed outlier: 6.665A pdb=" N SER B 727 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL B 715 " --> pdb=" O SER B 727 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 945 through 951 removed outlier: 5.906A pdb=" N GLY B1032 " --> pdb=" O GLU B1042 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLU B1042 " --> pdb=" O GLY B1032 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU B1185 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL B1177 " --> pdb=" O LEU B1185 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ALA B1187 " --> pdb=" O ALA B1175 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ALA B1175 " --> pdb=" O ALA B1187 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG B1097 " --> pdb=" O LEU B1108 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 967 through 969 removed outlier: 3.797A pdb=" N GLN B 962 " --> pdb=" O VAL B 969 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1677 through 1680 removed outlier: 3.542A pdb=" N ARG B1425 " --> pdb=" O ARG B1422 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 11.029A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 15.293A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE B1350 " --> pdb=" O ALA B1390 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N VAL B1392 " --> pdb=" O ILE B1350 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU B1352 " --> pdb=" O VAL B1392 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N SER B1234 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU B1303 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N LEU B1236 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N VAL B1305 " --> pdb=" O LEU B1236 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE B1238 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER B1239 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLY B1264 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B1274 " --> pdb=" O ALA B1263 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 1502 through 1505 removed outlier: 7.927A pdb=" N LEU B1453 " --> pdb=" O ARG B1531 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B1533 " --> pdb=" O LEU B1453 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ALA B1455 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU B1535 " --> pdb=" O ALA B1455 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N PHE B1582 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LEU B1535 " --> pdb=" O PHE B1582 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B1584 " --> pdb=" O LEU B1535 " (cutoff:3.500A) 961 hydrogen bonds defined for protein. 2328 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: 25.75 Time building geometry restraints manager: 39.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.12: 24324 1.12 - 1.29: 4361 1.29 - 1.47: 8860 1.47 - 1.64: 11933 1.64 - 1.82: 68 Bond restraints: 49546 Sorted by residual: bond pdb=" N ALA B 323 " pdb=" H ALA B 323 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" CD1 PHE A 627 " pdb=" HD1 PHE A 627 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.79e+01 bond pdb=" N LEU A1151 " pdb=" H LEU A1151 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" N ALA A 107 " pdb=" H ALA A 107 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.78e+01 bond pdb=" NH1 ARG B 912 " pdb="HH11 ARG B 912 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.77e+01 ... (remaining 49541 not shown) Histogram of bond angle deviations from ideal: 95.92 - 103.82: 540 103.82 - 111.73: 52713 111.73 - 119.63: 20405 119.63 - 127.54: 15674 127.54 - 135.44: 332 Bond angle restraints: 89664 Sorted by residual: angle pdb=" C VAL A 916 " pdb=" N PRO A 917 " pdb=" CA PRO A 917 " ideal model delta sigma weight residual 119.66 124.23 -4.57 7.30e-01 1.88e+00 3.91e+01 angle pdb=" CA ASP B 64 " pdb=" CB ASP B 64 " pdb=" CG ASP B 64 " ideal model delta sigma weight residual 112.60 118.83 -6.23 1.00e+00 1.00e+00 3.89e+01 angle pdb=" N SER A 250 " pdb=" CA SER A 250 " pdb=" C SER A 250 " ideal model delta sigma weight residual 111.33 118.54 -7.21 1.21e+00 6.83e-01 3.55e+01 angle pdb=" N PRO A 928 " pdb=" CA PRO A 928 " pdb=" C PRO A 928 " ideal model delta sigma weight residual 110.70 117.95 -7.25 1.22e+00 6.72e-01 3.53e+01 angle pdb=" C VAL B 916 " pdb=" N PRO B 917 " pdb=" CA PRO B 917 " ideal model delta sigma weight residual 119.66 123.53 -3.87 7.20e-01 1.93e+00 2.89e+01 ... (remaining 89659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.54: 21611 21.54 - 43.07: 1151 43.07 - 64.61: 522 64.61 - 86.14: 36 86.14 - 107.68: 8 Dihedral angle restraints: 23328 sinusoidal: 12976 harmonic: 10352 Sorted by residual: dihedral pdb=" CA LYS A 249 " pdb=" C LYS A 249 " pdb=" N SER A 250 " pdb=" CA SER A 250 " ideal model delta harmonic sigma weight residual -180.00 -150.84 -29.16 0 5.00e+00 4.00e-02 3.40e+01 dihedral pdb=" CA THR A 397 " pdb=" C THR A 397 " pdb=" N VAL A 398 " pdb=" CA VAL A 398 " ideal model delta harmonic sigma weight residual -180.00 -151.02 -28.98 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA GLY A1279 " pdb=" C GLY A1279 " pdb=" N THR A1280 " pdb=" CA THR A1280 " ideal model delta harmonic sigma weight residual 180.00 151.47 28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 23325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2571 0.091 - 0.183: 1075 0.183 - 0.274: 185 0.274 - 0.365: 24 0.365 - 0.457: 13 Chirality restraints: 3868 Sorted by residual: chirality pdb=" CA ASP B1222 " pdb=" N ASP B1222 " pdb=" C ASP B1222 " pdb=" CB ASP B1222 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.21e+00 chirality pdb=" CA VAL B 862 " pdb=" N VAL B 862 " pdb=" C VAL B 862 " pdb=" CB VAL B 862 " both_signs ideal model delta sigma weight residual False 2.44 1.99 0.45 2.00e-01 2.50e+01 5.02e+00 chirality pdb=" CA GLN B 33 " pdb=" N GLN B 33 " pdb=" C GLN B 33 " pdb=" CB GLN B 33 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 ... (remaining 3865 not shown) Planarity restraints: 7786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1337 " -0.239 9.50e-02 1.11e+02 1.31e-01 2.47e+02 pdb=" NE ARG B1337 " -0.111 2.00e-02 2.50e+03 pdb=" CZ ARG B1337 " -0.067 2.00e-02 2.50e+03 pdb=" NH1 ARG B1337 " -0.036 2.00e-02 2.50e+03 pdb=" NH2 ARG B1337 " -0.034 2.00e-02 2.50e+03 pdb="HH11 ARG B1337 " 0.184 2.00e-02 2.50e+03 pdb="HH12 ARG B1337 " -0.050 2.00e-02 2.50e+03 pdb="HH21 ARG B1337 " 0.190 2.00e-02 2.50e+03 pdb="HH22 ARG B1337 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1337 " 0.239 9.50e-02 1.11e+02 1.30e-01 2.42e+02 pdb=" NE ARG A1337 " 0.086 2.00e-02 2.50e+03 pdb=" CZ ARG A1337 " 0.076 2.00e-02 2.50e+03 pdb=" NH1 ARG A1337 " 0.056 2.00e-02 2.50e+03 pdb=" NH2 ARG A1337 " 0.074 2.00e-02 2.50e+03 pdb="HH11 ARG A1337 " -0.182 2.00e-02 2.50e+03 pdb="HH12 ARG A1337 " 0.033 2.00e-02 2.50e+03 pdb="HH21 ARG A1337 " -0.192 2.00e-02 2.50e+03 pdb="HH22 ARG A1337 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1651 " -0.202 2.00e-02 2.50e+03 8.92e-02 2.39e+02 pdb=" CG TYR B1651 " 0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B1651 " 0.065 2.00e-02 2.50e+03 pdb=" CD2 TYR B1651 " 0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR B1651 " 0.044 2.00e-02 2.50e+03 pdb=" CE2 TYR B1651 " 0.063 2.00e-02 2.50e+03 pdb=" CZ TYR B1651 " 0.012 2.00e-02 2.50e+03 pdb=" OH TYR B1651 " -0.189 2.00e-02 2.50e+03 pdb=" HD1 TYR B1651 " 0.046 2.00e-02 2.50e+03 pdb=" HD2 TYR B1651 " 0.021 2.00e-02 2.50e+03 pdb=" HE1 TYR B1651 " 0.017 2.00e-02 2.50e+03 pdb=" HE2 TYR B1651 " 0.029 2.00e-02 2.50e+03 ... (remaining 7783 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3701 2.19 - 2.79: 86517 2.79 - 3.40: 135877 3.40 - 4.00: 179469 4.00 - 4.60: 262680 Nonbonded interactions: 668244 Sorted by model distance: nonbonded pdb=" HG SER A1591 " pdb=" OD2 ASP A1605 " model vdw 1.590 1.850 nonbonded pdb=" OE1 GLU B 654 " pdb=" HG SER B 787 " model vdw 1.596 1.850 nonbonded pdb=" HG SER B1512 " pdb=" OD1 ASP B1515 " model vdw 1.597 1.850 nonbonded pdb=" HG SER B 665 " pdb=" OD2 ASP B 668 " model vdw 1.597 1.850 nonbonded pdb=" OD1 ASP B 408 " pdb=" HG SER B 410 " model vdw 1.600 1.850 ... (remaining 668239 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.950 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: 0.690 Extract box with map and model: 14.200 Check model and map are aligned: 0.690 Set scattering table: 0.390 Process input model: 152.120 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.220 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 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 : 0.012 0.053 25198 Z= 0.835 Angle : 1.826 9.054 34402 Z= 1.229 Chirality : 0.097 0.457 3868 Planarity : 0.016 0.161 4658 Dihedral : 12.825 107.677 9074 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.86 % Favored : 96.11 % Rotamer: Outliers : 1.16 % Allowed : 2.89 % Favored : 95.95 % Cbeta Deviations : 0.41 % 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: -0.81 (0.13), residues: 3370 helix: -1.03 (0.12), residues: 1214 sheet: 1.08 (0.25), residues: 440 loop : -0.48 (0.14), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.115 0.021 TRP A 122 HIS 0.024 0.003 HIS A1461 PHE 0.071 0.014 PHE B 778 TYR 0.185 0.025 TYR B1651 ARG 0.012 0.001 ARG B 506 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 413 time to evaluate : 3.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 GLU cc_start: 0.8001 (tt0) cc_final: 0.7734 (tt0) REVERT: A 681 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7210 (mt-10) REVERT: A 806 LEU cc_start: 0.7349 (tp) cc_final: 0.7119 (tp) REVERT: A 1402 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7797 (p) REVERT: B 330 GLU cc_start: 0.8542 (tp30) cc_final: 0.7942 (tm-30) REVERT: B 387 MET cc_start: 0.9044 (mmm) cc_final: 0.8814 (mmm) REVERT: B 479 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7275 (tt) REVERT: B 497 ASP cc_start: 0.8156 (m-30) cc_final: 0.7891 (m-30) REVERT: B 806 LEU cc_start: 0.8287 (tp) cc_final: 0.7963 (tp) outliers start: 28 outliers final: 10 residues processed: 439 average time/residue: 1.1199 time to fit residues: 693.1843 Evaluate side-chains 157 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 3.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 720 GLU Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1402 THR Chi-restraints excluded: chain A residue 1519 LEU Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 1049 VAL Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 5.9990 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 263 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 2.9990 chunk 196 optimal weight: 0.9990 chunk 305 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 482 GLN A1461 HIS A1617 GLN ** B 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 25198 Z= 0.242 Angle : 0.687 8.549 34402 Z= 0.363 Chirality : 0.043 0.187 3868 Planarity : 0.007 0.074 4658 Dihedral : 7.162 94.103 3755 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.74 % Allowed : 6.94 % Favored : 91.32 % 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: -0.40 (0.14), residues: 3370 helix: -0.38 (0.14), residues: 1234 sheet: 0.96 (0.22), residues: 546 loop : -0.50 (0.15), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 423 HIS 0.008 0.002 HIS B 399 PHE 0.021 0.002 PHE A 850 TYR 0.019 0.002 TYR B 151 ARG 0.005 0.001 ARG A1570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 154 time to evaluate : 3.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 678 ARG cc_start: 0.6883 (mtt180) cc_final: 0.6649 (mpt-90) REVERT: A 681 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7295 (mt-10) REVERT: A 1284 ASP cc_start: 0.7159 (t70) cc_final: 0.6698 (t0) REVERT: A 1343 TYR cc_start: 0.7406 (m-80) cc_final: 0.6953 (m-80) REVERT: B 330 GLU cc_start: 0.8358 (tp30) cc_final: 0.7852 (tm-30) REVERT: B 479 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7053 (tt) REVERT: B 666 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8194 (mp) REVERT: B 674 THR cc_start: 0.7689 (p) cc_final: 0.7408 (t) REVERT: B 806 LEU cc_start: 0.8372 (tp) cc_final: 0.8066 (tp) REVERT: B 1067 GLU cc_start: 0.6206 (OUTLIER) cc_final: 0.5905 (mp0) REVERT: B 1632 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5943 (pm20) outliers start: 42 outliers final: 27 residues processed: 189 average time/residue: 0.9507 time to fit residues: 268.6949 Evaluate side-chains 147 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 600 LEU Chi-restraints excluded: chain A residue 739 HIS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1251 GLU Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1373 LEU Chi-restraints excluded: chain A residue 1469 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1708 GLU Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 827 VAL Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1183 VAL Chi-restraints excluded: chain B residue 1303 LEU Chi-restraints excluded: chain B residue 1411 MET Chi-restraints excluded: chain B residue 1580 THR Chi-restraints excluded: chain B residue 1632 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 chunk 253 optimal weight: 4.9990 chunk 207 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 305 optimal weight: 3.9990 chunk 330 optimal weight: 4.9990 chunk 272 optimal weight: 4.9990 chunk 303 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 25198 Z= 0.291 Angle : 0.607 7.779 34402 Z= 0.313 Chirality : 0.042 0.186 3868 Planarity : 0.006 0.050 4658 Dihedral : 6.220 85.184 3748 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.61 % Allowed : 7.73 % Favored : 90.66 % 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: -0.45 (0.14), residues: 3370 helix: -0.12 (0.14), residues: 1232 sheet: 0.35 (0.21), residues: 578 loop : -0.58 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1468 HIS 0.014 0.001 HIS A 743 PHE 0.013 0.002 PHE A 95 TYR 0.023 0.002 TYR A1343 ARG 0.006 0.001 ARG A1199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 127 time to evaluate : 3.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 PHE cc_start: 0.7426 (m-10) cc_final: 0.6675 (m-10) REVERT: A 1199 ARG cc_start: 0.5124 (tpp80) cc_final: 0.4915 (tpp80) REVERT: B 330 GLU cc_start: 0.8479 (tp30) cc_final: 0.7869 (tm-30) REVERT: B 479 LEU cc_start: 0.7711 (OUTLIER) cc_final: 0.7166 (tt) REVERT: B 666 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8290 (mp) REVERT: B 1067 GLU cc_start: 0.6093 (OUTLIER) cc_final: 0.5888 (mp0) outliers start: 39 outliers final: 30 residues processed: 157 average time/residue: 0.9746 time to fit residues: 232.1240 Evaluate side-chains 139 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1342 GLU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1708 GLU Chi-restraints excluded: chain A residue 1716 GLN Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1403 VAL Chi-restraints excluded: chain B residue 1411 MET Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 3.9990 chunk 229 optimal weight: 5.9990 chunk 158 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 205 optimal weight: 2.9990 chunk 306 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 290 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 763 GLN A1617 GLN B 374 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25198 Z= 0.204 Angle : 0.542 6.459 34402 Z= 0.273 Chirality : 0.041 0.155 3868 Planarity : 0.005 0.052 4658 Dihedral : 5.697 76.760 3748 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.45 % Allowed : 8.43 % Favored : 90.12 % 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: -0.27 (0.14), residues: 3370 helix: 0.10 (0.15), residues: 1234 sheet: 0.44 (0.21), residues: 576 loop : -0.54 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1468 HIS 0.009 0.001 HIS A1692 PHE 0.012 0.001 PHE A1029 TYR 0.009 0.001 TYR B 151 ARG 0.013 0.000 ARG B 576 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 110 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1284 ASP cc_start: 0.7080 (t0) cc_final: 0.6643 (t0) REVERT: B 330 GLU cc_start: 0.8481 (tp30) cc_final: 0.7856 (tm-30) REVERT: B 479 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7182 (tt) REVERT: B 666 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8342 (mp) REVERT: B 674 THR cc_start: 0.7397 (p) cc_final: 0.7149 (t) outliers start: 35 outliers final: 27 residues processed: 138 average time/residue: 0.9017 time to fit residues: 193.6921 Evaluate side-chains 127 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 98 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1288 LYS Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1617 GLN Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain A residue 1719 MET Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1411 MET Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 241 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 0.9990 chunk 224 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 291 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 113 GLN B 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 25198 Z= 0.261 Angle : 0.544 6.248 34402 Z= 0.275 Chirality : 0.041 0.157 3868 Planarity : 0.005 0.050 4658 Dihedral : 5.504 69.957 3748 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.36 % Allowed : 9.17 % Favored : 89.46 % 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 (0.14), residues: 3370 helix: 0.17 (0.15), residues: 1228 sheet: 0.14 (0.21), residues: 568 loop : -0.59 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1468 HIS 0.016 0.001 HIS A1692 PHE 0.010 0.001 PHE A 947 TYR 0.010 0.001 TYR A 151 ARG 0.010 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 3.617 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: B 330 GLU cc_start: 0.8515 (tp30) cc_final: 0.7869 (tm-30) REVERT: B 387 MET cc_start: 0.9103 (mmp) cc_final: 0.8847 (mmp) REVERT: B 479 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7208 (tt) outliers start: 33 outliers final: 24 residues processed: 134 average time/residue: 0.8952 time to fit residues: 189.3768 Evaluate side-chains 122 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 97 time to evaluate : 3.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 325 optimal weight: 4.9990 chunk 269 optimal weight: 0.0470 chunk 150 optimal weight: 0.7980 chunk 27 optimal weight: 0.0570 chunk 107 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 25198 Z= 0.195 Angle : 0.517 6.066 34402 Z= 0.258 Chirality : 0.040 0.155 3868 Planarity : 0.005 0.055 4658 Dihedral : 5.279 63.419 3748 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.28 % Allowed : 9.46 % Favored : 89.26 % 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: -0.27 (0.14), residues: 3370 helix: 0.28 (0.15), residues: 1232 sheet: 0.21 (0.21), residues: 564 loop : -0.59 (0.16), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1468 HIS 0.013 0.001 HIS A1692 PHE 0.008 0.001 PHE B 947 TYR 0.008 0.001 TYR A 151 ARG 0.003 0.000 ARG A 390 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 105 time to evaluate : 4.011 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: B 330 GLU cc_start: 0.8532 (tp30) cc_final: 0.7902 (tm-30) REVERT: B 479 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7201 (tt) REVERT: B 1179 SER cc_start: 0.8754 (p) cc_final: 0.8158 (m) outliers start: 31 outliers final: 22 residues processed: 132 average time/residue: 0.8784 time to fit residues: 184.6372 Evaluate side-chains 125 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 3.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1679 LEU Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1580 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 10.0000 chunk 36 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 0.7980 chunk 181 optimal weight: 1.9990 chunk 323 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A1014 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25198 Z= 0.190 Angle : 0.506 6.004 34402 Z= 0.252 Chirality : 0.040 0.214 3868 Planarity : 0.005 0.052 4658 Dihedral : 5.021 57.207 3747 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.16 % Allowed : 9.79 % Favored : 89.05 % 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: -0.18 (0.15), residues: 3370 helix: 0.37 (0.15), residues: 1244 sheet: 0.21 (0.21), residues: 600 loop : -0.56 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1630 HIS 0.011 0.001 HIS A1692 PHE 0.034 0.001 PHE A 778 TYR 0.008 0.001 TYR B 151 ARG 0.007 0.000 ARG A1199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 3.448 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: A 789 VAL cc_start: 0.7916 (t) cc_final: 0.7436 (m) REVERT: A 1199 ARG cc_start: 0.5671 (tpp80) cc_final: 0.5420 (tpp80) REVERT: B 330 GLU cc_start: 0.8568 (tp30) cc_final: 0.7938 (tm-30) REVERT: B 479 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7214 (tt) REVERT: B 674 THR cc_start: 0.7092 (p) cc_final: 0.6841 (t) REVERT: B 1179 SER cc_start: 0.8750 (p) cc_final: 0.8158 (m) outliers start: 28 outliers final: 22 residues processed: 141 average time/residue: 0.8503 time to fit residues: 189.2456 Evaluate side-chains 129 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 GLN Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 967 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.4708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 25198 Z= 0.379 Angle : 0.574 6.173 34402 Z= 0.293 Chirality : 0.042 0.161 3868 Planarity : 0.005 0.054 4658 Dihedral : 5.267 56.860 3746 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.40 % Allowed : 10.04 % Favored : 88.55 % 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 (0.14), residues: 3370 helix: 0.19 (0.15), residues: 1240 sheet: -0.07 (0.21), residues: 616 loop : -0.76 (0.16), residues: 1514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 914 HIS 0.015 0.001 HIS A1692 PHE 0.013 0.002 PHE A 947 TYR 0.012 0.002 TYR B 151 ARG 0.004 0.001 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 100 time to evaluate : 3.835 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: B 330 GLU cc_start: 0.8616 (tp30) cc_final: 0.8001 (tm-30) REVERT: B 479 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7327 (tt) REVERT: B 547 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.4731 (mt0) REVERT: B 674 THR cc_start: 0.7315 (p) cc_final: 0.7005 (t) REVERT: B 1483 GLU cc_start: 0.3604 (OUTLIER) cc_final: 0.2493 (pm20) outliers start: 34 outliers final: 25 residues processed: 130 average time/residue: 0.8641 time to fit residues: 178.3560 Evaluate side-chains 124 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 96 time to evaluate : 3.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain A residue 1707 ASP Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 547 GLN Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1483 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 2.9990 chunk 310 optimal weight: 7.9990 chunk 283 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 92 optimal weight: 0.6980 chunk 272 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 300 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 25198 Z= 0.285 Angle : 0.544 5.991 34402 Z= 0.274 Chirality : 0.041 0.156 3868 Planarity : 0.005 0.054 4658 Dihedral : 5.211 55.605 3746 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.32 % Allowed : 10.25 % Favored : 88.43 % 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: -0.44 (0.15), residues: 3370 helix: 0.23 (0.15), residues: 1228 sheet: -0.01 (0.21), residues: 614 loop : -0.74 (0.16), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A1630 HIS 0.014 0.001 HIS A1692 PHE 0.011 0.001 PHE A1427 TYR 0.010 0.001 TYR B 151 ARG 0.006 0.000 ARG B 390 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 101 time to evaluate : 3.386 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 789 VAL cc_start: 0.7750 (t) cc_final: 0.7501 (m) REVERT: B 330 GLU cc_start: 0.8589 (tp30) cc_final: 0.7992 (tm-30) REVERT: B 479 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7349 (tt) REVERT: B 1179 SER cc_start: 0.8690 (p) cc_final: 0.8111 (t) outliers start: 32 outliers final: 25 residues processed: 129 average time/residue: 0.8833 time to fit residues: 179.3023 Evaluate side-chains 122 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 96 time to evaluate : 2.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1067 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 6.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 334 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 266 optimal weight: 3.9990 chunk 27 optimal weight: 0.0040 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1370 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25198 Z= 0.265 Angle : 0.534 7.550 34402 Z= 0.268 Chirality : 0.041 0.193 3868 Planarity : 0.005 0.055 4658 Dihedral : 5.137 55.650 3746 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 1.16 % Allowed : 10.50 % Favored : 88.35 % 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: -0.39 (0.15), residues: 3370 helix: 0.31 (0.15), residues: 1220 sheet: 0.03 (0.21), residues: 608 loop : -0.75 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1630 HIS 0.014 0.001 HIS A1692 PHE 0.010 0.001 PHE B 947 TYR 0.011 0.001 TYR B 151 ARG 0.005 0.000 ARG B 390 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6740 Ramachandran restraints generated. 3370 Oldfield, 0 Emsley, 3370 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 3.244 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 789 VAL cc_start: 0.7776 (t) cc_final: 0.7540 (m) REVERT: B 330 GLU cc_start: 0.8572 (tp30) cc_final: 0.7985 (tm-30) REVERT: B 479 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7345 (tt) REVERT: B 674 THR cc_start: 0.7003 (p) cc_final: 0.6652 (t) REVERT: B 1483 GLU cc_start: 0.3684 (OUTLIER) cc_final: 0.2801 (pm20) outliers start: 28 outliers final: 26 residues processed: 127 average time/residue: 0.8817 time to fit residues: 176.3623 Evaluate side-chains 126 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 3.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 438 THR Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 503 HIS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 595 HIS Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 VAL Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1035 THR Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1174 ASP Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1378 THR Chi-restraints excluded: chain A residue 1433 ARG Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1693 ARG Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 625 VAL Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 824 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 1067 GLU Chi-restraints excluded: chain B residue 1483 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.9990 chunk 283 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 74 optimal weight: 0.3980 chunk 266 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.103604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085617 restraints weight = 185821.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.086704 restraints weight = 167507.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087393 restraints weight = 129172.975| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.5071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25198 Z= 0.164 Angle : 0.498 5.940 34402 Z= 0.246 Chirality : 0.040 0.153 3868 Planarity : 0.005 0.053 4658 Dihedral : 4.915 55.226 3746 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.03 % Allowed : 10.83 % Favored : 88.14 % 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: -0.15 (0.15), residues: 3370 helix: 0.49 (0.16), residues: 1198 sheet: 0.23 (0.21), residues: 604 loop : -0.61 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1630 HIS 0.013 0.001 HIS A1692 PHE 0.008 0.001 PHE B1238 TYR 0.008 0.001 TYR B 151 ARG 0.003 0.000 ARG B1143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7559.18 seconds wall clock time: 134 minutes 38.90 seconds (8078.90 seconds total)