Starting phenix.real_space_refine on Mon Apr 15 10:01:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqe_41503/04_2024/8tqe_41503.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqe_41503/04_2024/8tqe_41503.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqe_41503/04_2024/8tqe_41503.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqe_41503/04_2024/8tqe_41503.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqe_41503/04_2024/8tqe_41503.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tqe_41503/04_2024/8tqe_41503.pdb" } resolution = 3.1 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= 0.007 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: 4 Type Number sf(0) Gaussians S 365 5.16 5 C 63125 2.51 5 N 17075 2.21 5 O 19470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 52": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 256": "OE1" <-> "OE2" Residue "A ASP 260": "OD1" <-> "OD2" Residue "A GLU 269": "OE1" <-> "OE2" Residue "A TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 306": "OD1" <-> "OD2" Residue "A ASP 406": "OD1" <-> "OD2" Residue "A TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 658": "OE1" <-> "OE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 690": "OD1" <-> "OD2" Residue "A PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 878": "OD1" <-> "OD2" Residue "A GLU 988": "OE1" <-> "OE2" Residue "A GLU 1074": "OE1" <-> "OE2" Residue "A PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1185": "OE1" <-> "OE2" Residue "A PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1216": "OE1" <-> "OE2" Residue "A GLU 1226": "OE1" <-> "OE2" Residue "A GLU 1277": "OE1" <-> "OE2" Residue "A TYR 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1504": "OD1" <-> "OD2" Residue "A GLU 1572": "OE1" <-> "OE2" Residue "A PHE 1602": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1645": "OE1" <-> "OE2" Residue "A PHE 1659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1715": "OE1" <-> "OE2" Residue "A GLU 1747": "OE1" <-> "OE2" Residue "A ASP 1908": "OD1" <-> "OD2" Residue "A ASP 1926": "OD1" <-> "OD2" Residue "A GLU 2055": "OE1" <-> "OE2" Residue "A ASP 2079": "OD1" <-> "OD2" Residue "A ASP 2150": "OD1" <-> "OD2" Residue "A PHE 2176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2256": "OE1" <-> "OE2" Residue "A PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2309": "OE1" <-> "OE2" Residue "A GLU 2361": "OE1" <-> "OE2" Residue "A PHE 2423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2428": "OE1" <-> "OE2" Residue "A PHE 2488": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2513": "OD1" <-> "OD2" Residue "B ASP 39": "OD1" <-> "OD2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 269": "OE1" <-> "OE2" Residue "B GLU 289": "OE1" <-> "OE2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B ASP 338": "OD1" <-> "OD2" Residue "B ASP 339": "OD1" <-> "OD2" Residue "B PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 368": "OE1" <-> "OE2" Residue "B GLU 437": "OE1" <-> "OE2" Residue "B TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 516": "OD1" <-> "OD2" Residue "B ASP 517": "OD1" <-> "OD2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "B PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "B GLU 675": "OE1" <-> "OE2" Residue "B ASP 690": "OD1" <-> "OD2" Residue "B ASP 839": "OD1" <-> "OD2" Residue "B TYR 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 940": "OE1" <-> "OE2" Residue "B ASP 1071": "OD1" <-> "OD2" Residue "B GLU 1074": "OE1" <-> "OE2" Residue "B GLU 1119": "OE1" <-> "OE2" Residue "B GLU 1174": "OE1" <-> "OE2" Residue "B ASP 1210": "OD1" <-> "OD2" Residue "B ASP 1384": "OD1" <-> "OD2" Residue "B TYR 1402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1504": "OD1" <-> "OD2" Residue "B ASP 1506": "OD1" <-> "OD2" Residue "B PHE 1541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1552": "OE1" <-> "OE2" Residue "B ASP 1568": "OD1" <-> "OD2" Residue "B ASP 1577": "OD1" <-> "OD2" Residue "B ASP 1639": "OD1" <-> "OD2" Residue "B ASP 1674": "OD1" <-> "OD2" Residue "B TYR 1695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1710": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1721": "OE1" <-> "OE2" Residue "B GLU 1747": "OE1" <-> "OE2" Residue "B GLU 1927": "OE1" <-> "OE2" Residue "B GLU 2055": "OE1" <-> "OE2" Residue "B GLU 2118": "OE1" <-> "OE2" Residue "B ASP 2208": "OD1" <-> "OD2" Residue "B GLU 2222": "OE1" <-> "OE2" Residue "B ASP 2231": "OD1" <-> "OD2" Residue "B GLU 2256": "OE1" <-> "OE2" Residue "B PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2309": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C GLU 84": "OE1" <-> "OE2" Residue "C ASP 93": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C GLU 256": "OE1" <-> "OE2" Residue "C ASP 260": "OD1" <-> "OD2" Residue "C GLU 269": "OE1" <-> "OE2" Residue "C PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 304": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 339": "OD1" <-> "OD2" Residue "C ASP 341": "OD1" <-> "OD2" Residue "C PHE 363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 518": "OD1" <-> "OD2" Residue "C PHE 537": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 547": "OD1" <-> "OD2" Residue "C GLU 570": "OE1" <-> "OE2" Residue "C ASP 582": "OD1" <-> "OD2" Residue "C TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 652": "OE1" <-> "OE2" Residue "C GLU 658": "OE1" <-> "OE2" Residue "C PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 675": "OE1" <-> "OE2" Residue "C PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 778": "OE1" <-> "OE2" Residue "C TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1071": "OD1" <-> "OD2" Residue "C GLU 1074": "OE1" <-> "OE2" Residue "C ASP 1075": "OD1" <-> "OD2" Residue "C PHE 1084": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1142": "OE1" <-> "OE2" Residue "C GLU 1164": "OE1" <-> "OE2" Residue "C GLU 1185": "OE1" <-> "OE2" Residue "C TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1407": "OD1" <-> "OD2" Residue "C GLU 1444": "OE1" <-> "OE2" Residue "C PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1572": "OE1" <-> "OE2" Residue "C PHE 1659": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1674": "OD1" <-> "OD2" Residue "C GLU 1715": "OE1" <-> "OE2" Residue "C GLU 1739": "OE1" <-> "OE2" Residue "C GLU 1747": "OE1" <-> "OE2" Residue "C ASP 1908": "OD1" <-> "OD2" Residue "C ASP 1926": "OD1" <-> "OD2" Residue "C GLU 1927": "OE1" <-> "OE2" Residue "C GLU 2093": "OE1" <-> "OE2" Residue "C GLU 2128": "OE1" <-> "OE2" Residue "C ASP 2208": "OD1" <-> "OD2" Residue "C ASP 2231": "OD1" <-> "OD2" Residue "C GLU 2249": "OE1" <-> "OE2" Residue "C GLU 2256": "OE1" <-> "OE2" Residue "C TYR 2257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2357": "OE1" <-> "OE2" Residue "C GLU 2361": "OE1" <-> "OE2" Residue "C PHE 2423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2428": "OE1" <-> "OE2" Residue "C GLU 2451": "OE1" <-> "OE2" Residue "C PHE 2511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2523": "OE1" <-> "OE2" Residue "D ASP 182": "OD1" <-> "OD2" Residue "D GLU 256": "OE1" <-> "OE2" Residue "D GLU 269": "OE1" <-> "OE2" Residue "D TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 338": "OD1" <-> "OD2" Residue "D ASP 341": "OD1" <-> "OD2" Residue "D TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 518": "OD1" <-> "OD2" Residue "D ASP 582": "OD1" <-> "OD2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D PHE 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 811": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 878": "OD1" <-> "OD2" Residue "D ASP 913": "OD1" <-> "OD2" Residue "D TYR 937": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1071": "OD1" <-> "OD2" Residue "D GLU 1074": "OE1" <-> "OE2" Residue "D PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1224": "OD1" <-> "OD2" Residue "D PHE 1273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1277": "OE1" <-> "OE2" Residue "D ASP 1348": "OD1" <-> "OD2" Residue "D TYR 1389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1453": "OE1" <-> "OE2" Residue "D ASP 1674": "OD1" <-> "OD2" Residue "D GLU 1747": "OE1" <-> "OE2" Residue "D GLU 1844": "OE1" <-> "OE2" Residue "D GLU 1904": "OE1" <-> "OE2" Residue "D ASP 1926": "OD1" <-> "OD2" Residue "D ASP 2008": "OD1" <-> "OD2" Residue "D GLU 2082": "OE1" <-> "OE2" Residue "D GLU 2093": "OE1" <-> "OE2" Residue "D GLU 2128": "OE1" <-> "OE2" Residue "D ASP 2150": "OD1" <-> "OD2" Residue "D PHE 2176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 2257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 2296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 2309": "OE1" <-> "OE2" Residue "D GLU 2361": "OE1" <-> "OE2" Residue "D ASP 2452": "OD1" <-> "OD2" Residue "D PHE 2511": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 182": "OD1" <-> "OD2" Residue "E ASP 196": "OD1" <-> "OD2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ASP 260": "OD1" <-> "OD2" Residue "E GLU 269": "OE1" <-> "OE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 306": "OD1" <-> "OD2" Residue "E TYR 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 406": "OD1" <-> "OD2" Residue "E TYR 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 518": "OD1" <-> "OD2" Residue "E GLU 538": "OE1" <-> "OE2" Residue "E ASP 582": "OD1" <-> "OD2" Residue "E GLU 635": "OE1" <-> "OE2" Residue "E GLU 654": "OE1" <-> "OE2" Residue "E ASP 690": "OD1" <-> "OD2" Residue "E ASP 718": "OD1" <-> "OD2" Residue "E ASP 913": "OD1" <-> "OD2" Residue "E ASP 1071": "OD1" <-> "OD2" Residue "E PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1119": "OE1" <-> "OE2" Residue "E TYR 1120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1277": "OE1" <-> "OE2" Residue "E ASP 1364": "OD1" <-> "OD2" Residue "E ASP 1384": "OD1" <-> "OD2" Residue "E PHE 1452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1491": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 1639": "OD1" <-> "OD2" Residue "E GLU 1645": "OE1" <-> "OE2" Residue "E PHE 1678": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1734": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1747": "OE1" <-> "OE2" Residue "E GLU 1904": "OE1" <-> "OE2" Residue "E GLU 2128": "OE1" <-> "OE2" Residue "E GLU 2222": "OE1" <-> "OE2" Residue "E GLU 2256": "OE1" <-> "OE2" Residue "E GLU 2309": "OE1" <-> "OE2" Residue "E GLU 2354": "OE1" <-> "OE2" Residue "E PHE 2380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 2384": "OE1" <-> "OE2" Residue "E PHE 2423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 2513": "OD1" <-> "OD2" Time to flip residues: 0.22s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 100035 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 20007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2537, 20007 Classifications: {'peptide': 2537} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 4, 'PTRANS': 77, 'TRANS': 2451} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 20007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2537, 20007 Classifications: {'peptide': 2537} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 4, 'PTRANS': 77, 'TRANS': 2451} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 20007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2537, 20007 Classifications: {'peptide': 2537} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 4, 'PTRANS': 77, 'TRANS': 2451} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 20007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2537, 20007 Classifications: {'peptide': 2537} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'CIS': 5, 'PCIS': 4, 'PTRANS': 77, 'TRANS': 2450} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 20007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2537, 20007 Classifications: {'peptide': 2537} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'CIS': 4, 'PCIS': 4, 'PTRANS': 77, 'TRANS': 2451} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 37.79, per 1000 atoms: 0.38 Number of scatterers: 100035 At special positions: 0 Unit cell: (190.2, 190.2, 262.476, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 365 16.00 O 19470 8.00 N 17075 7.00 C 63125 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 29.12 Conformation dependent library (CDL) restraints added in 13.4 seconds 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23810 Finding SS restraints... Secondary structure from input PDB file: 466 helices and 103 sheets defined 48.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 12.93 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 42 through 72 removed outlier: 3.591A pdb=" N ARG A 70 " --> pdb=" O ARG A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 Processing helix chain 'A' and resid 78 through 83 removed outlier: 3.724A pdb=" N LEU A 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 97 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 161 through 178 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 272 through 277 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.710A pdb=" N TYR A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 459 Processing helix chain 'A' and resid 461 through 471 Processing helix chain 'A' and resid 479 through 497 Processing helix chain 'A' and resid 499 through 507 Processing helix chain 'A' and resid 521 through 528 Processing helix chain 'A' and resid 554 through 565 Processing helix chain 'A' and resid 567 through 579 Processing helix chain 'A' and resid 590 through 607 removed outlier: 3.775A pdb=" N HIS A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 621 Processing helix chain 'A' and resid 627 through 631 Processing helix chain 'A' and resid 634 through 654 removed outlier: 3.885A pdb=" N ARG A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 665 Processing helix chain 'A' and resid 673 through 684 Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 696 through 713 Proline residue: A 706 - end of helix Processing helix chain 'A' and resid 716 through 731 Processing helix chain 'A' and resid 736 through 745 Processing helix chain 'A' and resid 752 through 775 removed outlier: 4.195A pdb=" N GLN A 756 " --> pdb=" O ASN A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 788 Processing helix chain 'A' and resid 803 through 821 removed outlier: 3.926A pdb=" N GLY A 821 " --> pdb=" O ILE A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 833 Processing helix chain 'A' and resid 837 through 846 Processing helix chain 'A' and resid 848 through 860 Processing helix chain 'A' and resid 866 through 883 Processing helix chain 'A' and resid 886 through 895 Processing helix chain 'A' and resid 911 through 924 Processing helix chain 'A' and resid 927 through 954 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 984 through 1002 Processing helix chain 'A' and resid 1011 through 1014 Processing helix chain 'A' and resid 1015 through 1020 Processing helix chain 'A' and resid 1020 through 1025 Processing helix chain 'A' and resid 1026 through 1039 removed outlier: 4.422A pdb=" N VAL A1037 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N TYR A1038 " --> pdb=" O SER A1034 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1043 Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1069 through 1089 Processing helix chain 'A' and resid 1128 through 1130 No H-bonds generated for 'chain 'A' and resid 1128 through 1130' Processing helix chain 'A' and resid 1136 through 1140 Processing helix chain 'A' and resid 1211 through 1220 Processing helix chain 'A' and resid 1277 through 1284 removed outlier: 3.636A pdb=" N ARG A1283 " --> pdb=" O THR A1279 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR A1284 " --> pdb=" O ALA A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1291 removed outlier: 3.761A pdb=" N ASN A1289 " --> pdb=" O GLN A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1327 through 1329 No H-bonds generated for 'chain 'A' and resid 1327 through 1329' Processing helix chain 'A' and resid 1368 through 1373 Processing helix chain 'A' and resid 1373 through 1380 Processing helix chain 'A' and resid 1446 through 1450 removed outlier: 3.563A pdb=" N ARG A1450 " --> pdb=" O TYR A1447 " (cutoff:3.500A) Processing helix chain 'A' and resid 1472 through 1479 Processing helix chain 'A' and resid 1596 through 1600 removed outlier: 3.736A pdb=" N ILE A1600 " --> pdb=" O PRO A1597 " (cutoff:3.500A) Processing helix chain 'A' and resid 1625 through 1636 removed outlier: 3.985A pdb=" N GLN A1629 " --> pdb=" O LEU A1625 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL A1631 " --> pdb=" O ALA A1627 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A1632 " --> pdb=" O SER A1628 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ARG A1633 " --> pdb=" O GLN A1629 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N THR A1636 " --> pdb=" O SER A1632 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1642 removed outlier: 3.829A pdb=" N ILE A1641 " --> pdb=" O GLY A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1648 Processing helix chain 'A' and resid 1798 through 1807 Processing helix chain 'A' and resid 1807 through 1820 Processing helix chain 'A' and resid 1822 through 1831 Processing helix chain 'A' and resid 1852 through 1858 Processing helix chain 'A' and resid 1870 through 1878 Processing helix chain 'A' and resid 1879 through 1903 Processing helix chain 'A' and resid 1906 through 1925 Processing helix chain 'A' and resid 1940 through 1945 Processing helix chain 'A' and resid 1946 through 1963 removed outlier: 3.805A pdb=" N ARG A1962 " --> pdb=" O THR A1958 " (cutoff:3.500A) Processing helix chain 'A' and resid 1972 through 1976 Processing helix chain 'A' and resid 1984 through 2003 Processing helix chain 'A' and resid 2049 through 2137 Processing helix chain 'A' and resid 2139 through 2158 Processing helix chain 'A' and resid 2159 through 2170 Processing helix chain 'A' and resid 2186 through 2275 removed outlier: 3.597A pdb=" N GLU A2242 " --> pdb=" O ASP A2238 " (cutoff:3.500A) Processing helix chain 'A' and resid 2278 through 2316 removed outlier: 3.560A pdb=" N ASP A2298 " --> pdb=" O TYR A2294 " (cutoff:3.500A) Processing helix chain 'A' and resid 2329 through 2333 Processing helix chain 'A' and resid 2336 through 2356 removed outlier: 3.934A pdb=" N THR A2340 " --> pdb=" O MET A2336 " (cutoff:3.500A) Processing helix chain 'A' and resid 2368 through 2375 Processing helix chain 'A' and resid 2381 through 2392 Processing helix chain 'A' and resid 2418 through 2421 Processing helix chain 'A' and resid 2422 through 2426 removed outlier: 3.658A pdb=" N TYR A2426 " --> pdb=" O PHE A2423 " (cutoff:3.500A) Processing helix chain 'A' and resid 2518 through 2525 Processing helix chain 'B' and resid 3 through 12 Processing helix chain 'B' and resid 21 through 26 removed outlier: 3.508A pdb=" N LEU B 25 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN B 26 " --> pdb=" O ALA B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 42 through 72 removed outlier: 3.512A pdb=" N ARG B 70 " --> pdb=" O ARG B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 83 Processing helix chain 'B' and resid 86 through 97 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 161 through 178 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 243 through 252 Processing helix chain 'B' and resid 258 through 267 Processing helix chain 'B' and resid 272 through 277 Processing helix chain 'B' and resid 278 through 287 Processing helix chain 'B' and resid 289 through 298 removed outlier: 3.543A pdb=" N LYS B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 459 Processing helix chain 'B' and resid 461 through 471 Processing helix chain 'B' and resid 479 through 497 Processing helix chain 'B' and resid 499 through 508 removed outlier: 3.658A pdb=" N GLY B 508 " --> pdb=" O GLN B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 521 through 528 Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 567 through 579 Processing helix chain 'B' and resid 582 through 584 No H-bonds generated for 'chain 'B' and resid 582 through 584' Processing helix chain 'B' and resid 590 through 607 removed outlier: 3.793A pdb=" N HIS B 607 " --> pdb=" O LEU B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 621 Processing helix chain 'B' and resid 627 through 631 Processing helix chain 'B' and resid 634 through 654 removed outlier: 3.842A pdb=" N ARG B 638 " --> pdb=" O GLY B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 665 Processing helix chain 'B' and resid 673 through 684 Processing helix chain 'B' and resid 688 through 694 Processing helix chain 'B' and resid 696 through 713 Proline residue: B 706 - end of helix Processing helix chain 'B' and resid 716 through 731 Processing helix chain 'B' and resid 736 through 745 Processing helix chain 'B' and resid 752 through 775 removed outlier: 4.123A pdb=" N GLN B 756 " --> pdb=" O ASN B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 777 through 788 Processing helix chain 'B' and resid 803 through 821 removed outlier: 3.931A pdb=" N GLY B 821 " --> pdb=" O ILE B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 823 through 833 Processing helix chain 'B' and resid 837 through 846 Processing helix chain 'B' and resid 848 through 860 Processing helix chain 'B' and resid 866 through 883 Processing helix chain 'B' and resid 886 through 896 Processing helix chain 'B' and resid 911 through 924 Processing helix chain 'B' and resid 927 through 954 Processing helix chain 'B' and resid 963 through 972 Processing helix chain 'B' and resid 984 through 1002 Processing helix chain 'B' and resid 1011 through 1014 Processing helix chain 'B' and resid 1015 through 1020 Processing helix chain 'B' and resid 1020 through 1025 Processing helix chain 'B' and resid 1026 through 1039 removed outlier: 4.494A pdb=" N VAL B1037 " --> pdb=" O VAL B1033 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR B1038 " --> pdb=" O SER B1034 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1043 Processing helix chain 'B' and resid 1053 through 1063 Processing helix chain 'B' and resid 1069 through 1089 Processing helix chain 'B' and resid 1128 through 1130 No H-bonds generated for 'chain 'B' and resid 1128 through 1130' Processing helix chain 'B' and resid 1136 through 1140 removed outlier: 3.614A pdb=" N TRP B1140 " --> pdb=" O ALA B1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 1211 through 1220 Processing helix chain 'B' and resid 1277 through 1282 Processing helix chain 'B' and resid 1283 through 1291 removed outlier: 5.121A pdb=" N GLN B1286 " --> pdb=" O ARG B1283 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B1289 " --> pdb=" O GLN B1286 " (cutoff:3.500A) Processing helix chain 'B' and resid 1327 through 1329 No H-bonds generated for 'chain 'B' and resid 1327 through 1329' Processing helix chain 'B' and resid 1368 through 1380 removed outlier: 3.882A pdb=" N ILE B1375 " --> pdb=" O ARG B1371 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N SER B1376 " --> pdb=" O ASN B1372 " (cutoff:3.500A) Processing helix chain 'B' and resid 1472 through 1479 Processing helix chain 'B' and resid 1596 through 1600 removed outlier: 3.714A pdb=" N ILE B1600 " --> pdb=" O PRO B1597 " (cutoff:3.500A) Processing helix chain 'B' and resid 1625 through 1636 removed outlier: 3.944A pdb=" N GLN B1629 " --> pdb=" O LEU B1625 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL B1631 " --> pdb=" O ALA B1627 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N SER B1632 " --> pdb=" O SER B1628 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG B1633 " --> pdb=" O GLN B1629 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N THR B1636 " --> pdb=" O SER B1632 " (cutoff:3.500A) Processing helix chain 'B' and resid 1637 through 1642 removed outlier: 3.792A pdb=" N ILE B1641 " --> pdb=" O GLY B1637 " (cutoff:3.500A) Processing helix chain 'B' and resid 1643 through 1648 Processing helix chain 'B' and resid 1798 through 1807 Processing helix chain 'B' and resid 1807 through 1820 Processing helix chain 'B' and resid 1822 through 1831 Processing helix chain 'B' and resid 1852 through 1858 Processing helix chain 'B' and resid 1864 through 1868 removed outlier: 4.065A pdb=" N ASP B1867 " --> pdb=" O ASN B1864 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA B1868 " --> pdb=" O PRO B1865 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1864 through 1868' Processing helix chain 'B' and resid 1870 through 1878 Processing helix chain 'B' and resid 1879 through 1903 Processing helix chain 'B' and resid 1906 through 1925 Processing helix chain 'B' and resid 1940 through 1945 Processing helix chain 'B' and resid 1946 through 1963 removed outlier: 3.845A pdb=" N ARG B1962 " --> pdb=" O THR B1958 " (cutoff:3.500A) Processing helix chain 'B' and resid 1972 through 1976 Processing helix chain 'B' and resid 1984 through 2003 Processing helix chain 'B' and resid 2049 through 2137 Processing helix chain 'B' and resid 2139 through 2159 removed outlier: 3.926A pdb=" N GLY B2159 " --> pdb=" O GLN B2155 " (cutoff:3.500A) Processing helix chain 'B' and resid 2159 through 2170 Processing helix chain 'B' and resid 2186 through 2275 removed outlier: 3.634A pdb=" N GLU B2242 " --> pdb=" O ASP B2238 " (cutoff:3.500A) Processing helix chain 'B' and resid 2278 through 2316 removed outlier: 3.528A pdb=" N ASP B2298 " --> pdb=" O TYR B2294 " (cutoff:3.500A) Processing helix chain 'B' and resid 2329 through 2333 removed outlier: 3.507A pdb=" N THR B2332 " --> pdb=" O ASN B2329 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA B2333 " --> pdb=" O GLY B2330 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2329 through 2333' Processing helix chain 'B' and resid 2336 through 2355 Processing helix chain 'B' and resid 2368 through 2374 Processing helix chain 'B' and resid 2381 through 2392 Processing helix chain 'B' and resid 2418 through 2421 Processing helix chain 'B' and resid 2422 through 2426 removed outlier: 3.701A pdb=" N TYR B2426 " --> pdb=" O PHE B2423 " (cutoff:3.500A) Processing helix chain 'B' and resid 2518 through 2525 Processing helix chain 'C' and resid 3 through 12 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 42 through 72 removed outlier: 3.572A pdb=" N ARG C 70 " --> pdb=" O ARG C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 83 Processing helix chain 'C' and resid 86 through 97 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 161 through 178 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 200 through 214 Processing helix chain 'C' and resid 217 through 223 Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 252 Processing helix chain 'C' and resid 258 through 267 Processing helix chain 'C' and resid 272 through 277 Processing helix chain 'C' and resid 278 through 287 Processing helix chain 'C' and resid 289 through 298 removed outlier: 3.863A pdb=" N TYR C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 441 through 459 Processing helix chain 'C' and resid 461 through 471 Processing helix chain 'C' and resid 479 through 497 Processing helix chain 'C' and resid 499 through 508 removed outlier: 3.620A pdb=" N GLY C 508 " --> pdb=" O GLN C 504 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 528 Processing helix chain 'C' and resid 554 through 565 Processing helix chain 'C' and resid 567 through 579 Processing helix chain 'C' and resid 590 through 607 removed outlier: 3.691A pdb=" N HIS C 607 " --> pdb=" O LEU C 603 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 621 Processing helix chain 'C' and resid 627 through 631 Processing helix chain 'C' and resid 634 through 654 removed outlier: 3.824A pdb=" N ARG C 638 " --> pdb=" O GLY C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 665 Processing helix chain 'C' and resid 673 through 684 Processing helix chain 'C' and resid 688 through 694 Processing helix chain 'C' and resid 696 through 713 Proline residue: C 706 - end of helix Processing helix chain 'C' and resid 716 through 731 Processing helix chain 'C' and resid 736 through 745 Processing helix chain 'C' and resid 752 through 775 removed outlier: 4.134A pdb=" N GLN C 756 " --> pdb=" O ASN C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 777 through 788 Processing helix chain 'C' and resid 803 through 821 removed outlier: 3.943A pdb=" N GLY C 821 " --> pdb=" O ILE C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 833 Processing helix chain 'C' and resid 837 through 846 Processing helix chain 'C' and resid 848 through 860 Processing helix chain 'C' and resid 866 through 883 Processing helix chain 'C' and resid 886 through 895 Processing helix chain 'C' and resid 911 through 924 Processing helix chain 'C' and resid 927 through 954 Processing helix chain 'C' and resid 963 through 972 Processing helix chain 'C' and resid 984 through 1002 Processing helix chain 'C' and resid 1011 through 1014 Processing helix chain 'C' and resid 1015 through 1020 Processing helix chain 'C' and resid 1020 through 1025 Processing helix chain 'C' and resid 1026 through 1039 removed outlier: 4.382A pdb=" N VAL C1037 " --> pdb=" O VAL C1033 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR C1038 " --> pdb=" O SER C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1043 Processing helix chain 'C' and resid 1053 through 1063 Processing helix chain 'C' and resid 1069 through 1089 Processing helix chain 'C' and resid 1128 through 1130 No H-bonds generated for 'chain 'C' and resid 1128 through 1130' Processing helix chain 'C' and resid 1136 through 1140 removed outlier: 3.525A pdb=" N TRP C1140 " --> pdb=" O ALA C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1211 through 1220 Processing helix chain 'C' and resid 1277 through 1282 Processing helix chain 'C' and resid 1283 through 1291 removed outlier: 5.094A pdb=" N GLN C1286 " --> pdb=" O ARG C1283 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C1289 " --> pdb=" O GLN C1286 " (cutoff:3.500A) Processing helix chain 'C' and resid 1327 through 1329 No H-bonds generated for 'chain 'C' and resid 1327 through 1329' Processing helix chain 'C' and resid 1368 through 1380 removed outlier: 4.289A pdb=" N ILE C1375 " --> pdb=" O ARG C1371 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER C1376 " --> pdb=" O ASN C1372 " (cutoff:3.500A) Processing helix chain 'C' and resid 1446 through 1450 Processing helix chain 'C' and resid 1472 through 1479 Processing helix chain 'C' and resid 1596 through 1600 removed outlier: 3.772A pdb=" N ILE C1600 " --> pdb=" O PRO C1597 " (cutoff:3.500A) Processing helix chain 'C' and resid 1625 through 1636 removed outlier: 3.986A pdb=" N GLN C1629 " --> pdb=" O LEU C1625 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL C1631 " --> pdb=" O ALA C1627 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N SER C1632 " --> pdb=" O SER C1628 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG C1633 " --> pdb=" O GLN C1629 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N THR C1636 " --> pdb=" O SER C1632 " (cutoff:3.500A) Processing helix chain 'C' and resid 1637 through 1642 removed outlier: 3.862A pdb=" N ILE C1641 " --> pdb=" O GLY C1637 " (cutoff:3.500A) Processing helix chain 'C' and resid 1643 through 1648 Processing helix chain 'C' and resid 1798 through 1807 Processing helix chain 'C' and resid 1807 through 1820 Processing helix chain 'C' and resid 1822 through 1831 Processing helix chain 'C' and resid 1852 through 1858 Processing helix chain 'C' and resid 1864 through 1868 removed outlier: 3.918A pdb=" N ASP C1867 " --> pdb=" O ASN C1864 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ALA C1868 " --> pdb=" O PRO C1865 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1864 through 1868' Processing helix chain 'C' and resid 1870 through 1878 Processing helix chain 'C' and resid 1879 through 1903 removed outlier: 3.581A pdb=" N LYS C1883 " --> pdb=" O PRO C1879 " (cutoff:3.500A) Processing helix chain 'C' and resid 1906 through 1925 Processing helix chain 'C' and resid 1940 through 1945 Processing helix chain 'C' and resid 1946 through 1961 Processing helix chain 'C' and resid 1972 through 1976 Processing helix chain 'C' and resid 1984 through 2003 Processing helix chain 'C' and resid 2049 through 2137 Processing helix chain 'C' and resid 2139 through 2159 removed outlier: 3.884A pdb=" N GLY C2159 " --> pdb=" O GLN C2155 " (cutoff:3.500A) Processing helix chain 'C' and resid 2159 through 2170 Processing helix chain 'C' and resid 2186 through 2275 removed outlier: 3.664A pdb=" N GLU C2242 " --> pdb=" O ASP C2238 " (cutoff:3.500A) Processing helix chain 'C' and resid 2278 through 2316 removed outlier: 3.542A pdb=" N ASP C2298 " --> pdb=" O TYR C2294 " (cutoff:3.500A) Processing helix chain 'C' and resid 2329 through 2333 removed outlier: 3.592A pdb=" N THR C2332 " --> pdb=" O ASN C2329 " (cutoff:3.500A) Processing helix chain 'C' and resid 2336 through 2356 Processing helix chain 'C' and resid 2368 through 2374 Processing helix chain 'C' and resid 2381 through 2392 Processing helix chain 'C' and resid 2418 through 2421 Processing helix chain 'C' and resid 2422 through 2426 removed outlier: 3.737A pdb=" N TYR C2426 " --> pdb=" O PHE C2423 " (cutoff:3.500A) Processing helix chain 'C' and resid 2518 through 2525 Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 21 through 26 Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 42 through 72 removed outlier: 3.587A pdb=" N ARG D 70 " --> pdb=" O ARG D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 78 through 83 removed outlier: 3.760A pdb=" N LEU D 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 97 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 161 through 178 Processing helix chain 'D' and resid 180 through 191 removed outlier: 3.844A pdb=" N THR D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 214 Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 243 through 252 Processing helix chain 'D' and resid 258 through 267 Processing helix chain 'D' and resid 272 through 277 Processing helix chain 'D' and resid 278 through 287 Processing helix chain 'D' and resid 289 through 298 removed outlier: 3.909A pdb=" N TYR D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 441 through 459 Processing helix chain 'D' and resid 461 through 473 Processing helix chain 'D' and resid 479 through 497 Processing helix chain 'D' and resid 499 through 507 Processing helix chain 'D' and resid 521 through 528 Processing helix chain 'D' and resid 554 through 565 Processing helix chain 'D' and resid 567 through 579 Processing helix chain 'D' and resid 590 through 607 removed outlier: 3.732A pdb=" N HIS D 607 " --> pdb=" O LEU D 603 " (cutoff:3.500A) Processing helix chain 'D' and resid 610 through 621 Processing helix chain 'D' and resid 627 through 631 Processing helix chain 'D' and resid 634 through 654 removed outlier: 4.120A pdb=" N ARG D 638 " --> pdb=" O GLY D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 665 Processing helix chain 'D' and resid 673 through 684 Processing helix chain 'D' and resid 685 through 687 No H-bonds generated for 'chain 'D' and resid 685 through 687' Processing helix chain 'D' and resid 688 through 694 Processing helix chain 'D' and resid 696 through 713 Proline residue: D 706 - end of helix Processing helix chain 'D' and resid 716 through 731 Processing helix chain 'D' and resid 736 through 745 Processing helix chain 'D' and resid 752 through 775 removed outlier: 4.270A pdb=" N GLN D 756 " --> pdb=" O ASN D 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 777 through 788 Processing helix chain 'D' and resid 803 through 821 removed outlier: 3.946A pdb=" N GLY D 821 " --> pdb=" O ILE D 817 " (cutoff:3.500A) Processing helix chain 'D' and resid 823 through 833 Processing helix chain 'D' and resid 837 through 846 Processing helix chain 'D' and resid 848 through 860 Processing helix chain 'D' and resid 866 through 883 Processing helix chain 'D' and resid 886 through 895 Processing helix chain 'D' and resid 911 through 924 Processing helix chain 'D' and resid 927 through 954 Processing helix chain 'D' and resid 963 through 972 Processing helix chain 'D' and resid 984 through 1002 Processing helix chain 'D' and resid 1011 through 1014 Processing helix chain 'D' and resid 1015 through 1020 Processing helix chain 'D' and resid 1020 through 1025 Processing helix chain 'D' and resid 1026 through 1039 removed outlier: 4.398A pdb=" N VAL D1037 " --> pdb=" O VAL D1033 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR D1038 " --> pdb=" O SER D1034 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1043 Processing helix chain 'D' and resid 1053 through 1063 Processing helix chain 'D' and resid 1069 through 1089 Processing helix chain 'D' and resid 1128 through 1130 No H-bonds generated for 'chain 'D' and resid 1128 through 1130' Processing helix chain 'D' and resid 1136 through 1140 removed outlier: 3.630A pdb=" N TRP D1140 " --> pdb=" O ALA D1137 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1220 Processing helix chain 'D' and resid 1277 through 1284 removed outlier: 3.541A pdb=" N ARG D1283 " --> pdb=" O THR D1279 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D1284 " --> pdb=" O ALA D1280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1285 through 1291 removed outlier: 3.698A pdb=" N ASN D1289 " --> pdb=" O GLN D1286 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1329 No H-bonds generated for 'chain 'D' and resid 1327 through 1329' Processing helix chain 'D' and resid 1368 through 1380 removed outlier: 4.047A pdb=" N ASN D1372 " --> pdb=" O ASN D1368 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS D1373 " --> pdb=" O VAL D1369 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER D1376 " --> pdb=" O ASN D1372 " (cutoff:3.500A) Processing helix chain 'D' and resid 1446 through 1450 removed outlier: 3.585A pdb=" N ALA D1449 " --> pdb=" O ASN D1446 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG D1450 " --> pdb=" O TYR D1447 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1446 through 1450' Processing helix chain 'D' and resid 1472 through 1478 Processing helix chain 'D' and resid 1596 through 1600 removed outlier: 3.876A pdb=" N ILE D1600 " --> pdb=" O PRO D1597 " (cutoff:3.500A) Processing helix chain 'D' and resid 1625 through 1636 removed outlier: 4.003A pdb=" N GLN D1629 " --> pdb=" O LEU D1625 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL D1631 " --> pdb=" O ALA D1627 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER D1632 " --> pdb=" O SER D1628 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG D1633 " --> pdb=" O GLN D1629 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR D1636 " --> pdb=" O SER D1632 " (cutoff:3.500A) Processing helix chain 'D' and resid 1637 through 1642 removed outlier: 3.896A pdb=" N ILE D1641 " --> pdb=" O GLY D1637 " (cutoff:3.500A) Processing helix chain 'D' and resid 1643 through 1648 Processing helix chain 'D' and resid 1798 through 1807 Processing helix chain 'D' and resid 1807 through 1820 Processing helix chain 'D' and resid 1822 through 1831 Processing helix chain 'D' and resid 1852 through 1858 Processing helix chain 'D' and resid 1870 through 1878 Processing helix chain 'D' and resid 1879 through 1903 removed outlier: 3.548A pdb=" N LYS D1883 " --> pdb=" O PRO D1879 " (cutoff:3.500A) Processing helix chain 'D' and resid 1906 through 1925 Processing helix chain 'D' and resid 1940 through 1945 Processing helix chain 'D' and resid 1946 through 1961 Processing helix chain 'D' and resid 1984 through 2003 Processing helix chain 'D' and resid 2049 through 2137 Processing helix chain 'D' and resid 2139 through 2158 Processing helix chain 'D' and resid 2159 through 2170 Processing helix chain 'D' and resid 2186 through 2275 removed outlier: 3.694A pdb=" N GLU D2242 " --> pdb=" O ASP D2238 " (cutoff:3.500A) Processing helix chain 'D' and resid 2278 through 2316 removed outlier: 3.551A pdb=" N ASP D2298 " --> pdb=" O TYR D2294 " (cutoff:3.500A) Processing helix chain 'D' and resid 2329 through 2333 removed outlier: 3.549A pdb=" N THR D2332 " --> pdb=" O ASN D2329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA D2333 " --> pdb=" O GLY D2330 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2329 through 2333' Processing helix chain 'D' and resid 2336 through 2356 Processing helix chain 'D' and resid 2368 through 2374 Processing helix chain 'D' and resid 2381 through 2392 Processing helix chain 'D' and resid 2418 through 2421 Processing helix chain 'D' and resid 2422 through 2426 removed outlier: 3.540A pdb=" N TYR D2426 " --> pdb=" O PHE D2423 " (cutoff:3.500A) Processing helix chain 'D' and resid 2518 through 2525 Processing helix chain 'E' and resid 3 through 12 Processing helix chain 'E' and resid 21 through 26 Processing helix chain 'E' and resid 29 through 37 Processing helix chain 'E' and resid 42 through 72 removed outlier: 3.556A pdb=" N ARG E 70 " --> pdb=" O ARG E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 3.730A pdb=" N LEU E 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 97 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 161 through 178 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 200 through 214 Processing helix chain 'E' and resid 217 through 223 Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 243 through 252 Processing helix chain 'E' and resid 258 through 267 Processing helix chain 'E' and resid 272 through 277 Processing helix chain 'E' and resid 278 through 287 Processing helix chain 'E' and resid 289 through 298 removed outlier: 3.836A pdb=" N TYR E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 459 Processing helix chain 'E' and resid 461 through 471 Processing helix chain 'E' and resid 479 through 497 Processing helix chain 'E' and resid 499 through 508 removed outlier: 3.553A pdb=" N GLY E 508 " --> pdb=" O GLN E 504 " (cutoff:3.500A) Processing helix chain 'E' and resid 521 through 528 Processing helix chain 'E' and resid 554 through 565 Processing helix chain 'E' and resid 567 through 579 Processing helix chain 'E' and resid 590 through 607 removed outlier: 3.528A pdb=" N ILE E 594 " --> pdb=" O SER E 590 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N HIS E 607 " --> pdb=" O LEU E 603 " (cutoff:3.500A) Processing helix chain 'E' and resid 610 through 621 Processing helix chain 'E' and resid 634 through 654 removed outlier: 3.802A pdb=" N ARG E 638 " --> pdb=" O GLY E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 665 Processing helix chain 'E' and resid 673 through 684 Processing helix chain 'E' and resid 685 through 687 No H-bonds generated for 'chain 'E' and resid 685 through 687' Processing helix chain 'E' and resid 688 through 694 Processing helix chain 'E' and resid 696 through 713 Proline residue: E 706 - end of helix Processing helix chain 'E' and resid 716 through 731 Processing helix chain 'E' and resid 736 through 745 Processing helix chain 'E' and resid 753 through 775 Processing helix chain 'E' and resid 777 through 788 Processing helix chain 'E' and resid 803 through 821 removed outlier: 3.955A pdb=" N GLY E 821 " --> pdb=" O ILE E 817 " (cutoff:3.500A) Processing helix chain 'E' and resid 823 through 833 Processing helix chain 'E' and resid 837 through 846 Processing helix chain 'E' and resid 848 through 860 Processing helix chain 'E' and resid 866 through 883 Processing helix chain 'E' and resid 886 through 895 Processing helix chain 'E' and resid 911 through 924 Processing helix chain 'E' and resid 927 through 954 Processing helix chain 'E' and resid 963 through 972 Processing helix chain 'E' and resid 984 through 1002 Processing helix chain 'E' and resid 1011 through 1014 Processing helix chain 'E' and resid 1015 through 1020 Processing helix chain 'E' and resid 1020 through 1025 Processing helix chain 'E' and resid 1026 through 1039 removed outlier: 4.434A pdb=" N VAL E1037 " --> pdb=" O VAL E1033 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N TYR E1038 " --> pdb=" O SER E1034 " (cutoff:3.500A) Processing helix chain 'E' and resid 1040 through 1043 Processing helix chain 'E' and resid 1053 through 1063 Processing helix chain 'E' and resid 1069 through 1089 Processing helix chain 'E' and resid 1128 through 1130 No H-bonds generated for 'chain 'E' and resid 1128 through 1130' Processing helix chain 'E' and resid 1136 through 1140 Processing helix chain 'E' and resid 1211 through 1220 Processing helix chain 'E' and resid 1277 through 1282 Processing helix chain 'E' and resid 1283 through 1291 removed outlier: 5.131A pdb=" N GLN E1286 " --> pdb=" O ARG E1283 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASN E1289 " --> pdb=" O GLN E1286 " (cutoff:3.500A) Processing helix chain 'E' and resid 1327 through 1329 No H-bonds generated for 'chain 'E' and resid 1327 through 1329' Processing helix chain 'E' and resid 1368 through 1380 removed outlier: 4.093A pdb=" N ILE E1375 " --> pdb=" O ARG E1371 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N SER E1376 " --> pdb=" O ASN E1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 1446 through 1450 removed outlier: 3.806A pdb=" N ARG E1450 " --> pdb=" O TYR E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1472 through 1479 Processing helix chain 'E' and resid 1596 through 1600 removed outlier: 3.731A pdb=" N ILE E1600 " --> pdb=" O PRO E1597 " (cutoff:3.500A) Processing helix chain 'E' and resid 1625 through 1636 removed outlier: 3.967A pdb=" N GLN E1629 " --> pdb=" O LEU E1625 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL E1631 " --> pdb=" O ALA E1627 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER E1632 " --> pdb=" O SER E1628 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG E1633 " --> pdb=" O GLN E1629 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N THR E1636 " --> pdb=" O SER E1632 " (cutoff:3.500A) Processing helix chain 'E' and resid 1637 through 1642 removed outlier: 3.799A pdb=" N ILE E1641 " --> pdb=" O GLY E1637 " (cutoff:3.500A) Processing helix chain 'E' and resid 1643 through 1648 Processing helix chain 'E' and resid 1798 through 1807 Processing helix chain 'E' and resid 1807 through 1820 Processing helix chain 'E' and resid 1822 through 1831 Processing helix chain 'E' and resid 1852 through 1858 Processing helix chain 'E' and resid 1864 through 1868 removed outlier: 3.936A pdb=" N ASP E1867 " --> pdb=" O ASN E1864 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA E1868 " --> pdb=" O PRO E1865 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1864 through 1868' Processing helix chain 'E' and resid 1870 through 1878 Processing helix chain 'E' and resid 1879 through 1903 removed outlier: 3.634A pdb=" N LYS E1883 " --> pdb=" O PRO E1879 " (cutoff:3.500A) Processing helix chain 'E' and resid 1906 through 1925 Processing helix chain 'E' and resid 1940 through 1946 Processing helix chain 'E' and resid 1946 through 1963 removed outlier: 3.912A pdb=" N ARG E1962 " --> pdb=" O THR E1958 " (cutoff:3.500A) Processing helix chain 'E' and resid 1972 through 1976 Processing helix chain 'E' and resid 1984 through 2003 Processing helix chain 'E' and resid 2049 through 2137 Processing helix chain 'E' and resid 2139 through 2159 removed outlier: 3.909A pdb=" N GLY E2159 " --> pdb=" O GLN E2155 " (cutoff:3.500A) Processing helix chain 'E' and resid 2159 through 2170 Processing helix chain 'E' and resid 2186 through 2275 removed outlier: 3.712A pdb=" N GLU E2242 " --> pdb=" O ASP E2238 " (cutoff:3.500A) Processing helix chain 'E' and resid 2278 through 2316 removed outlier: 3.539A pdb=" N ASP E2298 " --> pdb=" O TYR E2294 " (cutoff:3.500A) Processing helix chain 'E' and resid 2329 through 2333 removed outlier: 3.574A pdb=" N THR E2332 " --> pdb=" O ASN E2329 " (cutoff:3.500A) Processing helix chain 'E' and resid 2336 through 2356 Processing helix chain 'E' and resid 2368 through 2374 Processing helix chain 'E' and resid 2381 through 2392 Processing helix chain 'E' and resid 2418 through 2421 Processing helix chain 'E' and resid 2518 through 2525 Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA3, first strand: chain 'A' and resid 346 through 351 removed outlier: 3.581A pdb=" N TYR A 346 " --> pdb=" O ALA A 361 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLN A 356 " --> pdb=" O TYR A 400 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TYR A 400 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 358 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 386 Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 Processing sheet with id=AA6, first strand: chain 'A' and resid 1144 through 1146 removed outlier: 4.901A pdb=" N TYR A1120 " --> pdb=" O ILE A1146 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A1106 " --> pdb=" O HIS A1097 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N HIS A1097 " --> pdb=" O LEU A1106 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TRP A1108 " --> pdb=" O ALA A1095 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A1095 " --> pdb=" O TRP A1108 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL A1110 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1157 through 1162 removed outlier: 3.547A pdb=" N PHE A1162 " --> pdb=" O ARG A1165 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG A1165 " --> pdb=" O PHE A1162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1228 through 1235 Processing sheet with id=AA9, first strand: chain 'A' and resid 1293 through 1294 removed outlier: 3.597A pdb=" N ILE A1293 " --> pdb=" O VAL A1302 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N LEU A1301 " --> pdb=" O GLU A1605 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N GLU A1605 " --> pdb=" O LEU A1301 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1313 through 1314 removed outlier: 6.575A pdb=" N VAL A1580 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A1575 " --> pdb=" O VAL A1580 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ASP A1513 " --> pdb=" O LYS A1574 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1319 through 1325 removed outlier: 6.754A pdb=" N GLY A1336 " --> pdb=" O MET A1321 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A1323 " --> pdb=" O GLU A1334 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU A1334 " --> pdb=" O SER A1323 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE A1325 " --> pdb=" O VAL A1332 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL A1332 " --> pdb=" O ILE A1325 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY A1336 " --> pdb=" O ALA A1358 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A1358 " --> pdb=" O GLY A1336 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR A1547 " --> pdb=" O ALA A1534 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1340 through 1346 removed outlier: 3.803A pdb=" N GLN A1340 " --> pdb=" O HIS A1355 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER A1346 " --> pdb=" O ASN A1349 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1464 through 1465 removed outlier: 8.875A pdb=" N THR A1413 " --> pdb=" O ALA A1396 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ALA A1396 " --> pdb=" O THR A1413 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1400 through 1403 removed outlier: 3.834A pdb=" N LYS A1400 " --> pdb=" O GLN A1498 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N SER A1496 " --> pdb=" O TYR A1402 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1705 through 1712 Processing sheet with id=AB7, first strand: chain 'A' and resid 1692 through 1698 removed outlier: 6.661A pdb=" N ILE A1680 " --> pdb=" O TYR A1694 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N SER A1696 " --> pdb=" O PHE A1678 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N PHE A1678 " --> pdb=" O SER A1696 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1763 through 1765 Processing sheet with id=AB9, first strand: chain 'A' and resid 1840 through 1841 Processing sheet with id=AC1, first strand: chain 'A' and resid 2360 through 2367 removed outlier: 6.641A pdb=" N ILE A2529 " --> pdb=" O VAL A2441 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A2441 " --> pdb=" O ILE A2529 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N HIS A2531 " --> pdb=" O VAL A2439 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL A2439 " --> pdb=" O HIS A2531 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ARG A2533 " --> pdb=" O LYS A2437 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2396 through 2399 Processing sheet with id=AC3, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AC4, first strand: chain 'B' and resid 299 through 300 removed outlier: 5.391A pdb=" N MET B 299 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N GLY B 318 " --> pdb=" O MET B 299 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLY B 431 " --> pdb=" O THR B 337 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 346 through 351 removed outlier: 3.798A pdb=" N TYR B 346 " --> pdb=" O ALA B 361 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 382 through 386 Processing sheet with id=AC7, first strand: chain 'B' and resid 543 through 545 Processing sheet with id=AC8, first strand: chain 'B' and resid 1144 through 1146 removed outlier: 4.690A pdb=" N TYR B1120 " --> pdb=" O ILE B1146 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B1106 " --> pdb=" O HIS B1097 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N HIS B1097 " --> pdb=" O LEU B1106 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TRP B1108 " --> pdb=" O ALA B1095 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ALA B1095 " --> pdb=" O TRP B1108 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B1110 " --> pdb=" O VAL B1093 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1157 through 1162 removed outlier: 3.622A pdb=" N PHE B1162 " --> pdb=" O ARG B1165 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ARG B1165 " --> pdb=" O PHE B1162 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1228 through 1235 Processing sheet with id=AD2, first strand: chain 'B' and resid 1293 through 1294 removed outlier: 3.526A pdb=" N ILE B1293 " --> pdb=" O VAL B1302 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU B1301 " --> pdb=" O GLU B1605 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N GLU B1605 " --> pdb=" O LEU B1301 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1313 through 1314 removed outlier: 6.586A pdb=" N VAL B1580 " --> pdb=" O ALA B1575 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA B1575 " --> pdb=" O VAL B1580 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS B1574 " --> pdb=" O ASP B1513 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASP B1513 " --> pdb=" O LYS B1574 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1319 through 1325 removed outlier: 6.681A pdb=" N GLY B1336 " --> pdb=" O MET B1321 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER B1323 " --> pdb=" O GLU B1334 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B1334 " --> pdb=" O SER B1323 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE B1325 " --> pdb=" O VAL B1332 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B1332 " --> pdb=" O ILE B1325 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY B1336 " --> pdb=" O ALA B1358 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ALA B1358 " --> pdb=" O GLY B1336 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N THR B1547 " --> pdb=" O ALA B1534 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1340 through 1346 removed outlier: 3.824A pdb=" N GLN B1340 " --> pdb=" O HIS B1355 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER B1346 " --> pdb=" O ASN B1349 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1421 through 1425 Processing sheet with id=AD7, first strand: chain 'B' and resid 1401 through 1404 removed outlier: 6.906A pdb=" N SER B1496 " --> pdb=" O TYR B1402 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1437 through 1440 Processing sheet with id=AD9, first strand: chain 'B' and resid 1705 through 1712 removed outlier: 4.679A pdb=" N PHE B1659 " --> pdb=" O ALA B1785 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 1692 through 1698 removed outlier: 6.626A pdb=" N ILE B1680 " --> pdb=" O TYR B1694 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER B1696 " --> pdb=" O PHE B1678 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE B1678 " --> pdb=" O SER B1696 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 1763 through 1765 Processing sheet with id=AE3, first strand: chain 'B' and resid 1840 through 1841 Processing sheet with id=AE4, first strand: chain 'B' and resid 2175 through 2177 Processing sheet with id=AE5, first strand: chain 'B' and resid 2360 through 2367 removed outlier: 6.647A pdb=" N ILE B2529 " --> pdb=" O VAL B2441 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL B2441 " --> pdb=" O ILE B2529 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N HIS B2531 " --> pdb=" O VAL B2439 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL B2439 " --> pdb=" O HIS B2531 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG B2533 " --> pdb=" O LYS B2437 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 2396 through 2399 Processing sheet with id=AE7, first strand: chain 'C' and resid 159 through 160 Processing sheet with id=AE8, first strand: chain 'C' and resid 299 through 300 removed outlier: 4.115A pdb=" N LYS C 326 " --> pdb=" O VAL C 321 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY C 431 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE C 434 " --> pdb=" O GLY C 412 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY C 412 " --> pdb=" O PHE C 434 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 346 through 351 removed outlier: 3.768A pdb=" N TYR C 346 " --> pdb=" O ALA C 361 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 382 through 386 Processing sheet with id=AF2, first strand: chain 'C' and resid 543 through 545 Processing sheet with id=AF3, first strand: chain 'C' and resid 1144 through 1146 removed outlier: 4.831A pdb=" N TYR C1120 " --> pdb=" O ILE C1146 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C1106 " --> pdb=" O HIS C1097 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N HIS C1097 " --> pdb=" O LEU C1106 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP C1108 " --> pdb=" O ALA C1095 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA C1095 " --> pdb=" O TRP C1108 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C1110 " --> pdb=" O VAL C1093 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1157 through 1162 removed outlier: 3.581A pdb=" N ARG C1165 " --> pdb=" O PHE C1162 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1228 through 1235 Processing sheet with id=AF6, first strand: chain 'C' and resid 1293 through 1294 removed outlier: 3.571A pdb=" N ILE C1293 " --> pdb=" O VAL C1302 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N LEU C1301 " --> pdb=" O GLU C1605 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU C1605 " --> pdb=" O LEU C1301 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 1313 through 1314 removed outlier: 6.652A pdb=" N VAL C1580 " --> pdb=" O ALA C1575 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA C1575 " --> pdb=" O VAL C1580 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C1574 " --> pdb=" O ASP C1513 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP C1513 " --> pdb=" O LYS C1574 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 1319 through 1325 removed outlier: 6.833A pdb=" N ASN C1320 " --> pdb=" O ASN C1337 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN C1337 " --> pdb=" O ASN C1320 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N GLY C1322 " --> pdb=" O ASN C1335 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASN C1335 " --> pdb=" O GLY C1322 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLY C1336 " --> pdb=" O ALA C1358 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ALA C1358 " --> pdb=" O GLY C1336 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N THR C1547 " --> pdb=" O ALA C1534 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 1340 through 1346 removed outlier: 3.816A pdb=" N GLN C1340 " --> pdb=" O HIS C1355 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C1346 " --> pdb=" O ASN C1349 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'C' and resid 1464 through 1465 removed outlier: 8.719A pdb=" N THR C1413 " --> pdb=" O ALA C1396 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA C1396 " --> pdb=" O THR C1413 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1401 through 1403 removed outlier: 7.014A pdb=" N SER C1496 " --> pdb=" O TYR C1402 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE C1452 " --> pdb=" O LEU C1440 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 1705 through 1712 removed outlier: 3.589A pdb=" N ASN C1781 " --> pdb=" O VAL C1663 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 1692 through 1698 removed outlier: 6.651A pdb=" N ILE C1680 " --> pdb=" O TYR C1694 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N SER C1696 " --> pdb=" O PHE C1678 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N PHE C1678 " --> pdb=" O SER C1696 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 1763 through 1765 Processing sheet with id=AG6, first strand: chain 'C' and resid 1840 through 1841 Processing sheet with id=AG7, first strand: chain 'C' and resid 2175 through 2177 Processing sheet with id=AG8, first strand: chain 'C' and resid 2360 through 2367 removed outlier: 5.405A pdb=" N THR C2535 " --> pdb=" O LEU C2436 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N LEU C2436 " --> pdb=" O THR C2535 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 2396 through 2399 Processing sheet with id=AH1, first strand: chain 'D' and resid 159 through 160 Processing sheet with id=AH2, first strand: chain 'D' and resid 299 through 300 removed outlier: 5.471A pdb=" N MET D 299 " --> pdb=" O SER D 316 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N GLY D 318 " --> pdb=" O MET D 299 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY D 412 " --> pdb=" O PHE D 434 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 347 through 351 removed outlier: 5.940A pdb=" N GLN D 356 " --> pdb=" O TYR D 400 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N TYR D 400 " --> pdb=" O GLN D 356 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE D 358 " --> pdb=" O SER D 398 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'D' and resid 382 through 386 Processing sheet with id=AH5, first strand: chain 'D' and resid 543 through 545 Processing sheet with id=AH6, first strand: chain 'D' and resid 1144 through 1146 removed outlier: 4.852A pdb=" N TYR D1120 " --> pdb=" O ILE D1146 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D1106 " --> pdb=" O HIS D1097 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N HIS D1097 " --> pdb=" O LEU D1106 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TRP D1108 " --> pdb=" O ALA D1095 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA D1095 " --> pdb=" O TRP D1108 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N VAL D1110 " --> pdb=" O VAL D1093 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 1157 through 1162 removed outlier: 3.526A pdb=" N PHE D1162 " --> pdb=" O ARG D1165 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG D1165 " --> pdb=" O PHE D1162 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'D' and resid 1228 through 1235 Processing sheet with id=AH9, first strand: chain 'D' and resid 1293 through 1294 removed outlier: 3.589A pdb=" N ILE D1293 " --> pdb=" O VAL D1302 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU D1301 " --> pdb=" O GLU D1605 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLU D1605 " --> pdb=" O LEU D1301 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'D' and resid 1313 through 1314 removed outlier: 6.459A pdb=" N VAL D1580 " --> pdb=" O ALA D1575 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA D1575 " --> pdb=" O VAL D1580 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP D1513 " --> pdb=" O LYS D1574 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'D' and resid 1319 through 1325 removed outlier: 6.588A pdb=" N GLY D1336 " --> pdb=" O MET D1321 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER D1323 " --> pdb=" O GLU D1334 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLU D1334 " --> pdb=" O SER D1323 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE D1325 " --> pdb=" O VAL D1332 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL D1332 " --> pdb=" O ILE D1325 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY D1336 " --> pdb=" O ALA D1358 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ALA D1358 " --> pdb=" O GLY D1336 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR D1547 " --> pdb=" O ALA D1534 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'D' and resid 1340 through 1346 removed outlier: 3.816A pdb=" N GLN D1340 " --> pdb=" O HIS D1355 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER D1346 " --> pdb=" O ASN D1349 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'D' and resid 1464 through 1465 removed outlier: 8.780A pdb=" N THR D1413 " --> pdb=" O ALA D1396 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N ALA D1396 " --> pdb=" O THR D1413 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'D' and resid 1400 through 1403 removed outlier: 3.551A pdb=" N LYS D1400 " --> pdb=" O GLN D1498 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N SER D1496 " --> pdb=" O TYR D1402 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'D' and resid 1705 through 1712 Processing sheet with id=AI7, first strand: chain 'D' and resid 1692 through 1698 removed outlier: 6.593A pdb=" N ILE D1680 " --> pdb=" O TYR D1694 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER D1696 " --> pdb=" O PHE D1678 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N PHE D1678 " --> pdb=" O SER D1696 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'D' and resid 1763 through 1765 Processing sheet with id=AI9, first strand: chain 'D' and resid 1840 through 1841 Processing sheet with id=AJ1, first strand: chain 'D' and resid 2360 through 2367 removed outlier: 6.637A pdb=" N ILE D2529 " --> pdb=" O VAL D2441 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL D2441 " --> pdb=" O ILE D2529 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS D2531 " --> pdb=" O VAL D2439 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL D2439 " --> pdb=" O HIS D2531 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ARG D2533 " --> pdb=" O LYS D2437 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 2396 through 2399 Processing sheet with id=AJ3, first strand: chain 'E' and resid 159 through 160 Processing sheet with id=AJ4, first strand: chain 'E' and resid 299 through 300 removed outlier: 5.364A pdb=" N MET E 299 " --> pdb=" O SER E 316 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N GLY E 318 " --> pdb=" O MET E 299 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLY E 431 " --> pdb=" O THR E 337 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE E 434 " --> pdb=" O GLY E 412 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY E 412 " --> pdb=" O PHE E 434 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'E' and resid 346 through 351 removed outlier: 3.717A pdb=" N TYR E 346 " --> pdb=" O ALA E 361 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N GLN E 356 " --> pdb=" O TYR E 400 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR E 400 " --> pdb=" O GLN E 356 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE E 358 " --> pdb=" O SER E 398 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'E' and resid 382 through 386 Processing sheet with id=AJ7, first strand: chain 'E' and resid 543 through 545 Processing sheet with id=AJ8, first strand: chain 'E' and resid 1144 through 1146 removed outlier: 4.863A pdb=" N TYR E1120 " --> pdb=" O ILE E1146 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU E1106 " --> pdb=" O HIS E1097 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N HIS E1097 " --> pdb=" O LEU E1106 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TRP E1108 " --> pdb=" O ALA E1095 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ALA E1095 " --> pdb=" O TRP E1108 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL E1110 " --> pdb=" O VAL E1093 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'E' and resid 1157 through 1162 removed outlier: 3.617A pdb=" N PHE E1162 " --> pdb=" O ARG E1165 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG E1165 " --> pdb=" O PHE E1162 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'E' and resid 1228 through 1235 Processing sheet with id=AK2, first strand: chain 'E' and resid 1293 through 1294 removed outlier: 3.523A pdb=" N ILE E1293 " --> pdb=" O VAL E1302 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU E1301 " --> pdb=" O GLU E1605 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU E1605 " --> pdb=" O LEU E1301 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'E' and resid 1313 through 1314 removed outlier: 6.272A pdb=" N VAL E1580 " --> pdb=" O ALA E1575 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA E1575 " --> pdb=" O VAL E1580 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS E1574 " --> pdb=" O ASP E1513 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASP E1513 " --> pdb=" O LYS E1574 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'E' and resid 1319 through 1325 removed outlier: 6.706A pdb=" N GLY E1336 " --> pdb=" O MET E1321 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER E1323 " --> pdb=" O GLU E1334 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU E1334 " --> pdb=" O SER E1323 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE E1325 " --> pdb=" O VAL E1332 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N VAL E1332 " --> pdb=" O ILE E1325 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY E1336 " --> pdb=" O ALA E1358 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA E1358 " --> pdb=" O GLY E1336 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'E' and resid 1340 through 1346 removed outlier: 3.773A pdb=" N GLN E1340 " --> pdb=" O HIS E1355 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'E' and resid 1464 through 1465 removed outlier: 8.909A pdb=" N THR E1413 " --> pdb=" O ALA E1396 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N ALA E1396 " --> pdb=" O THR E1413 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'E' and resid 1401 through 1403 removed outlier: 6.929A pdb=" N SER E1496 " --> pdb=" O TYR E1402 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'E' and resid 1705 through 1712 removed outlier: 4.656A pdb=" N PHE E1659 " --> pdb=" O ALA E1785 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'E' and resid 1692 through 1698 removed outlier: 6.740A pdb=" N ILE E1680 " --> pdb=" O TYR E1694 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N SER E1696 " --> pdb=" O PHE E1678 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N PHE E1678 " --> pdb=" O SER E1696 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'E' and resid 1763 through 1765 Processing sheet with id=AL2, first strand: chain 'E' and resid 1840 through 1841 Processing sheet with id=AL3, first strand: chain 'E' and resid 2360 through 2367 removed outlier: 6.625A pdb=" N ILE E2529 " --> pdb=" O VAL E2441 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL E2441 " --> pdb=" O ILE E2529 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS E2531 " --> pdb=" O VAL E2439 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL E2439 " --> pdb=" O HIS E2531 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG E2533 " --> pdb=" O LYS E2437 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'E' and resid 2396 through 2399 5416 hydrogen bonds defined for protein. 15399 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: 77.74 Time building geometry restraints manager: 32.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 33300 1.34 - 1.46: 23587 1.46 - 1.58: 44508 1.58 - 1.70: 0 1.70 - 1.82: 670 Bond restraints: 102065 Sorted by residual: bond pdb=" CG PRO C 798 " pdb=" CD PRO C 798 " ideal model delta sigma weight residual 1.503 1.355 0.148 3.40e-02 8.65e+02 1.88e+01 bond pdb=" C ASN D 822 " pdb=" N PRO D 823 " ideal model delta sigma weight residual 1.334 1.353 -0.019 8.40e-03 1.42e+04 5.16e+00 bond pdb=" C SER A1457 " pdb=" N PRO A1458 " ideal model delta sigma weight residual 1.331 1.358 -0.028 1.31e-02 5.83e+03 4.49e+00 bond pdb=" CG PRO D1455 " pdb=" CD PRO D1455 " ideal model delta sigma weight residual 1.503 1.568 -0.065 3.40e-02 8.65e+02 3.64e+00 bond pdb=" C SER B1457 " pdb=" N PRO B1458 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.34e-02 5.57e+03 3.53e+00 ... (remaining 102060 not shown) Histogram of bond angle deviations from ideal: 91.30 - 102.91: 543 102.91 - 114.51: 61171 114.51 - 126.12: 75466 126.12 - 137.73: 1375 137.73 - 149.34: 15 Bond angle restraints: 138570 Sorted by residual: angle pdb=" C THR D2515 " pdb=" N ASP D2516 " pdb=" CA ASP D2516 " ideal model delta sigma weight residual 121.70 149.34 -27.64 1.80e+00 3.09e-01 2.36e+02 angle pdb=" C GLN D 26 " pdb=" N TYR D 27 " pdb=" CA TYR D 27 " ideal model delta sigma weight residual 121.70 148.61 -26.91 1.80e+00 3.09e-01 2.24e+02 angle pdb=" C GLN B 26 " pdb=" N TYR B 27 " pdb=" CA TYR B 27 " ideal model delta sigma weight residual 121.70 148.22 -26.52 1.80e+00 3.09e-01 2.17e+02 angle pdb=" C GLN E 26 " pdb=" N TYR E 27 " pdb=" CA TYR E 27 " ideal model delta sigma weight residual 121.70 148.18 -26.48 1.80e+00 3.09e-01 2.16e+02 angle pdb=" C GLN C 26 " pdb=" N TYR C 27 " pdb=" CA TYR C 27 " ideal model delta sigma weight residual 121.70 148.03 -26.33 1.80e+00 3.09e-01 2.14e+02 ... (remaining 138565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 53565 17.97 - 35.94: 5779 35.94 - 53.91: 1261 53.91 - 71.87: 322 71.87 - 89.84: 113 Dihedral angle restraints: 61040 sinusoidal: 23980 harmonic: 37060 Sorted by residual: dihedral pdb=" CA SER B 398 " pdb=" C SER B 398 " pdb=" N ASN B 399 " pdb=" CA ASN B 399 " ideal model delta harmonic sigma weight residual 180.00 145.73 34.27 0 5.00e+00 4.00e-02 4.70e+01 dihedral pdb=" CA SER E 398 " pdb=" C SER E 398 " pdb=" N ASN E 399 " pdb=" CA ASN E 399 " ideal model delta harmonic sigma weight residual 180.00 146.30 33.70 0 5.00e+00 4.00e-02 4.54e+01 dihedral pdb=" CA SER A 398 " pdb=" C SER A 398 " pdb=" N ASN A 399 " pdb=" CA ASN A 399 " ideal model delta harmonic sigma weight residual 180.00 146.38 33.62 0 5.00e+00 4.00e-02 4.52e+01 ... (remaining 61037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 13386 0.059 - 0.119: 1987 0.119 - 0.178: 153 0.178 - 0.237: 2 0.237 - 0.297: 2 Chirality restraints: 15530 Sorted by residual: chirality pdb=" CB THR A1460 " pdb=" CA THR A1460 " pdb=" OG1 THR A1460 " pdb=" CG2 THR A1460 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB THR B1460 " pdb=" CA THR B1460 " pdb=" OG1 THR B1460 " pdb=" CG2 THR B1460 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA ASP A 338 " pdb=" N ASP A 338 " pdb=" C ASP A 338 " pdb=" CB ASP A 338 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 15527 not shown) Planarity restraints: 18005 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER E1457 " 0.080 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO E1458 " -0.207 5.00e-02 4.00e+02 pdb=" CA PRO E1458 " 0.062 5.00e-02 4.00e+02 pdb=" CD PRO E1458 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B1457 " -0.072 5.00e-02 4.00e+02 1.09e-01 1.90e+01 pdb=" N PRO B1458 " 0.188 5.00e-02 4.00e+02 pdb=" CA PRO B1458 " -0.057 5.00e-02 4.00e+02 pdb=" CD PRO B1458 " -0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1457 " 0.054 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO A1458 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A1458 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1458 " 0.047 5.00e-02 4.00e+02 ... (remaining 18002 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1443 2.67 - 3.23: 93857 3.23 - 3.79: 157282 3.79 - 4.34: 218112 4.34 - 4.90: 364938 Nonbonded interactions: 835632 Sorted by model distance: nonbonded pdb=" OH TYR B1039 " pdb=" O GLU B1982 " model vdw 2.114 2.440 nonbonded pdb=" OH TYR A1039 " pdb=" O GLU A1982 " model vdw 2.119 2.440 nonbonded pdb=" OG1 THR D1624 " pdb=" OH TYR D1802 " model vdw 2.140 2.440 nonbonded pdb=" OH TYR C1039 " pdb=" O GLU C1982 " model vdw 2.141 2.440 nonbonded pdb=" OH TYR E1039 " pdb=" O GLU E1982 " model vdw 2.144 2.440 ... (remaining 835627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 13.220 Check model and map are aligned: 1.130 Set scattering table: 0.730 Process input model: 244.900 Find NCS groups from input model: 5.980 Set up NCS constraints: 0.540 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: 0.030 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 271.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 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 : 0.004 0.148 102065 Z= 0.273 Angle : 0.646 27.638 138570 Z= 0.367 Chirality : 0.042 0.297 15530 Planarity : 0.004 0.120 18005 Dihedral : 16.173 89.843 37230 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.28 % Favored : 95.42 % Rotamer: Outliers : 0.16 % Allowed : 16.62 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.49 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.08), residues: 12675 helix: 2.22 (0.07), residues: 5750 sheet: -0.09 (0.11), residues: 2075 loop : -1.29 (0.09), residues: 4850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1143 HIS 0.006 0.001 HIS A 130 PHE 0.024 0.002 PHE C 347 TYR 0.024 0.001 TYR A 416 ARG 0.013 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 669 time to evaluate : 8.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1436 ARG cc_start: 0.6639 (ptm-80) cc_final: 0.6201 (ttp80) REVERT: A 1519 MET cc_start: 0.8020 (mpp) cc_final: 0.7502 (mpp) REVERT: A 1738 TRP cc_start: 0.8749 (m100) cc_final: 0.8537 (m100) REVERT: B 1428 HIS cc_start: 0.6170 (m90) cc_final: 0.5737 (m90) REVERT: B 1436 ARG cc_start: 0.6899 (ttp80) cc_final: 0.6580 (ttp-110) REVERT: C 2092 MET cc_start: 0.8188 (mmm) cc_final: 0.7960 (tpp) REVERT: E 801 GLN cc_start: 0.7488 (mm-40) cc_final: 0.7261 (mm-40) REVERT: E 1421 TYR cc_start: 0.6546 (m-10) cc_final: 0.6043 (m-10) outliers start: 17 outliers final: 9 residues processed: 683 average time/residue: 0.9039 time to fit residues: 1072.2068 Evaluate side-chains 656 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 647 time to evaluate : 8.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 2306 MET Chi-restraints excluded: chain C residue 2411 ILE Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain E residue 961 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 1068 optimal weight: 10.0000 chunk 958 optimal weight: 6.9990 chunk 532 optimal weight: 6.9990 chunk 327 optimal weight: 6.9990 chunk 646 optimal weight: 20.0000 chunk 512 optimal weight: 4.9990 chunk 991 optimal weight: 3.9990 chunk 383 optimal weight: 2.9990 chunk 602 optimal weight: 3.9990 chunk 737 optimal weight: 7.9990 chunk 1148 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN A 507 ASN A 921 ASN ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 HIS B 323 ASN B 354 ASN ** B1416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN B2240 GLN B2318 ASN C 213 HIS ** C 513 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 ASN C1299 ASN C1688 ASN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1661 ASN D2160 GLN ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1299 ASN E1401 HIS E1795 ASN E1815 GLN E1934 GLN E2160 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.0635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 102065 Z= 0.441 Angle : 0.646 17.524 138570 Z= 0.344 Chirality : 0.045 0.185 15530 Planarity : 0.005 0.098 18005 Dihedral : 4.931 42.818 13921 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.05 % Favored : 94.66 % Rotamer: Outliers : 2.97 % Allowed : 15.98 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.42 (0.07), residues: 12675 helix: 1.86 (0.07), residues: 5775 sheet: -0.24 (0.11), residues: 2085 loop : -1.48 (0.09), residues: 4815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C1143 HIS 0.008 0.002 HIS C 762 PHE 0.025 0.002 PHE E1196 TYR 0.027 0.002 TYR A 416 ARG 0.007 0.001 ARG D1026 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 694 time to evaluate : 8.585 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 437 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7464 (mt-10) REVERT: A 507 ASN cc_start: 0.8633 (OUTLIER) cc_final: 0.8396 (p0) REVERT: A 745 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7438 (mm) REVERT: A 845 MET cc_start: 0.8557 (mtp) cc_final: 0.8173 (mtp) REVERT: A 1162 PHE cc_start: 0.8826 (OUTLIER) cc_final: 0.8488 (p90) REVERT: A 1333 MET cc_start: 0.8505 (ttm) cc_final: 0.8239 (ttm) REVERT: A 1436 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.5964 (ttp80) REVERT: A 1519 MET cc_start: 0.8102 (mpp) cc_final: 0.7704 (mpp) REVERT: A 1698 MET cc_start: 0.8761 (tpp) cc_final: 0.8546 (mmm) REVERT: A 1757 ASP cc_start: 0.7807 (OUTLIER) cc_final: 0.7399 (t0) REVERT: A 1935 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7747 (pp30) REVERT: A 2423 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7678 (m-80) REVERT: B 95 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.8323 (mtp) REVERT: B 284 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8316 (mtmt) REVERT: B 776 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8726 (mp) REVERT: B 1011 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8297 (p0) REVERT: B 1162 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8130 (p90) REVERT: B 1373 LYS cc_start: 0.7253 (mmtt) cc_final: 0.7050 (mmpt) REVERT: B 1428 HIS cc_start: 0.6105 (m90) cc_final: 0.5833 (m90) REVERT: B 2364 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7576 (tpt90) REVERT: B 2373 GLN cc_start: 0.7436 (tp40) cc_final: 0.7055 (mm-40) REVERT: C 47 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7438 (ttp-170) REVERT: C 360 ARG cc_start: 0.8266 (ttt180) cc_final: 0.7860 (ttt180) REVERT: C 1117 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8268 (mp) REVERT: C 1525 HIS cc_start: 0.7102 (OUTLIER) cc_final: 0.6730 (t-90) REVERT: C 2272 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8602 (mp) REVERT: C 2364 ARG cc_start: 0.8279 (OUTLIER) cc_final: 0.8042 (tpt-90) REVERT: D 27 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.6792 (t80) REVERT: D 229 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7872 (mt0) REVERT: D 333 THR cc_start: 0.9335 (OUTLIER) cc_final: 0.9119 (t) REVERT: D 415 ILE cc_start: 0.6893 (OUTLIER) cc_final: 0.6670 (tp) REVERT: D 904 LYS cc_start: 0.1448 (OUTLIER) cc_final: 0.0836 (ptmm) REVERT: D 1011 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8328 (p0) REVERT: D 1065 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (mp10) REVERT: D 1154 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8810 (mttt) REVERT: D 1266 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9231 (m) REVERT: D 1525 HIS cc_start: 0.6964 (m90) cc_final: 0.6674 (t-90) REVERT: D 1935 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7870 (pp30) REVERT: D 2040 VAL cc_start: 0.7816 (OUTLIER) cc_final: 0.7565 (m) REVERT: D 2272 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8763 (mp) REVERT: E 33 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8148 (tt) REVERT: E 165 SER cc_start: 0.9239 (OUTLIER) cc_final: 0.9020 (t) REVERT: E 243 SER cc_start: 0.8937 (OUTLIER) cc_final: 0.8483 (t) REVERT: E 306 ASP cc_start: 0.6285 (m-30) cc_final: 0.5714 (m-30) REVERT: E 544 VAL cc_start: 0.8147 (m) cc_final: 0.7740 (p) REVERT: E 801 GLN cc_start: 0.7536 (mm-40) cc_final: 0.7194 (mm-40) REVERT: E 1011 ASP cc_start: 0.8776 (OUTLIER) cc_final: 0.8477 (p0) REVERT: E 1162 PHE cc_start: 0.8883 (OUTLIER) cc_final: 0.7751 (p90) REVERT: E 1421 TYR cc_start: 0.6674 (m-10) cc_final: 0.6238 (m-10) REVERT: E 1525 HIS cc_start: 0.7046 (m90) cc_final: 0.6564 (t-90) REVERT: E 2272 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8481 (mp) outliers start: 322 outliers final: 172 residues processed: 951 average time/residue: 0.8883 time to fit residues: 1486.2303 Evaluate side-chains 873 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 664 time to evaluate : 8.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1162 PHE Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1370 ILE Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1457 SER Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1757 ASP Chi-restraints excluded: chain A residue 1769 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 1948 THR Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2422 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain A residue 2526 SER Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 95 MET Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 337 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 761 CYS Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1279 THR Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1457 SER Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1561 THR Chi-restraints excluded: chain B residue 1576 LYS Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1780 LEU Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2031 VAL Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2318 ASN Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain B residue 2478 VAL Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 856 MET Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1117 LEU Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1399 VAL Chi-restraints excluded: chain C residue 1465 VAL Chi-restraints excluded: chain C residue 1488 SER Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2031 VAL Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2271 LEU Chi-restraints excluded: chain C residue 2272 LEU Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2364 ARG Chi-restraints excluded: chain C residue 2411 ILE Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2478 VAL Chi-restraints excluded: chain C residue 2515 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 543 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 771 VAL Chi-restraints excluded: chain D residue 904 LYS Chi-restraints excluded: chain D residue 1011 ASP Chi-restraints excluded: chain D residue 1065 GLN Chi-restraints excluded: chain D residue 1102 SER Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1154 LYS Chi-restraints excluded: chain D residue 1162 PHE Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1279 THR Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1685 VAL Chi-restraints excluded: chain D residue 1705 THR Chi-restraints excluded: chain D residue 1935 GLN Chi-restraints excluded: chain D residue 1948 THR Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2069 THR Chi-restraints excluded: chain D residue 2146 MET Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2351 VAL Chi-restraints excluded: chain D residue 2411 ILE Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain D residue 2501 VAL Chi-restraints excluded: chain D residue 2515 THR Chi-restraints excluded: chain E residue 27 TYR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 981 ILE Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1279 THR Chi-restraints excluded: chain E residue 1369 VAL Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1531 ASP Chi-restraints excluded: chain E residue 1581 LEU Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1705 THR Chi-restraints excluded: chain E residue 1754 LEU Chi-restraints excluded: chain E residue 1965 VAL Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2031 VAL Chi-restraints excluded: chain E residue 2272 LEU Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2422 ILE Chi-restraints excluded: chain E residue 2501 VAL Chi-restraints excluded: chain E residue 2515 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 638 optimal weight: 9.9990 chunk 356 optimal weight: 3.9990 chunk 956 optimal weight: 8.9990 chunk 782 optimal weight: 9.9990 chunk 316 optimal weight: 8.9990 chunk 1150 optimal weight: 10.0000 chunk 1243 optimal weight: 6.9990 chunk 1024 optimal weight: 1.9990 chunk 1141 optimal weight: 7.9990 chunk 392 optimal weight: 0.9980 chunk 923 optimal weight: 0.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 513 GLN ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN C1299 ASN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1401 HIS ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1299 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.0718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 102065 Z= 0.301 Angle : 0.571 17.453 138570 Z= 0.307 Chirality : 0.042 0.198 15530 Planarity : 0.004 0.087 18005 Dihedral : 4.722 41.976 13910 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.59 % Favored : 95.12 % Rotamer: Outliers : 3.04 % Allowed : 16.47 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.07), residues: 12675 helix: 2.02 (0.07), residues: 5760 sheet: -0.18 (0.11), residues: 2060 loop : -1.43 (0.09), residues: 4855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C1143 HIS 0.005 0.001 HIS C 762 PHE 0.022 0.002 PHE C1162 TYR 0.019 0.002 TYR A 416 ARG 0.005 0.000 ARG D1026 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1023 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 330 poor density : 693 time to evaluate : 10.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 243 SER cc_start: 0.9073 (OUTLIER) cc_final: 0.8576 (t) REVERT: A 537 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.6020 (m-10) REVERT: A 612 ASN cc_start: 0.8469 (OUTLIER) cc_final: 0.8173 (m-40) REVERT: A 626 LYS cc_start: 0.8188 (OUTLIER) cc_final: 0.7859 (ttmm) REVERT: A 745 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7558 (mm) REVERT: A 776 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8389 (mp) REVERT: A 830 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8317 (mtp) REVERT: A 845 MET cc_start: 0.8573 (mtp) cc_final: 0.8199 (mtp) REVERT: A 908 ASN cc_start: 0.7385 (OUTLIER) cc_final: 0.6770 (m-40) REVERT: A 1162 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8460 (p90) REVERT: A 1164 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7886 (mm-30) REVERT: A 1333 MET cc_start: 0.8506 (ttm) cc_final: 0.8195 (ttm) REVERT: A 1436 ARG cc_start: 0.6718 (ptm-80) cc_final: 0.6051 (ttp80) REVERT: A 1519 MET cc_start: 0.8072 (mpp) cc_final: 0.7706 (mpp) REVERT: A 1536 LEU cc_start: 0.8163 (OUTLIER) cc_final: 0.7706 (tt) REVERT: A 1757 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7386 (t0) REVERT: A 1935 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7609 (pp30) REVERT: A 2040 VAL cc_start: 0.7399 (OUTLIER) cc_final: 0.7122 (m) REVERT: A 2272 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8637 (mp) REVERT: A 2423 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7775 (m-80) REVERT: B 284 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8303 (mtmt) REVERT: B 516 ASP cc_start: 0.7266 (t70) cc_final: 0.6536 (t70) REVERT: B 776 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8731 (mp) REVERT: B 1011 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8257 (p0) REVERT: B 1129 ARG cc_start: 0.8897 (OUTLIER) cc_final: 0.8351 (mmt180) REVERT: B 1162 PHE cc_start: 0.8816 (OUTLIER) cc_final: 0.7933 (p90) REVERT: B 1164 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8229 (mm-30) REVERT: B 1991 TRP cc_start: 0.9637 (OUTLIER) cc_final: 0.9101 (m-10) REVERT: B 2373 GLN cc_start: 0.7452 (tp40) cc_final: 0.7095 (mm-40) REVERT: C 47 ARG cc_start: 0.8024 (OUTLIER) cc_final: 0.7448 (ttp-170) REVERT: C 360 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7920 (ttt180) REVERT: C 415 ILE cc_start: 0.6557 (OUTLIER) cc_final: 0.6287 (tp) REVERT: C 516 ASP cc_start: 0.7579 (t70) cc_final: 0.7252 (t70) REVERT: C 1400 LYS cc_start: 0.6336 (mttm) cc_final: 0.5341 (mmmt) REVERT: C 1402 TYR cc_start: 0.7525 (t80) cc_final: 0.7217 (t80) REVERT: C 1525 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6641 (t-90) REVERT: C 1935 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8071 (pp30) REVERT: D 27 TYR cc_start: 0.7763 (OUTLIER) cc_final: 0.6885 (t80) REVERT: D 33 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8069 (tt) REVERT: D 165 SER cc_start: 0.9106 (OUTLIER) cc_final: 0.8856 (t) REVERT: D 229 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7823 (mt0) REVERT: D 333 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9104 (t) REVERT: D 360 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.7999 (ttt-90) REVERT: D 415 ILE cc_start: 0.6521 (OUTLIER) cc_final: 0.6285 (tp) REVERT: D 776 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8653 (mp) REVERT: D 904 LYS cc_start: 0.1251 (OUTLIER) cc_final: 0.0766 (ptmm) REVERT: D 1011 ASP cc_start: 0.8565 (OUTLIER) cc_final: 0.8260 (p0) REVERT: D 1065 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.8272 (mp10) REVERT: D 1158 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8819 (ptp-110) REVERT: D 1266 THR cc_start: 0.9458 (OUTLIER) cc_final: 0.9233 (m) REVERT: D 1444 GLU cc_start: 0.4239 (OUTLIER) cc_final: 0.3626 (tt0) REVERT: D 1525 HIS cc_start: 0.6967 (m90) cc_final: 0.6682 (t-90) REVERT: D 1661 ASN cc_start: 0.8598 (m110) cc_final: 0.8373 (m-40) REVERT: D 1935 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7667 (pt0) REVERT: D 2040 VAL cc_start: 0.7815 (OUTLIER) cc_final: 0.7567 (m) REVERT: E 33 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8231 (tt) REVERT: E 165 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.9007 (t) REVERT: E 243 SER cc_start: 0.8858 (OUTLIER) cc_final: 0.8387 (t) REVERT: E 415 ILE cc_start: 0.6525 (OUTLIER) cc_final: 0.6219 (tp) REVERT: E 437 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7157 (mt-10) REVERT: E 544 VAL cc_start: 0.8147 (m) cc_final: 0.7755 (p) REVERT: E 801 GLN cc_start: 0.7522 (mm-40) cc_final: 0.7310 (mm-40) REVERT: E 1011 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8442 (p0) REVERT: E 1162 PHE cc_start: 0.8815 (OUTLIER) cc_final: 0.7497 (p90) REVERT: E 1421 TYR cc_start: 0.6644 (m-10) cc_final: 0.6185 (m-10) REVERT: E 1494 PHE cc_start: 0.6607 (m-80) cc_final: 0.6366 (m-80) REVERT: E 1525 HIS cc_start: 0.6995 (m90) cc_final: 0.6524 (t-90) REVERT: E 1757 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7173 (t0) outliers start: 330 outliers final: 202 residues processed: 960 average time/residue: 0.9486 time to fit residues: 1612.1064 Evaluate side-chains 916 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 663 time to evaluate : 9.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 537 PHE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1162 PHE Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1457 SER Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1639 ASP Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1757 ASP Chi-restraints excluded: chain A residue 1769 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2040 VAL Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1394 ILE Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1540 SER Chi-restraints excluded: chain B residue 1576 LYS Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2026 LEU Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1161 ILE Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1488 SER Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1935 GLN Chi-restraints excluded: chain C residue 1948 THR Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2031 VAL Chi-restraints excluded: chain C residue 2271 LEU Chi-restraints excluded: chain C residue 2306 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2411 ILE Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain C residue 2478 VAL Chi-restraints excluded: chain C residue 2515 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 317 THR Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 543 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 904 LYS Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1011 ASP Chi-restraints excluded: chain D residue 1065 GLN Chi-restraints excluded: chain D residue 1102 SER Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1158 ARG Chi-restraints excluded: chain D residue 1162 PHE Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1279 THR Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1370 ILE Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1685 VAL Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1935 GLN Chi-restraints excluded: chain D residue 1948 THR Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2161 VAL Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain D residue 2463 ILE Chi-restraints excluded: chain D residue 2475 SER Chi-restraints excluded: chain D residue 2501 VAL Chi-restraints excluded: chain D residue 2515 THR Chi-restraints excluded: chain E residue 27 TYR Chi-restraints excluded: chain E residue 33 LEU Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 862 ASN Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 981 ILE Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1130 MET Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1279 THR Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1412 ILE Chi-restraints excluded: chain E residue 1418 THR Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1531 ASP Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1748 THR Chi-restraints excluded: chain E residue 1757 ASP Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1948 THR Chi-restraints excluded: chain E residue 1965 VAL Chi-restraints excluded: chain E residue 1975 LEU Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2031 VAL Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2478 VAL Chi-restraints excluded: chain E residue 2501 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 1137 optimal weight: 6.9990 chunk 865 optimal weight: 5.9990 chunk 597 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 549 optimal weight: 4.9990 chunk 772 optimal weight: 8.9990 chunk 1154 optimal weight: 9.9990 chunk 1222 optimal weight: 7.9990 chunk 603 optimal weight: 0.8980 chunk 1094 optimal weight: 0.7980 chunk 329 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1446 ASN ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN B2318 ASN C 411 ASN C1299 ASN C1492 GLN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1397 ASN E 645 GLN E1815 GLN E2160 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.0819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 102065 Z= 0.212 Angle : 0.526 17.314 138570 Z= 0.284 Chirality : 0.040 0.217 15530 Planarity : 0.004 0.077 18005 Dihedral : 4.520 40.784 13910 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.82 % Favored : 94.90 % Rotamer: Outliers : 3.20 % Allowed : 16.81 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.78 (0.08), residues: 12675 helix: 2.25 (0.07), residues: 5765 sheet: -0.25 (0.11), residues: 2135 loop : -1.33 (0.09), residues: 4775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1143 HIS 0.005 0.001 HIS A2476 PHE 0.018 0.001 PHE D1162 TYR 0.015 0.001 TYR D1421 ARG 0.004 0.000 ARG D1026 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1042 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 694 time to evaluate : 8.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8607 (mt) REVERT: A 165 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8857 (t) REVERT: A 243 SER cc_start: 0.9019 (OUTLIER) cc_final: 0.8552 (t) REVERT: A 437 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7382 (mt-10) REVERT: A 612 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8224 (m-40) REVERT: A 626 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7741 (ttmm) REVERT: A 675 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6855 (mm-30) REVERT: A 745 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7495 (mm) REVERT: A 776 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8387 (mp) REVERT: A 830 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8305 (mtp) REVERT: A 845 MET cc_start: 0.8572 (mtp) cc_final: 0.8205 (mtp) REVERT: A 1011 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8207 (p0) REVERT: A 1164 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7790 (mm-30) REVERT: A 1333 MET cc_start: 0.8495 (ttm) cc_final: 0.8160 (ttm) REVERT: A 1436 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.6134 (ttp80) REVERT: A 1519 MET cc_start: 0.8004 (mpp) cc_final: 0.7709 (mpp) REVERT: A 1935 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7606 (pp30) REVERT: A 1991 TRP cc_start: 0.9534 (OUTLIER) cc_final: 0.8919 (m-90) REVERT: A 2364 ARG cc_start: 0.8042 (OUTLIER) cc_final: 0.7297 (tpt90) REVERT: A 2423 PHE cc_start: 0.8208 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: A 2513 ASP cc_start: 0.7208 (OUTLIER) cc_final: 0.6698 (t0) REVERT: B 284 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8317 (mtmt) REVERT: B 516 ASP cc_start: 0.7237 (t70) cc_final: 0.6879 (t70) REVERT: B 776 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8732 (mp) REVERT: B 822 ASN cc_start: 0.8142 (OUTLIER) cc_final: 0.7941 (t0) REVERT: B 1129 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8373 (mmt180) REVERT: B 1162 PHE cc_start: 0.8713 (OUTLIER) cc_final: 0.7963 (p90) REVERT: B 1164 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8193 (mm-30) REVERT: B 1991 TRP cc_start: 0.9628 (OUTLIER) cc_final: 0.9104 (m-10) REVERT: B 2092 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8340 (tpp) REVERT: B 2137 ASP cc_start: 0.7778 (t0) cc_final: 0.7453 (t70) REVERT: B 2364 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7684 (tpt90) REVERT: B 2373 GLN cc_start: 0.7447 (tp40) cc_final: 0.7090 (mm-40) REVERT: C 47 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7412 (ttp80) REVERT: C 315 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8857 (tp) REVERT: C 360 ARG cc_start: 0.8261 (ttt180) cc_final: 0.7928 (ttt180) REVERT: C 516 ASP cc_start: 0.7489 (t70) cc_final: 0.7110 (t70) REVERT: C 1400 LYS cc_start: 0.6320 (mttm) cc_final: 0.5324 (mmmt) REVERT: C 1525 HIS cc_start: 0.6985 (OUTLIER) cc_final: 0.6668 (t-90) REVERT: C 1935 GLN cc_start: 0.8594 (OUTLIER) cc_final: 0.7937 (pp30) REVERT: C 2272 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8658 (mp) REVERT: C 2351 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8640 (t) REVERT: D 27 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6792 (t80) REVERT: D 33 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8107 (tt) REVERT: D 165 SER cc_start: 0.9082 (OUTLIER) cc_final: 0.8841 (t) REVERT: D 229 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7799 (mt0) REVERT: D 333 THR cc_start: 0.9263 (OUTLIER) cc_final: 0.9054 (t) REVERT: D 360 ARG cc_start: 0.8395 (ttt-90) cc_final: 0.8021 (ttt-90) REVERT: D 415 ILE cc_start: 0.6454 (OUTLIER) cc_final: 0.6235 (tp) REVERT: D 776 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8669 (mp) REVERT: D 904 LYS cc_start: 0.1244 (OUTLIER) cc_final: 0.0733 (ptmm) REVERT: D 908 ASN cc_start: 0.6758 (OUTLIER) cc_final: 0.6506 (t0) REVERT: D 1011 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8207 (p0) REVERT: D 1065 GLN cc_start: 0.8478 (OUTLIER) cc_final: 0.8205 (mp10) REVERT: D 1266 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9234 (m) REVERT: D 1444 GLU cc_start: 0.4304 (OUTLIER) cc_final: 0.3634 (tt0) REVERT: D 1525 HIS cc_start: 0.6952 (m90) cc_final: 0.6717 (t-90) REVERT: D 1780 LEU cc_start: 0.8104 (mt) cc_final: 0.7771 (mt) REVERT: D 1935 GLN cc_start: 0.8259 (OUTLIER) cc_final: 0.7832 (pt0) REVERT: D 2040 VAL cc_start: 0.7811 (OUTLIER) cc_final: 0.7564 (m) REVERT: D 2373 GLN cc_start: 0.7306 (tp40) cc_final: 0.7030 (tp40) REVERT: D 2412 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7432 (mt-10) REVERT: E 243 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8359 (t) REVERT: E 415 ILE cc_start: 0.6644 (OUTLIER) cc_final: 0.6317 (tp) REVERT: E 437 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: E 544 VAL cc_start: 0.8135 (m) cc_final: 0.7722 (p) REVERT: E 764 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8145 (mtm) REVERT: E 801 GLN cc_start: 0.7511 (mm-40) cc_final: 0.7296 (mm-40) REVERT: E 1162 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7448 (p90) REVERT: E 1421 TYR cc_start: 0.6599 (m-10) cc_final: 0.6165 (m-10) REVERT: E 1494 PHE cc_start: 0.6625 (m-80) cc_final: 0.6370 (m-80) REVERT: E 1525 HIS cc_start: 0.6989 (m90) cc_final: 0.6521 (t-90) REVERT: E 1757 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7174 (t0) REVERT: E 2412 GLU cc_start: 0.7391 (mt-10) cc_final: 0.6859 (mp0) outliers start: 348 outliers final: 205 residues processed: 979 average time/residue: 0.8690 time to fit residues: 1492.7957 Evaluate side-chains 927 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 668 time to evaluate : 8.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1457 SER Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1639 ASP Chi-restraints excluded: chain A residue 1769 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 182 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 536 ILE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1279 THR Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1540 SER Chi-restraints excluded: chain B residue 1576 LYS Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2092 MET Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2318 ASN Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1161 ILE Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1399 VAL Chi-restraints excluded: chain C residue 1465 VAL Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1935 GLN Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2031 VAL Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2271 LEU Chi-restraints excluded: chain C residue 2272 LEU Chi-restraints excluded: chain C residue 2306 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2411 ILE Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain C residue 2478 VAL Chi-restraints excluded: chain C residue 2515 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 904 LYS Chi-restraints excluded: chain D residue 908 ASN Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain D residue 1011 ASP Chi-restraints excluded: chain D residue 1065 GLN Chi-restraints excluded: chain D residue 1102 SER Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1162 PHE Chi-restraints excluded: chain D residue 1220 ASP Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1279 THR Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1685 VAL Chi-restraints excluded: chain D residue 1705 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1935 GLN Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2069 THR Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain D residue 2501 VAL Chi-restraints excluded: chain D residue 2515 THR Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 862 ASN Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 981 ILE Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1279 THR Chi-restraints excluded: chain E residue 1399 VAL Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1412 ILE Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1531 ASP Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1705 THR Chi-restraints excluded: chain E residue 1754 LEU Chi-restraints excluded: chain E residue 1757 ASP Chi-restraints excluded: chain E residue 1786 THR Chi-restraints excluded: chain E residue 1812 MET Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1908 ASP Chi-restraints excluded: chain E residue 1965 VAL Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2031 VAL Chi-restraints excluded: chain E residue 2285 MET Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2478 VAL Chi-restraints excluded: chain E residue 2501 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 1018 optimal weight: 3.9990 chunk 694 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 910 optimal weight: 10.0000 chunk 504 optimal weight: 5.9990 chunk 1043 optimal weight: 4.9990 chunk 845 optimal weight: 9.9990 chunk 1 optimal weight: 0.3980 chunk 624 optimal weight: 10.0000 chunk 1097 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN ** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN C1299 ASN ** C1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1397 ASN ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1397 ASN E2160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 102065 Z= 0.324 Angle : 0.571 17.429 138570 Z= 0.306 Chirality : 0.042 0.213 15530 Planarity : 0.004 0.074 18005 Dihedral : 4.614 41.129 13909 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.97 % Favored : 94.74 % Rotamer: Outliers : 3.99 % Allowed : 16.59 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.65 (0.08), residues: 12675 helix: 2.11 (0.07), residues: 5760 sheet: -0.24 (0.11), residues: 2120 loop : -1.39 (0.09), residues: 4795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1143 HIS 0.005 0.001 HIS E 130 PHE 0.023 0.002 PHE C1162 TYR 0.018 0.002 TYR D1421 ARG 0.007 0.000 ARG C1129 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 687 time to evaluate : 8.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8553 (mt) REVERT: A 165 SER cc_start: 0.9187 (OUTLIER) cc_final: 0.8914 (t) REVERT: A 243 SER cc_start: 0.9066 (OUTLIER) cc_final: 0.8593 (t) REVERT: A 356 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7722 (mt0) REVERT: A 368 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7408 (mm-30) REVERT: A 437 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7454 (mt-10) REVERT: A 612 ASN cc_start: 0.8477 (OUTLIER) cc_final: 0.8244 (m-40) REVERT: A 626 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7863 (ttmm) REVERT: A 675 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6879 (mm-30) REVERT: A 745 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7530 (mm) REVERT: A 776 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8395 (mp) REVERT: A 830 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: A 845 MET cc_start: 0.8544 (mtp) cc_final: 0.8177 (mtp) REVERT: A 908 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6559 (m-40) REVERT: A 1164 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7885 (mm-30) REVERT: A 1333 MET cc_start: 0.8520 (ttm) cc_final: 0.8198 (ttm) REVERT: A 1436 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6159 (ttp80) REVERT: A 1519 MET cc_start: 0.8053 (mpp) cc_final: 0.7792 (mpp) REVERT: A 1536 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7656 (tt) REVERT: A 1757 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7414 (t0) REVERT: A 1935 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7623 (pp30) REVERT: A 1991 TRP cc_start: 0.9550 (OUTLIER) cc_final: 0.8908 (m-90) REVERT: A 2272 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8608 (mp) REVERT: A 2364 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7218 (tpt90) REVERT: A 2389 PHE cc_start: 0.8326 (m-10) cc_final: 0.8076 (m-10) REVERT: A 2423 PHE cc_start: 0.8248 (OUTLIER) cc_final: 0.7823 (m-80) REVERT: A 2513 ASP cc_start: 0.7145 (OUTLIER) cc_final: 0.6624 (t0) REVERT: B 33 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8198 (tt) REVERT: B 284 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8313 (mtmt) REVERT: B 516 ASP cc_start: 0.7288 (t70) cc_final: 0.6741 (t70) REVERT: B 550 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: B 689 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5844 (mt-10) REVERT: B 776 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8736 (mp) REVERT: B 822 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7941 (t0) REVERT: B 1011 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.8083 (p0) REVERT: B 1129 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8181 (mmt180) REVERT: B 1162 PHE cc_start: 0.8820 (OUTLIER) cc_final: 0.7975 (p90) REVERT: B 1164 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8223 (mm-30) REVERT: B 1991 TRP cc_start: 0.9642 (OUTLIER) cc_final: 0.9103 (m-10) REVERT: B 2092 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8390 (tpp) REVERT: B 2137 ASP cc_start: 0.7797 (t0) cc_final: 0.7464 (t70) REVERT: B 2364 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7663 (tpt90) REVERT: B 2373 GLN cc_start: 0.7466 (tp40) cc_final: 0.7099 (mm-40) REVERT: C 47 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7383 (ttp80) REVERT: C 86 ASP cc_start: 0.6703 (OUTLIER) cc_final: 0.6226 (t70) REVERT: C 227 MET cc_start: 0.8352 (ttt) cc_final: 0.8119 (tpp) REVERT: C 356 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7392 (mp10) REVERT: C 360 ARG cc_start: 0.8298 (ttt180) cc_final: 0.7952 (ttt180) REVERT: C 415 ILE cc_start: 0.6773 (OUTLIER) cc_final: 0.6523 (tp) REVERT: C 776 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8605 (mp) REVERT: C 1525 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6717 (t-90) REVERT: C 1935 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8009 (pp30) REVERT: C 2237 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.8331 (mtt) REVERT: C 2272 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8637 (mp) REVERT: C 2351 VAL cc_start: 0.9010 (OUTLIER) cc_final: 0.8650 (t) REVERT: D 27 TYR cc_start: 0.7627 (OUTLIER) cc_final: 0.6771 (t80) REVERT: D 33 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8039 (tt) REVERT: D 165 SER cc_start: 0.9134 (OUTLIER) cc_final: 0.8884 (t) REVERT: D 229 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.7839 (mt0) REVERT: D 333 THR cc_start: 0.9271 (OUTLIER) cc_final: 0.9052 (t) REVERT: D 415 ILE cc_start: 0.6575 (OUTLIER) cc_final: 0.6351 (tp) REVERT: D 776 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8664 (mp) REVERT: D 904 LYS cc_start: 0.1345 (OUTLIER) cc_final: 0.0799 (ptmm) REVERT: D 908 ASN cc_start: 0.6783 (OUTLIER) cc_final: 0.6537 (t0) REVERT: D 1011 ASP cc_start: 0.8537 (OUTLIER) cc_final: 0.8228 (p0) REVERT: D 1065 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8253 (mp10) REVERT: D 1158 ARG cc_start: 0.9258 (OUTLIER) cc_final: 0.8795 (ptp-110) REVERT: D 1266 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9239 (m) REVERT: D 1444 GLU cc_start: 0.4473 (OUTLIER) cc_final: 0.3902 (tt0) REVERT: D 1525 HIS cc_start: 0.7031 (OUTLIER) cc_final: 0.6730 (t-90) REVERT: D 1780 LEU cc_start: 0.8121 (mt) cc_final: 0.7779 (mt) REVERT: D 1935 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: D 2040 VAL cc_start: 0.7838 (OUTLIER) cc_final: 0.7605 (m) REVERT: D 2272 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8432 (mp) REVERT: D 2412 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7402 (mt-10) REVERT: E 20 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7755 (ttm) REVERT: E 165 SER cc_start: 0.9241 (OUTLIER) cc_final: 0.9024 (t) REVERT: E 227 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7627 (tpp) REVERT: E 243 SER cc_start: 0.8885 (OUTLIER) cc_final: 0.8402 (t) REVERT: E 415 ILE cc_start: 0.6755 (OUTLIER) cc_final: 0.6448 (tp) REVERT: E 437 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: E 544 VAL cc_start: 0.8155 (m) cc_final: 0.7744 (p) REVERT: E 801 GLN cc_start: 0.7443 (mm-40) cc_final: 0.7200 (mm-40) REVERT: E 1003 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8268 (mtt180) REVERT: E 1011 ASP cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (p0) REVERT: E 1162 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7566 (p90) REVERT: E 1174 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: E 1421 TYR cc_start: 0.6489 (m-10) cc_final: 0.6177 (m-10) REVERT: E 1494 PHE cc_start: 0.6824 (m-80) cc_final: 0.6484 (m-80) REVERT: E 1525 HIS cc_start: 0.6992 (m90) cc_final: 0.6527 (t-90) REVERT: E 1757 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7187 (t0) REVERT: E 2272 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8436 (mp) REVERT: E 2364 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6979 (tpt90) REVERT: E 2423 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.6820 (m-80) outliers start: 433 outliers final: 289 residues processed: 1039 average time/residue: 0.8631 time to fit residues: 1590.9358 Evaluate side-chains 1040 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 367 poor density : 673 time to evaluate : 8.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1399 VAL Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1457 SER Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1757 ASP Chi-restraints excluded: chain A residue 1769 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 1948 THR Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1978 LEU Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain A residue 2526 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 413 VAL Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1279 THR Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1413 THR Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1540 SER Chi-restraints excluded: chain B residue 1576 LYS Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1638 ILE Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1786 THR Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2031 VAL Chi-restraints excluded: chain B residue 2040 VAL Chi-restraints excluded: chain B residue 2092 MET Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2351 VAL Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain B residue 2478 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1161 ILE Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1399 VAL Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1465 VAL Chi-restraints excluded: chain C residue 1488 SER Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1639 ASP Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1935 GLN Chi-restraints excluded: chain C residue 1948 THR Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2031 VAL Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2237 MET Chi-restraints excluded: chain C residue 2271 LEU Chi-restraints excluded: chain C residue 2272 LEU Chi-restraints excluded: chain C residue 2306 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain C residue 2478 VAL Chi-restraints excluded: chain C residue 2515 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 543 THR Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 904 LYS Chi-restraints excluded: chain D residue 908 ASN Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 978 SER Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain D residue 1011 ASP Chi-restraints excluded: chain D residue 1022 THR Chi-restraints excluded: chain D residue 1065 GLN Chi-restraints excluded: chain D residue 1102 SER Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1158 ARG Chi-restraints excluded: chain D residue 1162 PHE Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain D residue 1220 ASP Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1279 THR Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1370 ILE Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1525 HIS Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1685 VAL Chi-restraints excluded: chain D residue 1705 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1765 THR Chi-restraints excluded: chain D residue 1784 ILE Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1935 GLN Chi-restraints excluded: chain D residue 1948 THR Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2069 THR Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain D residue 2463 ILE Chi-restraints excluded: chain D residue 2475 SER Chi-restraints excluded: chain D residue 2501 VAL Chi-restraints excluded: chain D residue 2515 THR Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 227 MET Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 856 MET Chi-restraints excluded: chain E residue 862 ASN Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 981 ILE Chi-restraints excluded: chain E residue 1003 ARG Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1130 MET Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1174 GLU Chi-restraints excluded: chain E residue 1279 THR Chi-restraints excluded: chain E residue 1399 VAL Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1412 ILE Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1457 SER Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1531 ASP Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1705 THR Chi-restraints excluded: chain E residue 1754 LEU Chi-restraints excluded: chain E residue 1757 ASP Chi-restraints excluded: chain E residue 1786 THR Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1948 THR Chi-restraints excluded: chain E residue 1965 VAL Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2027 LEU Chi-restraints excluded: chain E residue 2031 VAL Chi-restraints excluded: chain E residue 2041 LEU Chi-restraints excluded: chain E residue 2272 LEU Chi-restraints excluded: chain E residue 2364 ARG Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2423 PHE Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2478 VAL Chi-restraints excluded: chain E residue 2501 VAL Chi-restraints excluded: chain E residue 2515 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 411 optimal weight: 9.9990 chunk 1101 optimal weight: 1.9990 chunk 241 optimal weight: 9.9990 chunk 717 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 1223 optimal weight: 7.9990 chunk 1016 optimal weight: 6.9990 chunk 566 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 404 optimal weight: 5.9990 chunk 642 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1614 GLN B 762 HIS ** B1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN C1299 ASN ** C1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1446 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 102065 Z= 0.314 Angle : 0.566 17.442 138570 Z= 0.304 Chirality : 0.042 0.251 15530 Planarity : 0.004 0.071 18005 Dihedral : 4.621 40.776 13907 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.98 % Favored : 94.74 % Rotamer: Outliers : 4.17 % Allowed : 16.77 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.25 % Twisted General : 0.04 % 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: 0.62 (0.08), residues: 12675 helix: 2.11 (0.07), residues: 5750 sheet: -0.35 (0.11), residues: 2180 loop : -1.37 (0.09), residues: 4745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1143 HIS 0.007 0.001 HIS D1401 PHE 0.022 0.002 PHE C1162 TYR 0.017 0.002 TYR A 416 ARG 0.005 0.000 ARG A 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1150 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 453 poor density : 697 time to evaluate : 8.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8518 (mt) REVERT: A 165 SER cc_start: 0.9188 (OUTLIER) cc_final: 0.8917 (t) REVERT: A 243 SER cc_start: 0.9057 (OUTLIER) cc_final: 0.8587 (t) REVERT: A 328 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6953 (pt0) REVERT: A 437 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7485 (mt-10) REVERT: A 612 ASN cc_start: 0.8479 (OUTLIER) cc_final: 0.8245 (m-40) REVERT: A 626 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7897 (ttmm) REVERT: A 675 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6864 (mm-30) REVERT: A 745 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 776 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8397 (mp) REVERT: A 830 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8340 (mtp) REVERT: A 845 MET cc_start: 0.8543 (mtp) cc_final: 0.8185 (mtp) REVERT: A 908 ASN cc_start: 0.7127 (OUTLIER) cc_final: 0.6441 (m-40) REVERT: A 1164 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7882 (mm-30) REVERT: A 1333 MET cc_start: 0.8535 (ttm) cc_final: 0.8210 (ttm) REVERT: A 1436 ARG cc_start: 0.6815 (OUTLIER) cc_final: 0.6145 (ttp80) REVERT: A 1519 MET cc_start: 0.8047 (mpp) cc_final: 0.7793 (mpp) REVERT: A 1536 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7627 (tt) REVERT: A 1757 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7432 (t0) REVERT: A 1935 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7640 (pp30) REVERT: A 1991 TRP cc_start: 0.9545 (OUTLIER) cc_final: 0.8912 (m-90) REVERT: A 2272 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8614 (mp) REVERT: A 2364 ARG cc_start: 0.7938 (OUTLIER) cc_final: 0.7225 (tpt90) REVERT: A 2389 PHE cc_start: 0.8368 (m-10) cc_final: 0.8150 (m-10) REVERT: A 2423 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7830 (m-80) REVERT: A 2513 ASP cc_start: 0.7106 (OUTLIER) cc_final: 0.6599 (t0) REVERT: B 284 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8303 (mtmt) REVERT: B 516 ASP cc_start: 0.7288 (t70) cc_final: 0.6758 (t70) REVERT: B 689 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.5823 (mt-10) REVERT: B 776 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8739 (mp) REVERT: B 822 ASN cc_start: 0.8177 (OUTLIER) cc_final: 0.7933 (t0) REVERT: B 1011 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8076 (p0) REVERT: B 1129 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.8207 (mmt180) REVERT: B 1162 PHE cc_start: 0.8831 (OUTLIER) cc_final: 0.7925 (p90) REVERT: B 1164 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8225 (mm-30) REVERT: B 1991 TRP cc_start: 0.9640 (OUTLIER) cc_final: 0.9185 (m-10) REVERT: B 2092 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8394 (tpp) REVERT: B 2137 ASP cc_start: 0.7793 (t0) cc_final: 0.7442 (t70) REVERT: B 2364 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7741 (tpt90) REVERT: B 2373 GLN cc_start: 0.7345 (tp40) cc_final: 0.6975 (mm-40) REVERT: C 47 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7447 (ttp80) REVERT: C 86 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6362 (t70) REVERT: C 227 MET cc_start: 0.8371 (ttt) cc_final: 0.8140 (tpp) REVERT: C 315 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8854 (tp) REVERT: C 356 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.7380 (mp10) REVERT: C 360 ARG cc_start: 0.8314 (ttt180) cc_final: 0.7943 (ttt180) REVERT: C 374 ARG cc_start: 0.8053 (ttp80) cc_final: 0.7804 (ttp80) REVERT: C 415 ILE cc_start: 0.6766 (OUTLIER) cc_final: 0.6523 (tp) REVERT: C 516 ASP cc_start: 0.7465 (t70) cc_final: 0.7198 (t70) REVERT: C 776 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 1321 MET cc_start: 0.9230 (mmm) cc_final: 0.8994 (mmm) REVERT: C 1400 LYS cc_start: 0.6212 (mttm) cc_final: 0.5414 (mmmt) REVERT: C 1525 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6713 (t-90) REVERT: C 1764 MET cc_start: 0.7945 (tpt) cc_final: 0.7706 (mmm) REVERT: C 1935 GLN cc_start: 0.8620 (OUTLIER) cc_final: 0.7958 (pp30) REVERT: C 2237 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: C 2272 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8633 (mp) REVERT: D 27 TYR cc_start: 0.7631 (OUTLIER) cc_final: 0.6775 (t80) REVERT: D 33 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.8043 (tt) REVERT: D 165 SER cc_start: 0.9139 (OUTLIER) cc_final: 0.8890 (t) REVERT: D 229 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7829 (mt0) REVERT: D 333 THR cc_start: 0.9262 (OUTLIER) cc_final: 0.9053 (t) REVERT: D 415 ILE cc_start: 0.6580 (OUTLIER) cc_final: 0.6357 (tp) REVERT: D 776 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8647 (mp) REVERT: D 904 LYS cc_start: 0.1192 (OUTLIER) cc_final: 0.0816 (ptmm) REVERT: D 1011 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8218 (p0) REVERT: D 1065 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: D 1158 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8873 (ptp-110) REVERT: D 1266 THR cc_start: 0.9453 (OUTLIER) cc_final: 0.9234 (m) REVERT: D 1444 GLU cc_start: 0.4540 (OUTLIER) cc_final: 0.3991 (tt0) REVERT: D 1453 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.5784 (tm-30) REVERT: D 1525 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6720 (t-90) REVERT: D 1780 LEU cc_start: 0.8142 (mt) cc_final: 0.7826 (mt) REVERT: D 1935 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7739 (pt0) REVERT: D 2040 VAL cc_start: 0.7824 (OUTLIER) cc_final: 0.7601 (m) REVERT: D 2272 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8319 (mp) REVERT: D 2373 GLN cc_start: 0.7332 (tp40) cc_final: 0.7107 (tp40) REVERT: D 2412 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7429 (mt-10) REVERT: E 165 SER cc_start: 0.9242 (OUTLIER) cc_final: 0.9024 (t) REVERT: E 243 SER cc_start: 0.8882 (OUTLIER) cc_final: 0.8397 (t) REVERT: E 415 ILE cc_start: 0.6689 (OUTLIER) cc_final: 0.6432 (tp) REVERT: E 437 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7141 (mt-10) REVERT: E 544 VAL cc_start: 0.8144 (m) cc_final: 0.7735 (p) REVERT: E 801 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7305 (mm-40) REVERT: E 1003 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8290 (mtt180) REVERT: E 1162 PHE cc_start: 0.8888 (OUTLIER) cc_final: 0.7544 (p90) REVERT: E 1164 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8095 (mm-30) REVERT: E 1174 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: E 1421 TYR cc_start: 0.6631 (m-10) cc_final: 0.6295 (m-10) REVERT: E 1494 PHE cc_start: 0.6885 (m-80) cc_final: 0.6574 (m-80) REVERT: E 1525 HIS cc_start: 0.6994 (m90) cc_final: 0.6528 (t-90) REVERT: E 1757 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7200 (t0) REVERT: E 1970 ARG cc_start: 0.7411 (mmm-85) cc_final: 0.7133 (mmm-85) REVERT: E 2272 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8440 (mp) REVERT: E 2364 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.6927 (tpt90) REVERT: E 2423 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.6935 (m-80) REVERT: E 2519 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.7241 (ttmt) outliers start: 453 outliers final: 316 residues processed: 1065 average time/residue: 0.8654 time to fit residues: 1617.9081 Evaluate side-chains 1061 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 672 time to evaluate : 8.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 27 TYR Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 356 GLN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 540 ASP Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 626 LYS Chi-restraints excluded: chain A residue 671 ASN Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 830 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1028 SER Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1399 VAL Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1457 SER Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1478 LYS Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1639 ASP Chi-restraints excluded: chain A residue 1704 GLU Chi-restraints excluded: chain A residue 1757 ASP Chi-restraints excluded: chain A residue 1769 ILE Chi-restraints excluded: chain A residue 1770 VAL Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1935 GLN Chi-restraints excluded: chain A residue 1948 THR Chi-restraints excluded: chain A residue 1973 ASN Chi-restraints excluded: chain A residue 1978 LEU Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2178 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2272 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2478 VAL Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain A residue 2515 THR Chi-restraints excluded: chain A residue 2526 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 27 TYR Chi-restraints excluded: chain B residue 175 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 284 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 633 SER Chi-restraints excluded: chain B residue 647 THR Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 978 SER Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1003 ARG Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1279 THR Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1369 VAL Chi-restraints excluded: chain B residue 1430 MET Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1540 SER Chi-restraints excluded: chain B residue 1576 LYS Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1638 ILE Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1948 THR Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2031 VAL Chi-restraints excluded: chain B residue 2040 VAL Chi-restraints excluded: chain B residue 2092 MET Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain B residue 2478 VAL Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 226 VAL Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 356 GLN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 520 VAL Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 736 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 894 VAL Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 981 ILE Chi-restraints excluded: chain C residue 986 LEU Chi-restraints excluded: chain C residue 1022 THR Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1161 ILE Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1171 VAL Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1399 VAL Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1465 VAL Chi-restraints excluded: chain C residue 1488 SER Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1639 ASP Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1935 GLN Chi-restraints excluded: chain C residue 1948 THR Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2031 VAL Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2237 MET Chi-restraints excluded: chain C residue 2271 LEU Chi-restraints excluded: chain C residue 2272 LEU Chi-restraints excluded: chain C residue 2306 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2411 ILE Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain C residue 2478 VAL Chi-restraints excluded: chain C residue 2515 THR Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 269 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 315 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 415 ILE Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 536 ILE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 543 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 624 ASN Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 904 LYS Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 978 SER Chi-restraints excluded: chain D residue 986 LEU Chi-restraints excluded: chain D residue 1011 ASP Chi-restraints excluded: chain D residue 1022 THR Chi-restraints excluded: chain D residue 1028 SER Chi-restraints excluded: chain D residue 1065 GLN Chi-restraints excluded: chain D residue 1102 SER Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1158 ARG Chi-restraints excluded: chain D residue 1162 PHE Chi-restraints excluded: chain D residue 1171 VAL Chi-restraints excluded: chain D residue 1220 ASP Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1279 THR Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1370 ILE Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1453 GLU Chi-restraints excluded: chain D residue 1459 ASN Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1525 HIS Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1639 ASP Chi-restraints excluded: chain D residue 1685 VAL Chi-restraints excluded: chain D residue 1705 THR Chi-restraints excluded: chain D residue 1748 THR Chi-restraints excluded: chain D residue 1765 THR Chi-restraints excluded: chain D residue 1784 ILE Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1935 GLN Chi-restraints excluded: chain D residue 1948 THR Chi-restraints excluded: chain D residue 1978 LEU Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2069 THR Chi-restraints excluded: chain D residue 2161 VAL Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2361 GLU Chi-restraints excluded: chain D residue 2368 LEU Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain D residue 2463 ILE Chi-restraints excluded: chain D residue 2475 SER Chi-restraints excluded: chain D residue 2478 VAL Chi-restraints excluded: chain D residue 2501 VAL Chi-restraints excluded: chain D residue 2515 THR Chi-restraints excluded: chain E residue 27 TYR Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 243 SER Chi-restraints excluded: chain E residue 315 ILE Chi-restraints excluded: chain E residue 337 THR Chi-restraints excluded: chain E residue 343 ASN Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 415 ILE Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 427 THR Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 601 THR Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 856 MET Chi-restraints excluded: chain E residue 862 ASN Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 981 ILE Chi-restraints excluded: chain E residue 986 LEU Chi-restraints excluded: chain E residue 1003 ARG Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1130 MET Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1164 GLU Chi-restraints excluded: chain E residue 1171 VAL Chi-restraints excluded: chain E residue 1174 GLU Chi-restraints excluded: chain E residue 1279 THR Chi-restraints excluded: chain E residue 1399 VAL Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1412 ILE Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1457 SER Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1685 VAL Chi-restraints excluded: chain E residue 1705 THR Chi-restraints excluded: chain E residue 1748 THR Chi-restraints excluded: chain E residue 1754 LEU Chi-restraints excluded: chain E residue 1757 ASP Chi-restraints excluded: chain E residue 1786 THR Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1908 ASP Chi-restraints excluded: chain E residue 1948 THR Chi-restraints excluded: chain E residue 1965 VAL Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2027 LEU Chi-restraints excluded: chain E residue 2031 VAL Chi-restraints excluded: chain E residue 2271 LEU Chi-restraints excluded: chain E residue 2272 LEU Chi-restraints excluded: chain E residue 2285 MET Chi-restraints excluded: chain E residue 2364 ARG Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2422 ILE Chi-restraints excluded: chain E residue 2423 PHE Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2478 VAL Chi-restraints excluded: chain E residue 2501 VAL Chi-restraints excluded: chain E residue 2515 THR Chi-restraints excluded: chain E residue 2519 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 1180 optimal weight: 0.8980 chunk 137 optimal weight: 0.8980 chunk 697 optimal weight: 0.9990 chunk 893 optimal weight: 5.9990 chunk 692 optimal weight: 0.0970 chunk 1030 optimal weight: 0.9980 chunk 683 optimal weight: 7.9990 chunk 1219 optimal weight: 8.9990 chunk 763 optimal weight: 2.9990 chunk 743 optimal weight: 8.9990 chunk 562 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN A1539 ASN B 871 ASN B1311 GLN B1356 ASN ** B1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1388 GLN ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2262 GLN E 871 ASN E1356 ASN E2160 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 102065 Z= 0.138 Angle : 0.489 17.428 138570 Z= 0.266 Chirality : 0.038 0.211 15530 Planarity : 0.003 0.092 18005 Dihedral : 4.277 39.966 13907 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.27 % Favored : 95.50 % Rotamer: Outliers : 2.26 % Allowed : 18.72 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.08), residues: 12675 helix: 2.52 (0.07), residues: 5810 sheet: -0.22 (0.11), residues: 2140 loop : -1.24 (0.09), residues: 4725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1143 HIS 0.004 0.001 HIS D1401 PHE 0.018 0.001 PHE B1456 TYR 0.017 0.001 TYR B1481 ARG 0.004 0.000 ARG D2121 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 953 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 708 time to evaluate : 8.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 SER cc_start: 0.9108 (OUTLIER) cc_final: 0.8827 (t) REVERT: A 243 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8514 (t) REVERT: A 612 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8204 (m-40) REVERT: A 675 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6880 (mm-30) REVERT: A 686 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8184 (p) REVERT: A 745 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7517 (mm) REVERT: A 845 MET cc_start: 0.8478 (mtp) cc_final: 0.8130 (mtp) REVERT: A 908 ASN cc_start: 0.6807 (OUTLIER) cc_final: 0.6223 (m-40) REVERT: A 1011 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8166 (p0) REVERT: A 1023 VAL cc_start: 0.8960 (m) cc_final: 0.8753 (p) REVERT: A 1436 ARG cc_start: 0.6884 (OUTLIER) cc_final: 0.6382 (ttp80) REVERT: A 1519 MET cc_start: 0.8013 (mpp) cc_final: 0.7766 (mpp) REVERT: A 1536 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7593 (tt) REVERT: A 1698 MET cc_start: 0.8720 (mmt) cc_final: 0.8318 (mtp) REVERT: A 1989 ASP cc_start: 0.8282 (t0) cc_final: 0.8044 (t0) REVERT: A 1991 TRP cc_start: 0.9527 (OUTLIER) cc_final: 0.8888 (m-90) REVERT: A 2364 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7757 (ttt90) REVERT: A 2389 PHE cc_start: 0.8352 (m-10) cc_final: 0.8121 (m-10) REVERT: A 2423 PHE cc_start: 0.8200 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: A 2513 ASP cc_start: 0.7044 (OUTLIER) cc_final: 0.6544 (t0) REVERT: B 20 MET cc_start: 0.7847 (tpp) cc_final: 0.7571 (ttm) REVERT: B 314 ASN cc_start: 0.8347 (m110) cc_final: 0.8007 (m110) REVERT: B 516 ASP cc_start: 0.7203 (t70) cc_final: 0.6636 (t70) REVERT: B 776 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8750 (mp) REVERT: B 1011 ASP cc_start: 0.8301 (OUTLIER) cc_final: 0.7964 (p0) REVERT: B 1162 PHE cc_start: 0.8561 (OUTLIER) cc_final: 0.7884 (p90) REVERT: B 1991 TRP cc_start: 0.9608 (OUTLIER) cc_final: 0.9172 (m-10) REVERT: B 2137 ASP cc_start: 0.7729 (t0) cc_final: 0.7339 (t70) REVERT: B 2364 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7923 (tpt-90) REVERT: B 2373 GLN cc_start: 0.7237 (tp40) cc_final: 0.6890 (mm-40) REVERT: C 47 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7370 (ttp80) REVERT: C 315 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8764 (tp) REVERT: C 360 ARG cc_start: 0.8102 (ttt180) cc_final: 0.7895 (ttt180) REVERT: C 374 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7723 (ttp-170) REVERT: C 415 ILE cc_start: 0.6409 (OUTLIER) cc_final: 0.6152 (tp) REVERT: C 516 ASP cc_start: 0.7423 (t70) cc_final: 0.7092 (t70) REVERT: C 1402 TYR cc_start: 0.7254 (t80) cc_final: 0.6992 (t80) REVERT: C 1525 HIS cc_start: 0.6988 (m90) cc_final: 0.6688 (t-90) REVERT: C 1991 TRP cc_start: 0.9538 (OUTLIER) cc_final: 0.9151 (m-90) REVERT: C 2237 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8406 (mtt) REVERT: C 2351 VAL cc_start: 0.8923 (OUTLIER) cc_final: 0.8596 (t) REVERT: D 185 MET cc_start: 0.8623 (mmm) cc_final: 0.8276 (mmm) REVERT: D 229 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7807 (mt0) REVERT: D 399 ASN cc_start: 0.6799 (t0) cc_final: 0.6421 (t0) REVERT: D 776 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8625 (mp) REVERT: D 978 SER cc_start: 0.8769 (OUTLIER) cc_final: 0.8531 (p) REVERT: D 1444 GLU cc_start: 0.4131 (OUTLIER) cc_final: 0.3569 (tt0) REVERT: D 2040 VAL cc_start: 0.7794 (OUTLIER) cc_final: 0.7582 (m) REVERT: D 2272 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8356 (mp) REVERT: D 2373 GLN cc_start: 0.7438 (tp40) cc_final: 0.7183 (tp40) REVERT: D 2412 GLU cc_start: 0.7475 (mt-10) cc_final: 0.7175 (mt-10) REVERT: E 20 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7814 (ttm) REVERT: E 437 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7041 (mt-10) REVERT: E 801 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7269 (mm-40) REVERT: E 1011 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8323 (p0) REVERT: E 1162 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.7542 (p90) REVERT: E 1174 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7266 (mp0) REVERT: E 1421 TYR cc_start: 0.6601 (m-10) cc_final: 0.6174 (m-10) REVERT: E 1494 PHE cc_start: 0.6633 (m-80) cc_final: 0.6411 (m-80) REVERT: E 1525 HIS cc_start: 0.6973 (m90) cc_final: 0.6517 (t-90) REVERT: E 1970 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7132 (mmm-85) REVERT: E 2364 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.6851 (tpt90) REVERT: E 2412 GLU cc_start: 0.7352 (mt-10) cc_final: 0.6825 (mp0) REVERT: E 2423 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.6886 (m-80) REVERT: E 2519 LYS cc_start: 0.7602 (OUTLIER) cc_final: 0.7327 (ttmt) outliers start: 245 outliers final: 152 residues processed: 904 average time/residue: 0.9025 time to fit residues: 1425.3218 Evaluate side-chains 848 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 657 time to evaluate : 9.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1399 VAL Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1639 ASP Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1973 ASN Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1003 ARG Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1430 MET Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2040 VAL Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2275 LYS Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1399 VAL Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1465 VAL Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 1991 TRP Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2237 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 182 ASP Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 978 SER Chi-restraints excluded: chain D residue 1102 SER Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1639 ASP Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2161 VAL Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 182 ASP Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 418 TYR Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 862 ASN Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1174 GLU Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1457 SER Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1748 THR Chi-restraints excluded: chain E residue 1908 ASP Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2161 VAL Chi-restraints excluded: chain E residue 2364 ARG Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2423 PHE Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2501 VAL Chi-restraints excluded: chain E residue 2519 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 754 optimal weight: 9.9990 chunk 486 optimal weight: 10.0000 chunk 728 optimal weight: 0.8980 chunk 367 optimal weight: 0.2980 chunk 239 optimal weight: 20.0000 chunk 236 optimal weight: 5.9990 chunk 775 optimal weight: 0.9990 chunk 830 optimal weight: 8.9990 chunk 602 optimal weight: 3.9990 chunk 113 optimal weight: 10.0000 chunk 958 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1388 GLN A1446 ASN A1756 ASN ** B1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1401 HIS D1498 GLN D2262 GLN E 323 ASN E 354 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 102065 Z= 0.255 Angle : 0.534 17.444 138570 Z= 0.287 Chirality : 0.041 0.221 15530 Planarity : 0.004 0.093 18005 Dihedral : 4.382 41.306 13907 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.26 % Allowed : 4.77 % Favored : 94.97 % Rotamer: Outliers : 2.65 % Allowed : 18.46 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 0.94 (0.08), residues: 12675 helix: 2.41 (0.07), residues: 5780 sheet: -0.22 (0.11), residues: 2130 loop : -1.27 (0.09), residues: 4765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1143 HIS 0.004 0.001 HIS B 130 PHE 0.022 0.001 PHE D1162 TYR 0.016 0.001 TYR C1187 ARG 0.005 0.000 ARG D 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 674 time to evaluate : 8.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 22 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8593 (mt) REVERT: A 165 SER cc_start: 0.9152 (OUTLIER) cc_final: 0.8881 (t) REVERT: A 243 SER cc_start: 0.9059 (OUTLIER) cc_final: 0.8623 (t) REVERT: A 368 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7027 (mp0) REVERT: A 612 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8184 (m-40) REVERT: A 675 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6832 (mm-30) REVERT: A 686 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8165 (p) REVERT: A 745 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7559 (mm) REVERT: A 776 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8401 (mp) REVERT: A 845 MET cc_start: 0.8540 (mtp) cc_final: 0.8201 (mtp) REVERT: A 908 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6221 (m-40) REVERT: A 1003 ARG cc_start: 0.8734 (OUTLIER) cc_final: 0.8308 (mtt180) REVERT: A 1011 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.8165 (p0) REVERT: A 1164 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7764 (mm-30) REVERT: A 1333 MET cc_start: 0.8507 (ttm) cc_final: 0.8172 (ttm) REVERT: A 1436 ARG cc_start: 0.6842 (OUTLIER) cc_final: 0.6211 (ttp80) REVERT: A 1438 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7374 (tp) REVERT: A 1519 MET cc_start: 0.8055 (mpp) cc_final: 0.7809 (mpp) REVERT: A 1536 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7573 (tt) REVERT: A 1989 ASP cc_start: 0.8347 (t0) cc_final: 0.8057 (t0) REVERT: A 1991 TRP cc_start: 0.9553 (OUTLIER) cc_final: 0.8919 (m-90) REVERT: A 2364 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7317 (tpt90) REVERT: A 2389 PHE cc_start: 0.8399 (m-10) cc_final: 0.8196 (m-10) REVERT: A 2423 PHE cc_start: 0.8236 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: A 2513 ASP cc_start: 0.6987 (OUTLIER) cc_final: 0.6477 (t0) REVERT: B 20 MET cc_start: 0.7866 (tpp) cc_final: 0.7517 (ttm) REVERT: B 516 ASP cc_start: 0.7198 (t70) cc_final: 0.6652 (t70) REVERT: B 550 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6568 (tm-30) REVERT: B 661 TRP cc_start: 0.8320 (t60) cc_final: 0.8061 (t-100) REVERT: B 689 GLU cc_start: 0.6455 (OUTLIER) cc_final: 0.5828 (mt-10) REVERT: B 776 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8753 (mp) REVERT: B 1011 ASP cc_start: 0.8396 (OUTLIER) cc_final: 0.8002 (p0) REVERT: B 1129 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8148 (mmt180) REVERT: B 1162 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7898 (p90) REVERT: B 1164 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8208 (mm-30) REVERT: B 1991 TRP cc_start: 0.9630 (OUTLIER) cc_final: 0.9174 (m-10) REVERT: B 2137 ASP cc_start: 0.7709 (t0) cc_final: 0.7406 (t70) REVERT: B 2364 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7673 (tpt90) REVERT: B 2373 GLN cc_start: 0.7195 (tp40) cc_final: 0.6860 (mm-40) REVERT: C 47 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7393 (ttp80) REVERT: C 315 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8831 (tp) REVERT: C 360 ARG cc_start: 0.8264 (ttt180) cc_final: 0.7930 (ttt180) REVERT: C 374 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7853 (ttp80) REVERT: C 415 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.6263 (tp) REVERT: C 776 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 1525 HIS cc_start: 0.7023 (OUTLIER) cc_final: 0.6717 (t-90) REVERT: C 1764 MET cc_start: 0.7951 (tpt) cc_final: 0.7692 (mmm) REVERT: C 1935 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.7856 (pp30) REVERT: C 1991 TRP cc_start: 0.9562 (OUTLIER) cc_final: 0.9166 (m-90) REVERT: C 2237 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.8422 (mtt) REVERT: C 2351 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8649 (t) REVERT: D 27 TYR cc_start: 0.7419 (OUTLIER) cc_final: 0.6647 (t80) REVERT: D 229 GLN cc_start: 0.8084 (OUTLIER) cc_final: 0.7792 (mt0) REVERT: D 776 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8671 (mp) REVERT: D 978 SER cc_start: 0.8762 (OUTLIER) cc_final: 0.8517 (p) REVERT: D 1011 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8162 (p0) REVERT: D 1444 GLU cc_start: 0.4383 (OUTLIER) cc_final: 0.3847 (tt0) REVERT: D 1935 GLN cc_start: 0.8220 (OUTLIER) cc_final: 0.7825 (pt0) REVERT: D 2040 VAL cc_start: 0.7833 (OUTLIER) cc_final: 0.7618 (m) REVERT: D 2272 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8411 (mp) REVERT: D 2412 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7198 (mt-10) REVERT: E 20 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7869 (ttm) REVERT: E 165 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.9005 (t) REVERT: E 323 ASN cc_start: 0.5053 (OUTLIER) cc_final: 0.4713 (p0) REVERT: E 437 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: E 544 VAL cc_start: 0.8148 (m) cc_final: 0.7741 (p) REVERT: E 764 MET cc_start: 0.8432 (OUTLIER) cc_final: 0.8147 (mtm) REVERT: E 1011 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8322 (p0) REVERT: E 1162 PHE cc_start: 0.8726 (OUTLIER) cc_final: 0.7568 (p90) REVERT: E 1174 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7455 (mp0) REVERT: E 1421 TYR cc_start: 0.6680 (m-10) cc_final: 0.6249 (m-10) REVERT: E 1494 PHE cc_start: 0.6730 (m-80) cc_final: 0.6419 (m-80) REVERT: E 1525 HIS cc_start: 0.6998 (m90) cc_final: 0.6532 (t-90) REVERT: E 1644 MET cc_start: 0.8914 (tpt) cc_final: 0.8637 (tpt) REVERT: E 2364 ARG cc_start: 0.7860 (OUTLIER) cc_final: 0.6849 (tpt90) REVERT: E 2412 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6839 (mp0) REVERT: E 2423 PHE cc_start: 0.8327 (OUTLIER) cc_final: 0.6885 (m-80) REVERT: E 2519 LYS cc_start: 0.7535 (OUTLIER) cc_final: 0.7233 (ttmt) outliers start: 288 outliers final: 205 residues processed: 901 average time/residue: 0.9441 time to fit residues: 1495.3640 Evaluate side-chains 921 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 658 time to evaluate : 8.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ILE Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 368 GLU Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 413 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1003 ARG Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1055 MET Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1399 VAL Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1438 LEU Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1756 ASN Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1978 LEU Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 689 GLU Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 899 VAL Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1022 THR Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1028 SER Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1130 MET Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1279 THR Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1430 MET Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1576 LYS Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1765 THR Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2031 VAL Chi-restraints excluded: chain B residue 2040 VAL Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2275 LYS Chi-restraints excluded: chain B residue 2285 MET Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 27 TYR Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 413 VAL Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 736 ASP Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 776 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 978 SER Chi-restraints excluded: chain C residue 1011 ASP Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1161 ILE Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1461 ILE Chi-restraints excluded: chain C residue 1465 VAL Chi-restraints excluded: chain C residue 1488 SER Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1525 HIS Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1740 SER Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1935 GLN Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 1991 TRP Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2237 MET Chi-restraints excluded: chain C residue 2271 LEU Chi-restraints excluded: chain C residue 2306 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 20 MET Chi-restraints excluded: chain D residue 27 TYR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 290 LEU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 978 SER Chi-restraints excluded: chain D residue 1011 ASP Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1475 ASP Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1705 THR Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1935 GLN Chi-restraints excluded: chain D residue 1978 LEU Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2161 VAL Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2361 GLU Chi-restraints excluded: chain D residue 2368 LEU Chi-restraints excluded: chain D residue 2423 PHE Chi-restraints excluded: chain D residue 2463 ILE Chi-restraints excluded: chain D residue 2475 SER Chi-restraints excluded: chain D residue 2478 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 323 ASN Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 647 THR Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1130 MET Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1174 GLU Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1457 SER Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1812 MET Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2161 VAL Chi-restraints excluded: chain E residue 2364 ARG Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2423 PHE Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2501 VAL Chi-restraints excluded: chain E residue 2519 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 1109 optimal weight: 1.9990 chunk 1168 optimal weight: 6.9990 chunk 1065 optimal weight: 1.9990 chunk 1136 optimal weight: 8.9990 chunk 1167 optimal weight: 2.9990 chunk 683 optimal weight: 8.9990 chunk 494 optimal weight: 0.9980 chunk 892 optimal weight: 9.9990 chunk 348 optimal weight: 0.0970 chunk 1026 optimal weight: 5.9990 chunk 1074 optimal weight: 0.8980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1756 ASN ** B1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1510 ASN B1688 ASN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2262 GLN ** E 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 102065 Z= 0.160 Angle : 0.498 17.498 138570 Z= 0.269 Chirality : 0.039 0.246 15530 Planarity : 0.003 0.091 18005 Dihedral : 4.267 41.140 13907 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.37 % Favored : 95.39 % Rotamer: Outliers : 2.44 % Allowed : 18.72 % Favored : 78.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.08), residues: 12675 helix: 2.55 (0.07), residues: 5790 sheet: -0.21 (0.11), residues: 2180 loop : -1.18 (0.09), residues: 4705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D1143 HIS 0.004 0.001 HIS A2476 PHE 0.024 0.001 PHE A 347 TYR 0.014 0.001 TYR C1187 ARG 0.004 0.000 ARG D2121 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 934 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 265 poor density : 669 time to evaluate : 8.650 Fit side-chains revert: symmetry clash REVERT: A 165 SER cc_start: 0.9120 (OUTLIER) cc_final: 0.8853 (t) REVERT: A 243 SER cc_start: 0.8989 (OUTLIER) cc_final: 0.8570 (t) REVERT: A 315 ILE cc_start: 0.9098 (tt) cc_final: 0.8851 (tp) REVERT: A 612 ASN cc_start: 0.8417 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: A 675 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6819 (mm-30) REVERT: A 686 SER cc_start: 0.8491 (OUTLIER) cc_final: 0.8176 (p) REVERT: A 745 LEU cc_start: 0.7981 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 845 MET cc_start: 0.8480 (mtp) cc_final: 0.8140 (mtp) REVERT: A 908 ASN cc_start: 0.6769 (OUTLIER) cc_final: 0.6165 (m-40) REVERT: A 1011 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8161 (p0) REVERT: A 1023 VAL cc_start: 0.8980 (m) cc_final: 0.8755 (p) REVERT: A 1164 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7826 (mm-30) REVERT: A 1436 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.6295 (ttp80) REVERT: A 1519 MET cc_start: 0.8045 (mpp) cc_final: 0.7795 (mpp) REVERT: A 1536 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7576 (tt) REVERT: A 1698 MET cc_start: 0.8718 (mmt) cc_final: 0.8317 (mtp) REVERT: A 1989 ASP cc_start: 0.8283 (t0) cc_final: 0.8041 (t0) REVERT: A 1991 TRP cc_start: 0.9534 (OUTLIER) cc_final: 0.8877 (m-90) REVERT: A 2364 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7719 (ttt90) REVERT: A 2389 PHE cc_start: 0.8344 (m-10) cc_final: 0.8133 (m-10) REVERT: A 2423 PHE cc_start: 0.8209 (OUTLIER) cc_final: 0.7750 (m-80) REVERT: A 2513 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6493 (t0) REVERT: B 20 MET cc_start: 0.7752 (tpp) cc_final: 0.7503 (ttm) REVERT: B 516 ASP cc_start: 0.7205 (t70) cc_final: 0.6682 (t70) REVERT: B 550 GLU cc_start: 0.7131 (OUTLIER) cc_final: 0.6578 (tm-30) REVERT: B 661 TRP cc_start: 0.8316 (t60) cc_final: 0.8094 (t-100) REVERT: B 776 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8748 (mp) REVERT: B 822 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7935 (t0) REVERT: B 1011 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7980 (p0) REVERT: B 1162 PHE cc_start: 0.8604 (OUTLIER) cc_final: 0.7855 (p90) REVERT: B 1164 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8169 (mm-30) REVERT: B 1265 MET cc_start: 0.8336 (ttt) cc_final: 0.8132 (ttm) REVERT: B 1991 TRP cc_start: 0.9620 (OUTLIER) cc_final: 0.9173 (m-10) REVERT: B 2137 ASP cc_start: 0.7723 (t0) cc_final: 0.7345 (t70) REVERT: B 2364 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7925 (tpt-90) REVERT: B 2373 GLN cc_start: 0.7249 (tp40) cc_final: 0.6896 (mm-40) REVERT: C 20 MET cc_start: 0.7599 (tpp) cc_final: 0.7288 (ttt) REVERT: C 47 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.7378 (ttp80) REVERT: C 315 ILE cc_start: 0.9107 (OUTLIER) cc_final: 0.8812 (tp) REVERT: C 360 ARG cc_start: 0.8145 (ttt180) cc_final: 0.7912 (ttt180) REVERT: C 374 ARG cc_start: 0.8046 (ttp80) cc_final: 0.7763 (ttp-170) REVERT: C 415 ILE cc_start: 0.6442 (OUTLIER) cc_final: 0.6190 (tp) REVERT: C 516 ASP cc_start: 0.7413 (t70) cc_final: 0.7179 (t70) REVERT: C 1402 TYR cc_start: 0.7257 (t80) cc_final: 0.6982 (t80) REVERT: C 1488 SER cc_start: 0.5827 (OUTLIER) cc_final: 0.5621 (m) REVERT: C 1525 HIS cc_start: 0.6997 (m90) cc_final: 0.6686 (t-90) REVERT: C 1991 TRP cc_start: 0.9547 (OUTLIER) cc_final: 0.9152 (m-90) REVERT: C 2237 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8419 (mtt) REVERT: C 2351 VAL cc_start: 0.8941 (OUTLIER) cc_final: 0.8603 (t) REVERT: D 185 MET cc_start: 0.8635 (mmm) cc_final: 0.8244 (mmm) REVERT: D 229 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7813 (mt0) REVERT: D 360 ARG cc_start: 0.8462 (ttt-90) cc_final: 0.8229 (ttt-90) REVERT: D 399 ASN cc_start: 0.6840 (t0) cc_final: 0.6470 (t0) REVERT: D 776 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8646 (mp) REVERT: D 1266 THR cc_start: 0.9398 (OUTLIER) cc_final: 0.9190 (m) REVERT: D 1444 GLU cc_start: 0.4087 (OUTLIER) cc_final: 0.3586 (tt0) REVERT: D 1454 PHE cc_start: 0.8223 (m-80) cc_final: 0.7863 (m-80) REVERT: D 2040 VAL cc_start: 0.7798 (OUTLIER) cc_final: 0.7582 (m) REVERT: D 2272 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 2373 GLN cc_start: 0.7480 (tp40) cc_final: 0.7091 (tp40) REVERT: D 2412 GLU cc_start: 0.7391 (mt-10) cc_final: 0.7070 (mt-10) REVERT: E 20 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7855 (ttm) REVERT: E 165 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8972 (t) REVERT: E 213 HIS cc_start: 0.8284 (OUTLIER) cc_final: 0.7939 (m-70) REVERT: E 437 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7091 (mt-10) REVERT: E 544 VAL cc_start: 0.8130 (m) cc_final: 0.7743 (p) REVERT: E 1011 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8327 (p0) REVERT: E 1162 PHE cc_start: 0.8593 (OUTLIER) cc_final: 0.7509 (p90) REVERT: E 1164 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8065 (mm-30) REVERT: E 1174 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7388 (mp0) REVERT: E 1421 TYR cc_start: 0.6636 (m-10) cc_final: 0.6202 (m-10) REVERT: E 1494 PHE cc_start: 0.6588 (m-80) cc_final: 0.6352 (m-80) REVERT: E 1525 HIS cc_start: 0.6989 (m90) cc_final: 0.6529 (t-90) REVERT: E 1644 MET cc_start: 0.8895 (tpt) cc_final: 0.8566 (tpt) REVERT: E 2364 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.6826 (tpt90) REVERT: E 2423 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.6853 (m-80) outliers start: 265 outliers final: 189 residues processed: 885 average time/residue: 0.8941 time to fit residues: 1386.0588 Evaluate side-chains 890 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 655 time to evaluate : 8.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1399 VAL Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1462 LEU Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1973 ASN Chi-restraints excluded: chain A residue 1978 LEU Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 257 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 822 ASN Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1003 ARG Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1430 MET Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1725 LEU Chi-restraints excluded: chain B residue 1786 THR Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2040 VAL Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2275 LYS Chi-restraints excluded: chain B residue 2285 MET Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 213 HIS Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1461 ILE Chi-restraints excluded: chain C residue 1488 SER Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1730 GLN Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1948 THR Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 1991 TRP Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2237 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 540 ASP Chi-restraints excluded: chain D residue 543 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1978 LEU Chi-restraints excluded: chain D residue 2040 VAL Chi-restraints excluded: chain D residue 2161 VAL Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2361 GLU Chi-restraints excluded: chain D residue 2368 LEU Chi-restraints excluded: chain D residue 2463 ILE Chi-restraints excluded: chain D residue 2475 SER Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 568 SER Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 830 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 862 ASN Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 978 SER Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1055 MET Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1164 GLU Chi-restraints excluded: chain E residue 1174 GLU Chi-restraints excluded: chain E residue 1408 LEU Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1457 SER Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1603 LEU Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1812 MET Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2161 VAL Chi-restraints excluded: chain E residue 2364 ARG Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2423 PHE Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2501 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 1132 optimal weight: 2.9990 chunk 746 optimal weight: 0.9980 chunk 1201 optimal weight: 6.9990 chunk 733 optimal weight: 6.9990 chunk 569 optimal weight: 2.9990 chunk 835 optimal weight: 0.7980 chunk 1260 optimal weight: 10.0000 chunk 1159 optimal weight: 9.9990 chunk 1003 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 775 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1688 ASN B2262 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2262 GLN ** E 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E2295 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 102065 Z= 0.166 Angle : 0.494 17.464 138570 Z= 0.266 Chirality : 0.039 0.257 15530 Planarity : 0.003 0.088 18005 Dihedral : 4.174 40.892 13905 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.23 % Allowed : 4.59 % Favored : 95.18 % Rotamer: Outliers : 2.30 % Allowed : 18.79 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.08), residues: 12675 helix: 2.62 (0.07), residues: 5780 sheet: -0.17 (0.11), residues: 2170 loop : -1.17 (0.09), residues: 4725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B1143 HIS 0.004 0.001 HIS A2476 PHE 0.022 0.001 PHE A 347 TYR 0.017 0.001 TYR E1402 ARG 0.005 0.000 ARG D2121 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 25350 Ramachandran restraints generated. 12675 Oldfield, 0 Emsley, 12675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 923 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 673 time to evaluate : 8.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 165 SER cc_start: 0.9118 (OUTLIER) cc_final: 0.8852 (t) REVERT: A 243 SER cc_start: 0.8993 (OUTLIER) cc_final: 0.8578 (t) REVERT: A 315 ILE cc_start: 0.9086 (tt) cc_final: 0.8840 (tp) REVERT: A 612 ASN cc_start: 0.8347 (OUTLIER) cc_final: 0.8125 (m-40) REVERT: A 675 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6834 (mm-30) REVERT: A 686 SER cc_start: 0.8483 (OUTLIER) cc_final: 0.8160 (p) REVERT: A 745 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7456 (mm) REVERT: A 845 MET cc_start: 0.8487 (mtp) cc_final: 0.8155 (mtp) REVERT: A 908 ASN cc_start: 0.6766 (OUTLIER) cc_final: 0.6169 (m-40) REVERT: A 1011 ASP cc_start: 0.8360 (OUTLIER) cc_final: 0.8153 (p0) REVERT: A 1023 VAL cc_start: 0.9008 (m) cc_final: 0.8786 (p) REVERT: A 1164 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7762 (mm-30) REVERT: A 1333 MET cc_start: 0.8465 (ttm) cc_final: 0.8136 (ttm) REVERT: A 1436 ARG cc_start: 0.6938 (OUTLIER) cc_final: 0.6366 (ttp80) REVERT: A 1519 MET cc_start: 0.8045 (mpp) cc_final: 0.7797 (mpp) REVERT: A 1536 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 1698 MET cc_start: 0.8751 (mmt) cc_final: 0.8356 (mtp) REVERT: A 1989 ASP cc_start: 0.8261 (t0) cc_final: 0.7978 (t0) REVERT: A 1991 TRP cc_start: 0.9539 (OUTLIER) cc_final: 0.8891 (m-90) REVERT: A 2364 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7700 (ttt90) REVERT: A 2389 PHE cc_start: 0.8348 (m-10) cc_final: 0.8137 (m-10) REVERT: A 2423 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7726 (m-80) REVERT: A 2513 ASP cc_start: 0.6850 (OUTLIER) cc_final: 0.6364 (t0) REVERT: B 20 MET cc_start: 0.7802 (tpp) cc_final: 0.7590 (ttm) REVERT: B 516 ASP cc_start: 0.7179 (t70) cc_final: 0.6675 (t70) REVERT: B 550 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6553 (tm-30) REVERT: B 661 TRP cc_start: 0.8341 (t60) cc_final: 0.8121 (t-100) REVERT: B 776 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8751 (mp) REVERT: B 1011 ASP cc_start: 0.8314 (OUTLIER) cc_final: 0.7962 (p0) REVERT: B 1129 ARG cc_start: 0.8826 (OUTLIER) cc_final: 0.8150 (mmt180) REVERT: B 1162 PHE cc_start: 0.8578 (OUTLIER) cc_final: 0.7844 (p90) REVERT: B 1164 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.8132 (mm-30) REVERT: B 1265 MET cc_start: 0.8324 (ttt) cc_final: 0.8117 (ttm) REVERT: B 1421 TYR cc_start: 0.6086 (m-10) cc_final: 0.5716 (m-10) REVERT: B 1438 LEU cc_start: 0.7238 (mm) cc_final: 0.7014 (tp) REVERT: B 1991 TRP cc_start: 0.9615 (OUTLIER) cc_final: 0.9157 (m-10) REVERT: B 2137 ASP cc_start: 0.7714 (t0) cc_final: 0.7346 (t70) REVERT: B 2364 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7921 (tpt-90) REVERT: B 2373 GLN cc_start: 0.7238 (tp40) cc_final: 0.6894 (mm-40) REVERT: C 20 MET cc_start: 0.7778 (tpp) cc_final: 0.7573 (ttt) REVERT: C 47 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7390 (ttp80) REVERT: C 86 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6285 (t70) REVERT: C 315 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8811 (tp) REVERT: C 374 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7821 (ttp-170) REVERT: C 415 ILE cc_start: 0.6499 (OUTLIER) cc_final: 0.6232 (tp) REVERT: C 516 ASP cc_start: 0.7408 (t70) cc_final: 0.7167 (t70) REVERT: C 616 MET cc_start: 0.7673 (mtm) cc_final: 0.7274 (mtp) REVERT: C 1402 TYR cc_start: 0.7290 (t80) cc_final: 0.6984 (t80) REVERT: C 1421 TYR cc_start: 0.6474 (m-10) cc_final: 0.5904 (m-10) REVERT: C 1510 ASN cc_start: 0.7389 (m-40) cc_final: 0.6793 (m-40) REVERT: C 1525 HIS cc_start: 0.7004 (m90) cc_final: 0.6690 (t-90) REVERT: C 1991 TRP cc_start: 0.9548 (OUTLIER) cc_final: 0.9139 (m-90) REVERT: C 2104 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7362 (mmt-90) REVERT: C 2237 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8459 (mtt) REVERT: C 2351 VAL cc_start: 0.8935 (OUTLIER) cc_final: 0.8598 (t) REVERT: D 185 MET cc_start: 0.8610 (mmm) cc_final: 0.8176 (mmm) REVERT: D 229 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7811 (mt0) REVERT: D 399 ASN cc_start: 0.6770 (t0) cc_final: 0.6414 (t0) REVERT: D 776 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8654 (mp) REVERT: D 1266 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.9189 (m) REVERT: D 1444 GLU cc_start: 0.4571 (OUTLIER) cc_final: 0.4022 (tt0) REVERT: D 2272 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8386 (mp) REVERT: D 2373 GLN cc_start: 0.7524 (tp40) cc_final: 0.7137 (tp40) REVERT: D 2412 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6958 (mt-10) REVERT: E 20 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7866 (ttm) REVERT: E 165 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8972 (t) REVERT: E 213 HIS cc_start: 0.8289 (OUTLIER) cc_final: 0.7953 (m-70) REVERT: E 374 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7703 (ttp-170) REVERT: E 437 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: E 544 VAL cc_start: 0.8138 (m) cc_final: 0.7745 (p) REVERT: E 764 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8137 (mtm) REVERT: E 1011 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8315 (p0) REVERT: E 1162 PHE cc_start: 0.8565 (OUTLIER) cc_final: 0.7539 (p90) REVERT: E 1164 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.8051 (mm-30) REVERT: E 1174 GLU cc_start: 0.7843 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: E 1421 TYR cc_start: 0.6622 (m-10) cc_final: 0.6229 (m-10) REVERT: E 1525 HIS cc_start: 0.7003 (m90) cc_final: 0.6563 (t-90) REVERT: E 1644 MET cc_start: 0.8917 (tpt) cc_final: 0.8590 (tpt) REVERT: E 1764 MET cc_start: 0.7932 (tpt) cc_final: 0.7084 (tpp) REVERT: E 2364 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.6834 (tpt90) REVERT: E 2423 PHE cc_start: 0.8322 (OUTLIER) cc_final: 0.6883 (m-80) outliers start: 250 outliers final: 186 residues processed: 880 average time/residue: 0.9093 time to fit residues: 1406.0515 Evaluate side-chains 891 residues out of total 10870 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 658 time to evaluate : 8.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 243 SER Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 536 ILE Chi-restraints excluded: chain A residue 591 VAL Chi-restraints excluded: chain A residue 612 ASN Chi-restraints excluded: chain A residue 621 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 736 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 754 THR Chi-restraints excluded: chain A residue 764 MET Chi-restraints excluded: chain A residue 894 VAL Chi-restraints excluded: chain A residue 904 LYS Chi-restraints excluded: chain A residue 908 ASN Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 SER Chi-restraints excluded: chain A residue 981 ILE Chi-restraints excluded: chain A residue 1011 ASP Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1102 SER Chi-restraints excluded: chain A residue 1164 GLU Chi-restraints excluded: chain A residue 1242 LEU Chi-restraints excluded: chain A residue 1279 THR Chi-restraints excluded: chain A residue 1295 HIS Chi-restraints excluded: chain A residue 1302 VAL Chi-restraints excluded: chain A residue 1349 ASN Chi-restraints excluded: chain A residue 1399 VAL Chi-restraints excluded: chain A residue 1436 ARG Chi-restraints excluded: chain A residue 1465 VAL Chi-restraints excluded: chain A residue 1499 SER Chi-restraints excluded: chain A residue 1517 THR Chi-restraints excluded: chain A residue 1528 THR Chi-restraints excluded: chain A residue 1531 ASP Chi-restraints excluded: chain A residue 1536 LEU Chi-restraints excluded: chain A residue 1603 LEU Chi-restraints excluded: chain A residue 1636 THR Chi-restraints excluded: chain A residue 1754 LEU Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 1908 ASP Chi-restraints excluded: chain A residue 1965 VAL Chi-restraints excluded: chain A residue 1973 ASN Chi-restraints excluded: chain A residue 1978 LEU Chi-restraints excluded: chain A residue 1991 TRP Chi-restraints excluded: chain A residue 2008 ASP Chi-restraints excluded: chain A residue 2021 THR Chi-restraints excluded: chain A residue 2026 LEU Chi-restraints excluded: chain A residue 2271 LEU Chi-restraints excluded: chain A residue 2364 ARG Chi-restraints excluded: chain A residue 2411 ILE Chi-restraints excluded: chain A residue 2423 PHE Chi-restraints excluded: chain A residue 2463 ILE Chi-restraints excluded: chain A residue 2501 VAL Chi-restraints excluded: chain A residue 2513 ASP Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 317 THR Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 355 ASN Chi-restraints excluded: chain B residue 500 PHE Chi-restraints excluded: chain B residue 550 GLU Chi-restraints excluded: chain B residue 554 THR Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 776 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 961 LEU Chi-restraints excluded: chain B residue 986 LEU Chi-restraints excluded: chain B residue 1003 ARG Chi-restraints excluded: chain B residue 1011 ASP Chi-restraints excluded: chain B residue 1023 VAL Chi-restraints excluded: chain B residue 1055 MET Chi-restraints excluded: chain B residue 1129 ARG Chi-restraints excluded: chain B residue 1147 ASP Chi-restraints excluded: chain B residue 1162 PHE Chi-restraints excluded: chain B residue 1164 GLU Chi-restraints excluded: chain B residue 1295 HIS Chi-restraints excluded: chain B residue 1302 VAL Chi-restraints excluded: chain B residue 1465 VAL Chi-restraints excluded: chain B residue 1517 THR Chi-restraints excluded: chain B residue 1528 THR Chi-restraints excluded: chain B residue 1531 ASP Chi-restraints excluded: chain B residue 1603 LEU Chi-restraints excluded: chain B residue 1636 THR Chi-restraints excluded: chain B residue 1685 VAL Chi-restraints excluded: chain B residue 1725 LEU Chi-restraints excluded: chain B residue 1786 THR Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1973 ASN Chi-restraints excluded: chain B residue 1978 LEU Chi-restraints excluded: chain B residue 1991 TRP Chi-restraints excluded: chain B residue 2040 VAL Chi-restraints excluded: chain B residue 2146 MET Chi-restraints excluded: chain B residue 2161 VAL Chi-restraints excluded: chain B residue 2364 ARG Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2370 GLN Chi-restraints excluded: chain B residue 2411 ILE Chi-restraints excluded: chain B residue 2463 ILE Chi-restraints excluded: chain C residue 47 ARG Chi-restraints excluded: chain C residue 86 ASP Chi-restraints excluded: chain C residue 243 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 321 VAL Chi-restraints excluded: chain C residue 355 ASN Chi-restraints excluded: chain C residue 415 ILE Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 477 ILE Chi-restraints excluded: chain C residue 481 SER Chi-restraints excluded: chain C residue 536 ILE Chi-restraints excluded: chain C residue 591 VAL Chi-restraints excluded: chain C residue 621 SER Chi-restraints excluded: chain C residue 672 ILE Chi-restraints excluded: chain C residue 686 SER Chi-restraints excluded: chain C residue 749 LEU Chi-restraints excluded: chain C residue 961 LEU Chi-restraints excluded: chain C residue 1023 VAL Chi-restraints excluded: chain C residue 1028 SER Chi-restraints excluded: chain C residue 1162 PHE Chi-restraints excluded: chain C residue 1174 GLU Chi-restraints excluded: chain C residue 1302 VAL Chi-restraints excluded: chain C residue 1346 SER Chi-restraints excluded: chain C residue 1408 LEU Chi-restraints excluded: chain C residue 1461 ILE Chi-restraints excluded: chain C residue 1509 ILE Chi-restraints excluded: chain C residue 1517 THR Chi-restraints excluded: chain C residue 1531 ASP Chi-restraints excluded: chain C residue 1636 THR Chi-restraints excluded: chain C residue 1685 VAL Chi-restraints excluded: chain C residue 1915 MET Chi-restraints excluded: chain C residue 1948 THR Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1978 LEU Chi-restraints excluded: chain C residue 1991 TRP Chi-restraints excluded: chain C residue 2008 ASP Chi-restraints excluded: chain C residue 2104 ARG Chi-restraints excluded: chain C residue 2161 VAL Chi-restraints excluded: chain C residue 2237 MET Chi-restraints excluded: chain C residue 2351 VAL Chi-restraints excluded: chain C residue 2423 PHE Chi-restraints excluded: chain C residue 2463 ILE Chi-restraints excluded: chain C residue 2501 VAL Chi-restraints excluded: chain D residue 4 THR Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 437 GLU Chi-restraints excluded: chain D residue 500 PHE Chi-restraints excluded: chain D residue 520 VAL Chi-restraints excluded: chain D residue 543 THR Chi-restraints excluded: chain D residue 568 SER Chi-restraints excluded: chain D residue 591 VAL Chi-restraints excluded: chain D residue 617 LEU Chi-restraints excluded: chain D residue 672 ILE Chi-restraints excluded: chain D residue 761 CYS Chi-restraints excluded: chain D residue 764 MET Chi-restraints excluded: chain D residue 776 LEU Chi-restraints excluded: chain D residue 851 MET Chi-restraints excluded: chain D residue 862 ASN Chi-restraints excluded: chain D residue 961 LEU Chi-restraints excluded: chain D residue 1135 LEU Chi-restraints excluded: chain D residue 1242 LEU Chi-restraints excluded: chain D residue 1266 THR Chi-restraints excluded: chain D residue 1293 ILE Chi-restraints excluded: chain D residue 1295 HIS Chi-restraints excluded: chain D residue 1331 THR Chi-restraints excluded: chain D residue 1349 ASN Chi-restraints excluded: chain D residue 1395 ILE Chi-restraints excluded: chain D residue 1425 VAL Chi-restraints excluded: chain D residue 1438 LEU Chi-restraints excluded: chain D residue 1441 THR Chi-restraints excluded: chain D residue 1444 GLU Chi-restraints excluded: chain D residue 1464 THR Chi-restraints excluded: chain D residue 1465 VAL Chi-restraints excluded: chain D residue 1517 THR Chi-restraints excluded: chain D residue 1576 LYS Chi-restraints excluded: chain D residue 1603 LEU Chi-restraints excluded: chain D residue 1636 THR Chi-restraints excluded: chain D residue 1705 THR Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1915 MET Chi-restraints excluded: chain D residue 1978 LEU Chi-restraints excluded: chain D residue 2161 VAL Chi-restraints excluded: chain D residue 2272 LEU Chi-restraints excluded: chain D residue 2329 ASN Chi-restraints excluded: chain D residue 2361 GLU Chi-restraints excluded: chain D residue 2368 LEU Chi-restraints excluded: chain D residue 2463 ILE Chi-restraints excluded: chain D residue 2501 VAL Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 213 HIS Chi-restraints excluded: chain E residue 355 ASN Chi-restraints excluded: chain E residue 437 GLU Chi-restraints excluded: chain E residue 536 ILE Chi-restraints excluded: chain E residue 549 ASP Chi-restraints excluded: chain E residue 591 VAL Chi-restraints excluded: chain E residue 736 ASP Chi-restraints excluded: chain E residue 764 MET Chi-restraints excluded: chain E residue 830 MET Chi-restraints excluded: chain E residue 835 THR Chi-restraints excluded: chain E residue 961 LEU Chi-restraints excluded: chain E residue 1011 ASP Chi-restraints excluded: chain E residue 1162 PHE Chi-restraints excluded: chain E residue 1164 GLU Chi-restraints excluded: chain E residue 1174 GLU Chi-restraints excluded: chain E residue 1428 HIS Chi-restraints excluded: chain E residue 1457 SER Chi-restraints excluded: chain E residue 1465 VAL Chi-restraints excluded: chain E residue 1509 ILE Chi-restraints excluded: chain E residue 1517 THR Chi-restraints excluded: chain E residue 1636 THR Chi-restraints excluded: chain E residue 1639 ASP Chi-restraints excluded: chain E residue 1705 THR Chi-restraints excluded: chain E residue 1754 LEU Chi-restraints excluded: chain E residue 1812 MET Chi-restraints excluded: chain E residue 1890 LEU Chi-restraints excluded: chain E residue 1921 LEU Chi-restraints excluded: chain E residue 1978 LEU Chi-restraints excluded: chain E residue 2161 VAL Chi-restraints excluded: chain E residue 2364 ARG Chi-restraints excluded: chain E residue 2368 LEU Chi-restraints excluded: chain E residue 2407 SER Chi-restraints excluded: chain E residue 2423 PHE Chi-restraints excluded: chain E residue 2463 ILE Chi-restraints excluded: chain E residue 2501 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1265 random chunks: chunk 615 optimal weight: 0.9990 chunk 797 optimal weight: 9.9990 chunk 1069 optimal weight: 0.6980 chunk 307 optimal weight: 6.9990 chunk 925 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 1005 optimal weight: 0.7980 chunk 420 optimal weight: 7.9990 chunk 1032 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1349 ASN A1356 ASN A1388 GLN B1688 ASN B2295 GLN ** C 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2262 GLN E 354 ASN E 411 ASN E2262 GLN E2489 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.128923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.105795 restraints weight = 140072.779| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.05 r_work: 0.2933 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 102065 Z= 0.141 Angle : 0.481 17.450 138570 Z= 0.260 Chirality : 0.038 0.253 15530 Planarity : 0.003 0.087 18005 Dihedral : 4.069 39.497 13902 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.24 % Favored : 95.53 % Rotamer: Outliers : 2.15 % Allowed : 19.08 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.94 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.08), residues: 12675 helix: 2.74 (0.07), residues: 5780 sheet: -0.12 (0.11), residues: 2150 loop : -1.12 (0.09), residues: 4745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C1143 HIS 0.004 0.001 HIS A1881 PHE 0.033 0.001 PHE E 347 TYR 0.016 0.001 TYR E1402 ARG 0.010 0.000 ARG D 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22771.84 seconds wall clock time: 407 minutes 19.18 seconds (24439.18 seconds total)