Starting phenix.real_space_refine on Mon Mar 25 13:13:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/03_2024/8i4z_35189_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/03_2024/8i4z_35189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/03_2024/8i4z_35189.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/03_2024/8i4z_35189.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/03_2024/8i4z_35189_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i4z_35189/03_2024/8i4z_35189_trim_updated.pdb" } resolution = 3.97 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 15345 2.51 5 N 4563 2.21 5 O 4675 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 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 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 PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 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 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: 48977 Number of models: 1 Model: "" Number of chains: 3 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: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'ONF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.84, per 1000 atoms: 0.45 Number of scatterers: 48977 At special positions: 0 Unit cell: (200.25, 167.32, 128.16, 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 4675 8.00 N 4563 7.00 C 15345 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=0, symmetry=0 Time building additional restraints: 38.14 Conformation dependent library (CDL) restraints added in 5.4 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: 128 helices and 15 sheets defined 38.3% alpha, 15.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.47 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 removed outlier: 3.623A pdb=" N TRP A 122 " --> pdb=" O LEU A 118 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU A 123 " --> pdb=" O GLU A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 135 No H-bonds generated for 'chain 'A' and resid 132 through 135' Processing helix chain 'A' and resid 151 through 154 Processing helix chain 'A' and resid 161 through 171 removed outlier: 4.466A pdb=" N ASP A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N HIS A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY A 168 " --> pdb=" O LEU A 164 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N LEU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 184 removed outlier: 4.204A pdb=" N SER A 177 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG A 179 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N PHE A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 212 removed outlier: 4.118A pdb=" N SER A 200 " --> pdb=" O CYS A 197 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A 202 " --> pdb=" O SER A 199 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A 206 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 209 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG A 212 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 272 through 278 Processing helix chain 'A' and resid 303 through 318 removed outlier: 3.514A pdb=" N GLN A 308 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE A 312 " --> pdb=" O GLU A 309 " (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 350 Processing helix chain 'A' and resid 366 through 370 removed outlier: 3.613A pdb=" N ILE A 370 " --> pdb=" O LYS A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 391 removed outlier: 5.227A pdb=" N ALA A 378 " --> pdb=" O THR A 375 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA A 380 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 381 " --> pdb=" O ALA A 378 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 386 " --> pdb=" O VAL A 383 " (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 488 removed outlier: 4.014A pdb=" N ALA A 488 " --> pdb=" O GLU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 495 through 504 removed outlier: 3.714A pdb=" N THR A 504 " --> pdb=" O HIS A 500 " (cutoff:3.500A) 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: 4.684A pdb=" N GLY A 577 " --> pdb=" O ARG A 573 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LEU A 578 " --> pdb=" O THR A 574 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N TYR A 579 " --> pdb=" O ALA A 575 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU A 580 " --> pdb=" O ARG A 576 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA A 581 " --> pdb=" O GLY A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 600 removed outlier: 4.128A pdb=" N GLU A 587 " --> pdb=" O PRO A 583 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 588 " --> pdb=" O ALA A 584 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLY A 598 " --> pdb=" O GLU A 594 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LEU A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 600 " --> pdb=" O LEU A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 removed outlier: 3.559A 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: 4.174A pdb=" N VAL A 655 " --> pdb=" O ALA A 652 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 660 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 684 removed outlier: 3.807A pdb=" N ARG A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE A 679 " --> pdb=" O ALA A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 706 removed outlier: 3.683A pdb=" N SER A 705 " --> pdb=" O ARG A 701 " (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: 3.529A pdb=" N ARG A 741 " --> pdb=" O ALA A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 775 removed outlier: 3.907A pdb=" N GLU A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 770 " --> pdb=" O LEU A 766 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE A 772 " --> pdb=" O GLU A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 802 through 810 removed outlier: 3.684A pdb=" N ASP A 807 " --> pdb=" O GLU A 803 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N HIS A 808 " --> pdb=" O HIS A 804 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU A 809 " --> pdb=" O TRP A 805 " (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: 3.751A 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: 4.162A pdb=" N ALA A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLY A 958 " --> pdb=" O GLY A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 986 removed outlier: 3.505A pdb=" N LEU A 976 " --> pdb=" O ALA A 972 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS A 985 " --> pdb=" O ALA A 981 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY A 986 " --> pdb=" O ALA A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1064 No H-bonds generated for 'chain 'A' and resid 1062 through 1064' Processing helix chain 'A' and resid 1074 through 1084 removed outlier: 3.539A pdb=" N TRP A1082 " --> pdb=" O TYR A1078 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG A1083 " --> pdb=" O ARG A1079 " (cutoff:3.500A) removed outlier: 4.180A 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: 3.550A pdb=" N LEU A1134 " --> pdb=" O ALA A1131 " (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 1242 through 1254 Processing helix chain 'A' and resid 1283 through 1295 Processing helix chain 'A' and resid 1309 through 1312 removed outlier: 4.196A 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: 3.774A pdb=" N GLY A1330 " --> pdb=" O CYS A1326 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG A1331 " --> pdb=" O ARG A1327 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU A1345 " --> pdb=" O GLN A1341 " (cutoff:3.500A) removed outlier: 6.973A 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: 3.558A pdb=" N ALA A1375 " --> pdb=" O PRO A1372 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A1382 " --> pdb=" O SER A1379 " (cutoff:3.500A) removed outlier: 3.512A 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 removed outlier: 3.526A pdb=" N ARG A1443 " --> pdb=" O ARG A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1471 Processing helix chain 'A' and resid 1482 through 1485 removed outlier: 3.954A pdb=" N GLU A1485 " --> pdb=" O ALA A1482 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1482 through 1485' Processing helix chain 'A' and resid 1490 through 1497 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: 4.951A pdb=" N ALA A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLY A1563 " --> pdb=" O GLY A1559 " (cutoff:3.500A) Proline residue: A1564 - end of helix Processing helix chain 'A' and resid 1589 through 1593 Proline residue: A1593 - end of helix Processing helix chain 'A' and resid 1599 through 1618 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 1640 through 1648 Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1684 through 1691 Processing helix chain 'A' and resid 1716 through 1718 No H-bonds generated for 'chain 'A' and resid 1716 through 1718' 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 104 through 109 Processing helix chain 'B' and resid 112 through 127 removed outlier: 3.544A pdb=" N TRP B 122 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 135 No H-bonds generated for 'chain 'B' and resid 132 through 135' Processing helix chain 'B' and resid 151 through 154 Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.017A pdb=" N ASP B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N HIS B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLY B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU B 169 " --> pdb=" O ASP B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 183 removed outlier: 4.493A pdb=" N SER B 177 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 181 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 212 removed outlier: 4.416A pdb=" N SER B 200 " --> pdb=" O CYS B 197 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 202 " --> pdb=" O SER B 199 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 204 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 238 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 318 removed outlier: 3.761A pdb=" N ARG B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 348 Processing helix chain 'B' and resid 366 through 370 removed outlier: 3.510A pdb=" N ILE B 370 " --> pdb=" O LYS B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.712A pdb=" N GLY B 377 " --> pdb=" O GLN B 374 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA B 378 " --> pdb=" O THR B 375 " (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 492 removed outlier: 3.671A pdb=" N ARG B 480 " --> pdb=" O PRO B 476 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N ALA B 488 " --> pdb=" O GLU B 484 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR B 489 " --> pdb=" O ARG B 485 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N THR B 491 " --> pdb=" O ARG B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 505 removed outlier: 3.794A pdb=" N HIS B 503 " --> pdb=" O GLY B 499 " (cutoff:3.500A) removed outlier: 3.932A 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: 4.165A pdb=" N GLU B 570 " --> pdb=" O PRO B 566 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLY B 571 " --> pdb=" O ALA B 567 " (cutoff:3.500A) Proline residue: B 572 - end of helix removed outlier: 3.722A pdb=" N GLY B 577 " --> pdb=" O ARG B 573 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLU B 580 " --> pdb=" O ARG B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 599 removed outlier: 3.732A pdb=" N GLU B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N HIS B 595 " --> pdb=" O GLU B 591 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU B 599 " --> pdb=" O HIS B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 610 removed outlier: 3.820A pdb=" N GLU B 610 " --> pdb=" O ALA B 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 616 Processing helix chain 'B' and resid 620 through 639 Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.552A pdb=" N ALA B 660 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 684 removed outlier: 3.721A pdb=" N ALA B 671 " --> pdb=" O ALA B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 706 removed outlier: 3.693A 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 Processing helix chain 'B' and resid 759 through 775 removed outlier: 3.599A pdb=" N ARG B 770 " --> pdb=" O LEU B 766 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ALA B 771 " --> pdb=" O ALA B 767 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE B 772 " --> pdb=" O GLU B 768 " (cutoff:3.500A) removed outlier: 3.562A 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: 3.873A pdb=" N HIS B 808 " --> pdb=" O HIS B 804 " (cutoff:3.500A) Processing helix chain 'B' and resid 815 through 824 Processing helix chain 'B' and resid 839 through 847 Processing helix chain 'B' and resid 869 through 883 removed outlier: 4.363A 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 956 through 959 No H-bonds generated for 'chain 'B' and resid 956 through 959' Processing helix chain 'B' and resid 972 through 986 removed outlier: 5.574A pdb=" N GLY B 986 " --> pdb=" O ALA B 982 " (cutoff:3.500A) 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 1074 through 1084 removed outlier: 3.517A 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: 3.659A pdb=" N LEU B1128 " --> pdb=" O ALA B1125 " (cutoff:3.500A) removed outlier: 3.660A 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 1254 Processing helix chain 'B' and resid 1283 through 1295 removed outlier: 4.133A pdb=" N GLU B1292 " --> pdb=" O LYS B1288 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU B1293 " --> pdb=" O THR B1289 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B1294 " --> pdb=" O PHE B1290 " (cutoff:3.500A) Processing helix chain 'B' and resid 1309 through 1316 removed outlier: 3.934A 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: 3.734A pdb=" N GLU B1342 " --> pdb=" O GLY B1338 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU B1345 " --> pdb=" O GLN B1341 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N GLN B1346 " --> pdb=" O GLU B1342 " (cutoff:3.500A) Processing helix chain 'B' and resid 1368 through 1381 Proline residue: B1372 - end of helix removed outlier: 3.549A pdb=" N ALA B1375 " --> pdb=" O PRO B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1403 through 1412 removed outlier: 3.551A pdb=" N ARG B1412 " --> pdb=" O GLY B1408 " (cutoff:3.500A) Processing helix chain 'B' and resid 1438 through 1443 Processing helix chain 'B' and resid 1459 through 1471 removed outlier: 3.592A pdb=" N ALA B1464 " --> pdb=" O ARG B1460 " (cutoff:3.500A) Processing helix chain 'B' and resid 1482 through 1485 removed outlier: 3.702A 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 1524 removed outlier: 3.991A pdb=" N LEU B1519 " --> pdb=" O ASP B1515 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA B1520 " --> pdb=" O VAL B1516 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU B1521 " --> pdb=" O ALA B1517 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU B1522 " --> pdb=" O ARG B1518 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N CYS B1523 " --> pdb=" O LEU B1519 " (cutoff:3.500A) Processing helix chain 'B' and resid 1552 through 1573 removed outlier: 4.002A pdb=" N ALA B1558 " --> pdb=" O GLY B1554 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLY B1563 " --> pdb=" O GLY B1559 " (cutoff:3.500A) Proline residue: B1564 - end of helix Processing helix chain 'B' and resid 1589 through 1593 Proline residue: B1593 - end of helix Processing helix chain 'B' and resid 1599 through 1618 removed outlier: 3.677A pdb=" N ARG B1613 " --> pdb=" O THR B1609 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA B1618 " --> pdb=" O HIS B1614 " (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 1640 through 1648 Processing helix chain 'B' and resid 1655 through 1662 Processing helix chain 'B' and resid 1684 through 1689 removed outlier: 3.730A pdb=" N THR B1689 " --> pdb=" O ASP B1685 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 190 through 193 removed outlier: 8.744A pdb=" N VAL A 191 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.428A 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: 6.427A pdb=" N ALA A 144 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU A 218 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 8.471A pdb=" N TYR A 143 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU A 220 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N GLY A 145 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N GLY A 222 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 40 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N GLU A 270 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL A 38 " --> pdb=" O GLU A 270 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 284 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A 447 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N THR A 289 " --> pdb=" O HIS A 445 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N HIS A 445 " --> pdb=" O THR A 289 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE A 291 " --> pdb=" O ASN A 443 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ASN A 443 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ALA A 328 " --> pdb=" O GLY A 433 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR A 435 " --> pdb=" O ALA A 328 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N GLU A 330 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 6.516A 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: 3.527A 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: 3.700A pdb=" N GLY A 649 " --> pdb=" O LEU A 786 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ALA A 646 " --> pdb=" O THR A 550 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ARG A 829 " --> pdb=" O ALA A 551 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU A 553 " --> pdb=" O ARG A 829 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N VAL A 831 " --> pdb=" O LEU A 553 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY A 555 " --> pdb=" O VAL A 831 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LEU A 858 " --> pdb=" O LEU A 830 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N GLY A 832 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.707A 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: 3.796A pdb=" N ALA A 717 " --> pdb=" O VAL A 725 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N SER A 727 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 5.511A 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: 5.821A pdb=" N GLY A1032 " --> pdb=" O GLU A1042 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU A1042 " --> pdb=" O GLY A1032 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 993 " --> pdb=" O VAL A1049 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LEU A1185 " --> pdb=" O SER A1154 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N VAL A1177 " --> pdb=" O LEU A1185 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA A1187 " --> pdb=" O ALA A1175 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ALA A1175 " --> pdb=" O ALA A1187 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL A1161 " --> pdb=" O VAL A1109 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A1097 " --> pdb=" O LEU A1108 " (cutoff:3.500A) removed outlier: 4.226A 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: 3.665A pdb=" N GLU A1676 " --> pdb=" O VAL A1214 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG A1422 " --> pdb=" O ARG A1425 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ARG A1418 " --> pdb=" O ALA A1429 " (cutoff:3.500A) removed outlier: 11.027A pdb=" N LEU A1431 " --> pdb=" O ALA A1416 " (cutoff:3.500A) removed outlier: 15.490A pdb=" N ALA A1416 " --> pdb=" O LEU A1431 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N CYS A1389 " --> pdb=" O GLY A1417 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU A1419 " --> pdb=" O CYS A1389 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLN A1391 " --> pdb=" O LEU A1419 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL A1421 " --> pdb=" O GLN A1391 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ASP A1393 " --> pdb=" O VAL A1421 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A1350 " --> pdb=" O ALA A1390 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A1392 " --> pdb=" O ILE A1350 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU A1352 " --> pdb=" O VAL A1392 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N LEU A1394 " --> pdb=" O LEU A1352 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER A1354 " --> pdb=" O LEU A1394 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N SER A1234 " --> pdb=" O ALA A1301 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N LEU A1303 " --> pdb=" O SER A1234 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A1236 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N VAL A1305 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N PHE A1238 " --> pdb=" O VAL A1305 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER A1239 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLY A1264 " --> pdb=" O SER A1239 " (cutoff:3.500A) removed outlier: 6.938A 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: 7.966A pdb=" N LEU A1453 " --> pdb=" O ARG A1531 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL A1533 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N ALA A1455 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A1535 " --> pdb=" O ALA A1455 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE A1582 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N LEU A1535 " --> pdb=" O PHE A1582 " (cutoff:3.500A) removed outlier: 6.567A 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: 8.828A pdb=" N VAL B 191 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL B 142 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 193 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA B 144 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 218 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N TYR B 143 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU B 220 " --> pdb=" O TYR B 143 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLY B 145 " --> pdb=" O LEU B 220 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLY B 222 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY B 40 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU B 270 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N VAL B 38 " --> pdb=" O GLU B 270 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA B 284 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 447 " --> pdb=" O ARG B 287 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 289 " --> pdb=" O HIS B 445 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N HIS B 445 " --> pdb=" O THR B 289 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ILE B 291 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 443 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS B 436 " --> pdb=" O GLY B 444 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA B 328 " --> pdb=" O GLY B 433 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N THR B 435 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N GLU B 330 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N LEU B 437 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 6.713A 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: 3.696A 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: 3.741A pdb=" N GLY B 649 " --> pdb=" O LEU B 786 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA B 646 " --> pdb=" O THR B 550 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ARG B 829 " --> pdb=" O ALA B 551 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU B 553 " --> pdb=" O ARG B 829 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL B 831 " --> pdb=" O LEU B 553 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLY B 555 " --> pdb=" O VAL B 831 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 858 " --> pdb=" O LEU B 830 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLY B 832 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 6.620A 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: 6.435A pdb=" N SER B 727 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N VAL B 715 " --> pdb=" O SER B 727 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 946 through 951 removed outlier: 5.785A pdb=" N GLY B1032 " --> pdb=" O GLU B1042 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1042 " --> pdb=" O GLY B1032 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU B1185 " --> pdb=" O SER B1154 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B1177 " --> pdb=" O LEU B1185 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA B1187 " --> pdb=" O ALA B1175 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ALA B1175 " --> pdb=" O ALA B1187 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG B1097 " --> pdb=" O LEU B1108 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL B1098 " --> pdb=" O LEU B1072 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA B1070 " --> pdb=" O LEU B1100 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 967 through 969 removed outlier: 3.730A 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: 5.680A pdb=" N ARG B1418 " --> pdb=" O ALA B1429 " (cutoff:3.500A) removed outlier: 10.976A pdb=" N LEU B1431 " --> pdb=" O ALA B1416 " (cutoff:3.500A) removed outlier: 15.326A pdb=" N ALA B1416 " --> pdb=" O LEU B1431 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N CYS B1389 " --> pdb=" O GLY B1417 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N LEU B1419 " --> pdb=" O CYS B1389 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLN B1391 " --> pdb=" O LEU B1419 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N VAL B1421 " --> pdb=" O GLN B1391 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP B1393 " --> pdb=" O VAL B1421 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE B1350 " --> pdb=" O ALA B1390 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N VAL B1392 " --> pdb=" O ILE B1350 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU B1352 " --> pdb=" O VAL B1392 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU B1394 " --> pdb=" O LEU B1352 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N SER B1354 " --> pdb=" O LEU B1394 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N SER B1234 " --> pdb=" O ALA B1301 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LEU B1303 " --> pdb=" O SER B1234 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B1236 " --> pdb=" O LEU B1303 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL B1305 " --> pdb=" O LEU B1236 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N PHE B1238 " --> pdb=" O VAL B1305 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER B1239 " --> pdb=" O LEU B1262 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY B1264 " --> pdb=" O SER B1239 " (cutoff:3.500A) removed outlier: 6.654A 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: 7.554A pdb=" N LEU B1453 " --> pdb=" O ARG B1531 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL B1533 " --> pdb=" O LEU B1453 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ALA B1455 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B1535 " --> pdb=" O ALA B1455 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE B1582 " --> pdb=" O VAL B1533 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N LEU B1535 " --> pdb=" O PHE B1582 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL B1584 " --> pdb=" O LEU B1535 " (cutoff:3.500A) 953 hydrogen bonds defined for protein. 2364 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: 24.76 Time building geometry restraints manager: 39.82 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: 4348 1.29 - 1.47: 8879 1.47 - 1.64: 11888 1.64 - 1.82: 68 Bond restraints: 49507 Sorted by residual: bond pdb=" N THR B1144 " pdb=" H THR B1144 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" N GLY A 319 " pdb=" H GLY A 319 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NH1 ARG A 867 " pdb="HH11 ARG A 867 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CD2 HIS A 881 " pdb=" HD2 HIS A 881 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N THR A1299 " pdb=" H THR A1299 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 ... (remaining 49502 not shown) Histogram of bond angle deviations from ideal: 95.74 - 103.66: 498 103.66 - 111.59: 52217 111.59 - 119.51: 20262 119.51 - 127.43: 16276 127.43 - 135.35: 363 Bond angle restraints: 89616 Sorted by residual: angle pdb=" CA ASP B 64 " pdb=" CB ASP B 64 " pdb=" CG ASP B 64 " ideal model delta sigma weight residual 112.60 118.85 -6.25 1.00e+00 1.00e+00 3.91e+01 angle pdb=" N PRO A 928 " pdb=" CA PRO A 928 " pdb=" C PRO A 928 " ideal model delta sigma weight residual 110.70 117.87 -7.17 1.22e+00 6.72e-01 3.46e+01 angle pdb=" CA PHE A 960 " pdb=" CB PHE A 960 " pdb=" CG PHE A 960 " ideal model delta sigma weight residual 113.80 119.40 -5.60 1.00e+00 1.00e+00 3.14e+01 angle pdb=" CB HIS A 930 " pdb=" CG HIS A 930 " pdb=" CD2 HIS A 930 " ideal model delta sigma weight residual 131.20 123.97 7.23 1.30e+00 5.92e-01 3.10e+01 angle pdb=" CA PHE B 947 " pdb=" CB PHE B 947 " pdb=" CG PHE B 947 " ideal model delta sigma weight residual 113.80 119.27 -5.47 1.00e+00 1.00e+00 2.99e+01 ... (remaining 89611 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 21242 18.00 - 35.99: 1233 35.99 - 53.99: 611 53.99 - 71.99: 198 71.99 - 89.98: 22 Dihedral angle restraints: 23306 sinusoidal: 12954 harmonic: 10352 Sorted by residual: dihedral pdb=" CA ARG A 545 " pdb=" C ARG A 545 " pdb=" N ALA A 546 " pdb=" CA ALA A 546 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA LEU B1413 " pdb=" C LEU B1413 " pdb=" N PRO B1414 " pdb=" CA PRO B1414 " ideal model delta harmonic sigma weight residual 180.00 151.00 29.00 0 5.00e+00 4.00e-02 3.36e+01 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 -151.05 -28.95 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 23303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 2504 0.087 - 0.175: 1125 0.175 - 0.262: 199 0.262 - 0.349: 30 0.349 - 0.436: 10 Chirality restraints: 3868 Sorted by residual: 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 4.76e+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 2.01 0.43 2.00e-01 2.50e+01 4.71e+00 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 2.09 0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 3865 not shown) Planarity restraints: 7781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 75 " -0.194 2.00e-02 2.50e+03 8.05e-02 2.59e+02 pdb=" CG TRP B 75 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TRP B 75 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP B 75 " 0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP B 75 " 0.076 2.00e-02 2.50e+03 pdb=" CE2 TRP B 75 " 0.039 2.00e-02 2.50e+03 pdb=" CE3 TRP B 75 " 0.080 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 75 " -0.024 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 75 " 0.029 2.00e-02 2.50e+03 pdb=" CH2 TRP B 75 " -0.044 2.00e-02 2.50e+03 pdb=" HD1 TRP B 75 " -0.052 2.00e-02 2.50e+03 pdb=" HE1 TRP B 75 " 0.112 2.00e-02 2.50e+03 pdb=" HE3 TRP B 75 " 0.099 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 75 " -0.076 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 75 " 0.021 2.00e-02 2.50e+03 pdb=" HH2 TRP B 75 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1337 " -0.282 9.50e-02 1.11e+02 1.41e-01 2.57e+02 pdb=" NE ARG B1337 " -0.116 2.00e-02 2.50e+03 pdb=" CZ ARG B1337 " -0.063 2.00e-02 2.50e+03 pdb=" NH1 ARG B1337 " -0.034 2.00e-02 2.50e+03 pdb=" NH2 ARG B1337 " -0.025 2.00e-02 2.50e+03 pdb="HH11 ARG B1337 " 0.184 2.00e-02 2.50e+03 pdb="HH12 ARG B1337 " -0.047 2.00e-02 2.50e+03 pdb="HH21 ARG B1337 " 0.193 2.00e-02 2.50e+03 pdb="HH22 ARG B1337 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1337 " 0.279 9.50e-02 1.11e+02 1.38e-01 2.39e+02 pdb=" NE ARG A1337 " 0.089 2.00e-02 2.50e+03 pdb=" CZ ARG A1337 " 0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG A1337 " 0.063 2.00e-02 2.50e+03 pdb=" NH2 ARG A1337 " 0.053 2.00e-02 2.50e+03 pdb="HH11 ARG A1337 " -0.191 2.00e-02 2.50e+03 pdb="HH12 ARG A1337 " 0.039 2.00e-02 2.50e+03 pdb="HH21 ARG A1337 " -0.180 2.00e-02 2.50e+03 pdb="HH22 ARG A1337 " 0.040 2.00e-02 2.50e+03 ... (remaining 7778 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.19: 3691 2.19 - 2.79: 86532 2.79 - 3.40: 135694 3.40 - 4.00: 178622 4.00 - 4.60: 262007 Nonbonded interactions: 666546 Sorted by model distance: nonbonded pdb=" HG SER B 665 " pdb=" OD2 ASP B 668 " model vdw 1.591 1.850 nonbonded pdb=" HG SER B1591 " pdb=" OD2 ASP B1605 " model vdw 1.592 1.850 nonbonded pdb=" OD1 ASP B 408 " pdb=" HG SER B 410 " model vdw 1.598 1.850 nonbonded pdb=" HG SER A1591 " pdb=" OD2 ASP A1605 " model vdw 1.608 1.850 nonbonded pdb=" OE1 GLU B 654 " pdb=" HG SER B 787 " model vdw 1.611 1.850 ... (remaining 666541 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 33 through 1719) 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: 4.300 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: 0.530 Extract box with map and model: 14.220 Check model and map are aligned: 0.720 Set scattering table: 0.440 Process input model: 156.380 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 181.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 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 0.046 25159 Z= 0.838 Angle : 1.806 8.674 34354 Z= 1.217 Chirality : 0.096 0.436 3868 Planarity : 0.016 0.171 4653 Dihedral : 12.609 89.982 9052 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 0.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.80 % Favored : 96.17 % Rotamer: Outliers : 0.74 % Allowed : 2.73 % Favored : 96.53 % Cbeta Deviations : 0.27 % 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: -0.79 (0.13), residues: 3370 helix: -0.89 (0.13), residues: 1214 sheet: 1.02 (0.24), residues: 446 loop : -0.57 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.020 TRP A1099 HIS 0.018 0.003 HIS A1461 PHE 0.085 0.013 PHE A 778 TYR 0.133 0.022 TYR B1651 ARG 0.014 0.001 ARG B 115 *********************** 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 502 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 484 time to evaluate : 3.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TRP cc_start: 0.8641 (t-100) cc_final: 0.8221 (t-100) REVERT: A 704 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7842 (tt) REVERT: A 873 LEU cc_start: 0.8682 (tp) cc_final: 0.8472 (tp) REVERT: A 1103 ASP cc_start: 0.8043 (p0) cc_final: 0.7809 (p0) REVERT: A 1459 THR cc_start: 0.8561 (p) cc_final: 0.8290 (t) REVERT: B 330 GLU cc_start: 0.8882 (tp30) cc_final: 0.8673 (tm-30) REVERT: B 595 HIS cc_start: 0.7478 (m90) cc_final: 0.7136 (m-70) REVERT: B 789 VAL cc_start: 0.9000 (t) cc_final: 0.8797 (p) REVERT: B 1029 PHE cc_start: 0.6765 (m-80) cc_final: 0.6515 (m-10) REVERT: B 1605 ASP cc_start: 0.7223 (m-30) cc_final: 0.6957 (m-30) REVERT: B 1639 GLU cc_start: 0.0792 (tt0) cc_final: -0.0549 (tt0) outliers start: 18 outliers final: 5 residues processed: 499 average time/residue: 1.1677 time to fit residues: 829.9213 Evaluate side-chains 202 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 196 time to evaluate : 3.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 1637 SER Chi-restraints excluded: chain B residue 1146 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 1.9990 chunk 254 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 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: 0.9980 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN A 183 GLN A 374 GLN A 482 GLN A 963 GLN A1189 GLN ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS ** B 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1409 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 25159 Z= 0.282 Angle : 0.681 7.986 34354 Z= 0.364 Chirality : 0.043 0.166 3868 Planarity : 0.007 0.062 4653 Dihedral : 6.436 76.326 3720 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.34 % Favored : 97.63 % Rotamer: Outliers : 1.61 % Allowed : 7.52 % Favored : 90.87 % 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: -0.55 (0.14), residues: 3370 helix: -0.30 (0.14), residues: 1238 sheet: 0.57 (0.22), residues: 524 loop : -0.63 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 423 HIS 0.008 0.002 HIS A 634 PHE 0.013 0.002 PHE A 95 TYR 0.020 0.002 TYR A 151 ARG 0.006 0.001 ARG B 605 *********************** 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 237 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 198 time to evaluate : 3.724 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: A 274 ASP cc_start: 0.8033 (m-30) cc_final: 0.7727 (t70) REVERT: A 330 GLU cc_start: 0.8443 (tp30) cc_final: 0.8139 (tm-30) REVERT: A 704 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7782 (tt) REVERT: A 1459 THR cc_start: 0.8608 (p) cc_final: 0.8239 (t) REVERT: B 1605 ASP cc_start: 0.7228 (m-30) cc_final: 0.6932 (m-30) REVERT: B 1639 GLU cc_start: 0.0424 (tt0) cc_final: 0.0008 (tt0) REVERT: B 1717 ASN cc_start: 0.2076 (p0) cc_final: 0.1617 (m110) outliers start: 39 outliers final: 26 residues processed: 225 average time/residue: 0.9229 time to fit residues: 316.5127 Evaluate side-chains 175 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 4.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1134 LEU Chi-restraints excluded: chain A residue 1161 VAL Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1404 VAL Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain B residue 399 HIS Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 794 VAL Chi-restraints excluded: chain B residue 940 VAL Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1300 VAL Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1635 ASP 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: 2.9990 chunk 253 optimal weight: 3.9990 chunk 207 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 272 optimal weight: 2.9990 chunk 303 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 245 optimal weight: 8.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25159 Z= 0.264 Angle : 0.595 6.255 34354 Z= 0.311 Chirality : 0.042 0.148 3868 Planarity : 0.005 0.064 4653 Dihedral : 5.699 78.936 3716 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 1.40 % Allowed : 8.35 % Favored : 90.25 % 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: -0.51 (0.14), residues: 3370 helix: -0.10 (0.14), residues: 1244 sheet: 0.28 (0.21), residues: 584 loop : -0.66 (0.16), residues: 1542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1684 HIS 0.018 0.001 HIS B 399 PHE 0.016 0.002 PHE A1582 TYR 0.016 0.002 TYR A 151 ARG 0.006 0.001 ARG A1693 *********************** 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 188 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 3.632 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: A 330 GLU cc_start: 0.8429 (tp30) cc_final: 0.8205 (tm-30) REVERT: A 704 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7820 (tt) REVERT: A 1459 THR cc_start: 0.8558 (p) cc_final: 0.8258 (t) REVERT: A 1545 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7378 (tt) REVERT: B 1605 ASP cc_start: 0.7169 (m-30) cc_final: 0.6796 (m-30) REVERT: B 1639 GLU cc_start: 0.0415 (tt0) cc_final: 0.0024 (tt0) REVERT: B 1717 ASN cc_start: 0.2425 (p0) cc_final: 0.1793 (m110) outliers start: 34 outliers final: 25 residues processed: 182 average time/residue: 0.9967 time to fit residues: 277.4435 Evaluate side-chains 156 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 4.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASP Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1286 VAL Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 719 ASP Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1635 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 2.9990 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 145 optimal weight: 9.9990 chunk 205 optimal weight: 0.9980 chunk 306 optimal weight: 2.9990 chunk 324 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 290 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 962 GLN A1167 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 374 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25159 Z= 0.246 Angle : 0.552 6.184 34354 Z= 0.283 Chirality : 0.041 0.151 3868 Planarity : 0.005 0.055 4653 Dihedral : 5.284 76.821 3714 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.09 % Favored : 96.88 % Rotamer: Outliers : 1.45 % Allowed : 8.72 % Favored : 89.83 % 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: -0.51 (0.14), residues: 3370 helix: 0.06 (0.15), residues: 1250 sheet: 0.21 (0.21), residues: 568 loop : -0.78 (0.15), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1099 HIS 0.008 0.001 HIS A1692 PHE 0.014 0.001 PHE A 95 TYR 0.012 0.002 TYR A 151 ARG 0.006 0.001 ARG B 741 *********************** 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 169 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 134 time to evaluate : 3.660 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 330 GLU cc_start: 0.8465 (tp30) cc_final: 0.7821 (tm-30) REVERT: A 704 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7802 (tt) REVERT: A 1459 THR cc_start: 0.8622 (p) cc_final: 0.8279 (t) REVERT: A 1545 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7379 (tt) REVERT: B 1018 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: B 1605 ASP cc_start: 0.7148 (m-30) cc_final: 0.6814 (m-30) REVERT: B 1639 GLU cc_start: 0.0322 (tt0) cc_final: 0.0061 (tt0) REVERT: B 1717 ASN cc_start: 0.2822 (p0) cc_final: 0.2059 (m110) outliers start: 35 outliers final: 22 residues processed: 160 average time/residue: 0.9101 time to fit residues: 225.8067 Evaluate side-chains 141 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 4.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 1018 GLU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1635 ASP Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.0030 chunk 184 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 241 optimal weight: 7.9990 chunk 134 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 224 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 291 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.9196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25159 Z= 0.158 Angle : 0.509 6.017 34354 Z= 0.256 Chirality : 0.040 0.150 3868 Planarity : 0.005 0.055 4653 Dihedral : 4.968 69.413 3714 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.70 % Favored : 97.27 % Rotamer: Outliers : 1.49 % Allowed : 8.97 % Favored : 89.55 % 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: -0.29 (0.14), residues: 3370 helix: 0.28 (0.15), residues: 1248 sheet: 0.24 (0.21), residues: 570 loop : -0.65 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B1468 HIS 0.006 0.001 HIS A1692 PHE 0.010 0.001 PHE A 95 TYR 0.012 0.001 TYR A 965 ARG 0.010 0.000 ARG B 359 *********************** 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 162 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 126 time to evaluate : 3.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8178 (mtt) cc_final: 0.7972 (mtt) REVERT: A 330 GLU cc_start: 0.8440 (tp30) cc_final: 0.7825 (tm-30) REVERT: A 704 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7731 (tt) REVERT: A 980 LEU cc_start: 0.8018 (tt) cc_final: 0.7733 (mt) REVERT: A 1167 HIS cc_start: 0.7537 (OUTLIER) cc_final: 0.7297 (m-70) REVERT: A 1459 THR cc_start: 0.8570 (p) cc_final: 0.8221 (t) REVERT: B 294 ASP cc_start: 0.7970 (p0) cc_final: 0.7704 (p0) REVERT: B 1323 ASP cc_start: 0.7459 (OUTLIER) cc_final: 0.7172 (t0) REVERT: B 1501 GLU cc_start: 0.4810 (mt-10) cc_final: 0.4225 (mt-10) REVERT: B 1605 ASP cc_start: 0.6996 (m-30) cc_final: 0.6702 (m-30) REVERT: B 1639 GLU cc_start: 0.0221 (tt0) cc_final: -0.0062 (tt0) REVERT: B 1717 ASN cc_start: 0.2925 (p0) cc_final: 0.2238 (m-40) outliers start: 36 outliers final: 24 residues processed: 154 average time/residue: 0.8373 time to fit residues: 206.2293 Evaluate side-chains 146 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1146 VAL Chi-restraints excluded: chain A residue 1167 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 5.9990 chunk 292 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 190 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 881 HIS ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1370 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.4869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25159 Z= 0.371 Angle : 0.596 6.883 34354 Z= 0.310 Chirality : 0.043 0.156 3868 Planarity : 0.006 0.055 4653 Dihedral : 5.292 74.385 3714 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.90 % Allowed : 9.09 % Favored : 89.01 % 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: -0.73 (0.14), residues: 3370 helix: 0.01 (0.15), residues: 1246 sheet: -0.15 (0.21), residues: 566 loop : -0.93 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1124 HIS 0.006 0.001 HIS A1692 PHE 0.019 0.002 PHE A 95 TYR 0.016 0.002 TYR B1706 ARG 0.006 0.001 ARG A 287 *********************** 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 167 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 121 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.8435 (tp30) cc_final: 0.8004 (tm-30) REVERT: A 704 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7831 (tt) REVERT: A 1167 HIS cc_start: 0.7551 (OUTLIER) cc_final: 0.7330 (m-70) REVERT: A 1251 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7661 (tp30) REVERT: B 294 ASP cc_start: 0.8099 (p0) cc_final: 0.7806 (p0) REVERT: B 604 VAL cc_start: 0.8148 (p) cc_final: 0.7857 (t) REVERT: B 1323 ASP cc_start: 0.7415 (OUTLIER) cc_final: 0.7046 (t0) outliers start: 46 outliers final: 32 residues processed: 158 average time/residue: 0.8187 time to fit residues: 207.7753 Evaluate side-chains 149 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1167 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1174 ASP Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1278 VAL Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1635 ASP Chi-restraints excluded: chain B residue 1705 SER Chi-restraints excluded: chain B residue 1719 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 9.9990 chunk 36 optimal weight: 5.9990 chunk 185 optimal weight: 0.9980 chunk 237 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 181 optimal weight: 0.9980 chunk 323 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25159 Z= 0.223 Angle : 0.529 6.346 34354 Z= 0.269 Chirality : 0.041 0.149 3868 Planarity : 0.005 0.051 4653 Dihedral : 5.059 68.597 3714 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 1.40 % Allowed : 10.00 % Favored : 88.60 % 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: -0.57 (0.14), residues: 3370 helix: 0.18 (0.15), residues: 1246 sheet: -0.13 (0.21), residues: 568 loop : -0.85 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 914 HIS 0.005 0.001 HIS A1692 PHE 0.012 0.001 PHE A 95 TYR 0.011 0.001 TYR A 151 ARG 0.005 0.000 ARG B 359 *********************** 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 149 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 3.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 227 MET cc_start: 0.8218 (mtt) cc_final: 0.8018 (mtt) REVERT: A 330 GLU cc_start: 0.8450 (tp30) cc_final: 0.7963 (tm-30) REVERT: A 704 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7785 (tt) REVERT: A 1167 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.7241 (m-70) REVERT: A 1251 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7671 (tp30) REVERT: B 294 ASP cc_start: 0.8051 (p0) cc_final: 0.7801 (p0) REVERT: B 424 ARG cc_start: 0.7657 (tpp-160) cc_final: 0.7308 (mtp85) REVERT: B 604 VAL cc_start: 0.8116 (p) cc_final: 0.7833 (t) REVERT: B 1323 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7103 (t0) outliers start: 34 outliers final: 28 residues processed: 141 average time/residue: 0.8568 time to fit residues: 189.8983 Evaluate side-chains 143 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 3.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 382 ILE Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1167 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Chi-restraints excluded: chain B residue 1719 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.7980 chunk 129 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 220 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 GLN B1391 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 25159 Z= 0.359 Angle : 0.584 6.755 34354 Z= 0.302 Chirality : 0.042 0.157 3868 Planarity : 0.006 0.054 4653 Dihedral : 5.276 68.099 3714 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer: Outliers : 1.69 % Allowed : 10.25 % Favored : 88.06 % 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: -0.86 (0.14), residues: 3370 helix: 0.05 (0.15), residues: 1234 sheet: -0.45 (0.20), residues: 578 loop : -1.05 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1124 HIS 0.005 0.001 HIS B 372 PHE 0.017 0.002 PHE A 95 TYR 0.016 0.002 TYR B1706 ARG 0.007 0.001 ARG A 287 *********************** 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 157 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 116 time to evaluate : 3.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 330 GLU cc_start: 0.8452 (tp30) cc_final: 0.8074 (tm-30) REVERT: A 704 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 1167 HIS cc_start: 0.7470 (OUTLIER) cc_final: 0.7231 (m-70) REVERT: A 1251 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7753 (tp30) REVERT: B 294 ASP cc_start: 0.8150 (p0) cc_final: 0.7932 (p0) REVERT: B 604 VAL cc_start: 0.8178 (p) cc_final: 0.7882 (t) REVERT: B 1323 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.6933 (t0) outliers start: 41 outliers final: 31 residues processed: 148 average time/residue: 0.8271 time to fit residues: 195.5094 Evaluate side-chains 146 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 859 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1167 HIS Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain A residue 1663 LEU Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 699 GLU Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1174 ASP Chi-restraints excluded: chain B residue 1196 MET Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1278 VAL Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1510 LEU Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1577 THR Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1635 ASP Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 4.9990 chunk 310 optimal weight: 7.9990 chunk 283 optimal weight: 4.9990 chunk 301 optimal weight: 0.0980 chunk 181 optimal weight: 2.9990 chunk 131 optimal weight: 0.3980 chunk 236 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 272 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25159 Z= 0.187 Angle : 0.513 6.269 34354 Z= 0.259 Chirality : 0.040 0.149 3868 Planarity : 0.005 0.051 4653 Dihedral : 4.904 56.793 3714 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 1.36 % Allowed : 10.62 % Favored : 88.02 % 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: -0.57 (0.14), residues: 3370 helix: 0.32 (0.15), residues: 1234 sheet: -0.30 (0.20), residues: 578 loop : -0.89 (0.15), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B1082 HIS 0.004 0.001 HIS B1497 PHE 0.010 0.001 PHE A1339 TYR 0.010 0.001 TYR A 151 ARG 0.006 0.000 ARG B 359 *********************** 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 154 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 4.308 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 227 MET cc_start: 0.8145 (mtt) cc_final: 0.7942 (mtt) REVERT: A 330 GLU cc_start: 0.8456 (tp30) cc_final: 0.8009 (tm-30) REVERT: A 704 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7769 (tt) REVERT: A 980 LEU cc_start: 0.8102 (tt) cc_final: 0.7724 (mt) REVERT: A 1251 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7731 (tp30) REVERT: B 604 VAL cc_start: 0.8145 (p) cc_final: 0.7853 (t) REVERT: B 1323 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7088 (t0) outliers start: 33 outliers final: 23 residues processed: 146 average time/residue: 0.9284 time to fit residues: 212.1770 Evaluate side-chains 139 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 3.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 8.9990 chunk 319 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 221 optimal weight: 9.9990 chunk 334 optimal weight: 0.7980 chunk 308 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25159 Z= 0.236 Angle : 0.524 6.292 34354 Z= 0.265 Chirality : 0.041 0.145 3868 Planarity : 0.005 0.051 4653 Dihedral : 4.717 56.831 3714 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 1.20 % Allowed : 10.91 % Favored : 87.89 % 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: -0.60 (0.14), residues: 3370 helix: 0.33 (0.15), residues: 1236 sheet: -0.36 (0.20), residues: 578 loop : -0.93 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1124 HIS 0.004 0.001 HIS A1367 PHE 0.011 0.001 PHE A 95 TYR 0.011 0.001 TYR A 151 ARG 0.009 0.000 ARG A1097 ********************** 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 143 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 114 time to evaluate : 3.793 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 227 MET cc_start: 0.8120 (mtt) cc_final: 0.7917 (mtt) REVERT: A 330 GLU cc_start: 0.8453 (tp30) cc_final: 0.7998 (tm-30) REVERT: A 704 LEU cc_start: 0.8184 (OUTLIER) cc_final: 0.7744 (tt) REVERT: A 1251 GLU cc_start: 0.8228 (mt-10) cc_final: 0.7736 (tp30) REVERT: B 604 VAL cc_start: 0.8149 (p) cc_final: 0.7853 (t) REVERT: B 1323 ASP cc_start: 0.7396 (OUTLIER) cc_final: 0.7019 (t0) outliers start: 29 outliers final: 24 residues processed: 139 average time/residue: 0.9090 time to fit residues: 198.6027 Evaluate side-chains 136 residues out of total 2420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 110 time to evaluate : 3.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 887 ILE Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1322 LEU Chi-restraints excluded: chain A residue 1501 GLU Chi-restraints excluded: chain A residue 1545 LEU Chi-restraints excluded: chain A residue 1580 THR Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1602 SER Chi-restraints excluded: chain B residue 365 SER Chi-restraints excluded: chain B residue 467 VAL Chi-restraints excluded: chain B residue 550 THR Chi-restraints excluded: chain B residue 761 ASP Chi-restraints excluded: chain B residue 835 LEU Chi-restraints excluded: chain B residue 947 PHE Chi-restraints excluded: chain B residue 1249 CYS Chi-restraints excluded: chain B residue 1278 VAL Chi-restraints excluded: chain B residue 1323 ASP Chi-restraints excluded: chain B residue 1505 HIS Chi-restraints excluded: chain B residue 1561 LEU Chi-restraints excluded: chain B residue 1609 THR Chi-restraints excluded: chain B residue 1692 HIS Chi-restraints excluded: chain B residue 1705 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 2.9990 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 245 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 266 optimal weight: 2.9990 chunk 111 optimal weight: 0.9980 chunk 274 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.093503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.074999 restraints weight = 198633.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.075711 restraints weight = 119858.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.076629 restraints weight = 97612.945| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.5525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 25159 Z= 0.325 Angle : 0.565 6.547 34354 Z= 0.289 Chirality : 0.042 0.152 3868 Planarity : 0.005 0.052 4653 Dihedral : 4.773 56.762 3714 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.70 % Favored : 94.27 % Rotamer: Outliers : 1.12 % Allowed : 10.95 % Favored : 87.93 % 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: -0.79 (0.14), residues: 3370 helix: 0.18 (0.15), residues: 1234 sheet: -0.52 (0.20), residues: 588 loop : -1.02 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B1124 HIS 0.005 0.001 HIS A 634 PHE 0.014 0.002 PHE A 95 TYR 0.014 0.002 TYR B1706 ARG 0.007 0.001 ARG A1097 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7718.37 seconds wall clock time: 137 minutes 18.39 seconds (8238.39 seconds total)