Starting phenix.real_space_refine on Thu Dec 14 07:18:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc4_12138/12_2023/7bc4_12138_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc4_12138/12_2023/7bc4_12138.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/7bc4_12138/12_2023/7bc4_12138.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc4_12138/12_2023/7bc4_12138.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc4_12138/12_2023/7bc4_12138_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bc4_12138/12_2023/7bc4_12138_updated.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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 95 5.16 5 C 17595 2.51 5 N 4640 2.21 5 O 5279 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 2": "NH1" <-> "NH2" Residue "A GLU 30": "OE1" <-> "OE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 42": "OE1" <-> "OE2" Residue "A GLU 46": "OE1" <-> "OE2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 329": "OD1" <-> "OD2" Residue "A ARG 331": "NH1" <-> "NH2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 379": "OE1" <-> "OE2" Residue "A TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A GLU 426": "OE1" <-> "OE2" Residue "A GLU 455": "OE1" <-> "OE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 482": "OD1" <-> "OD2" Residue "A ASP 487": "OD1" <-> "OD2" Residue "A TYR 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 612": "OD1" <-> "OD2" Residue "A GLU 636": "OE1" <-> "OE2" Residue "A ASP 640": "OD1" <-> "OD2" Residue "A ASP 642": "OD1" <-> "OD2" Residue "A ASP 649": "OD1" <-> "OD2" Residue "A ARG 697": "NH1" <-> "NH2" Residue "A PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 712": "NH1" <-> "NH2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 742": "NH1" <-> "NH2" Residue "A ASP 746": "OD1" <-> "OD2" Residue "A GLU 747": "OE1" <-> "OE2" Residue "A ASP 752": "OD1" <-> "OD2" Residue "A PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 844": "OE1" <-> "OE2" Residue "A ARG 882": "NH1" <-> "NH2" Residue "A ARG 925": "NH1" <-> "NH2" Residue "A ARG 932": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 954": "NH1" <-> "NH2" Residue "A ASP 962": "OD1" <-> "OD2" Residue "A ARG 969": "NH1" <-> "NH2" Residue "A ASP 1001": "OD1" <-> "OD2" Residue "A ARG 1021": "NH1" <-> "NH2" Residue "A ASP 1075": "OD1" <-> "OD2" Residue "A GLU 1083": "OE1" <-> "OE2" Residue "A ARG 1099": "NH1" <-> "NH2" Residue "A GLU 1107": "OE1" <-> "OE2" Residue "A GLU 1115": "OE1" <-> "OE2" Residue "A ASP 1117": "OD1" <-> "OD2" Residue "A ASP 1140": "OD1" <-> "OD2" Residue "A GLU 1145": "OE1" <-> "OE2" Residue "A GLU 1149": "OE1" <-> "OE2" Residue "A ARG 1159": "NH1" <-> "NH2" Residue "A GLU 1208": "OE1" <-> "OE2" Residue "A TYR 1224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1249": "NH1" <-> "NH2" Residue "A TYR 1252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1300": "OD1" <-> "OD2" Residue "A TYR 1319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1344": "OD1" <-> "OD2" Residue "A PHE 1363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1451": "OE1" <-> "OE2" Residue "A ASP 1452": "OD1" <-> "OD2" Residue "A ARG 1458": "NH1" <-> "NH2" Residue "A GLU 1460": "OE1" <-> "OE2" Residue "A GLU 1463": "OE1" <-> "OE2" Residue "A PHE 1471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1472": "OD1" <-> "OD2" Residue "A ARG 1480": "NH1" <-> "NH2" Residue "A GLU 1483": "OE1" <-> "OE2" Residue "A ARG 1486": "NH1" <-> "NH2" Residue "A ASP 1507": "OD1" <-> "OD2" Residue "A PHE 1532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1613": "OE1" <-> "OE2" Residue "A ARG 1620": "NH1" <-> "NH2" Residue "A PHE 1635": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1659": "OE1" <-> "OE2" Residue "A PHE 1661": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1662": "OE1" <-> "OE2" Residue "A GLU 1669": "OE1" <-> "OE2" Residue "A TYR 1672": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A ARG 1685": "NH1" <-> "NH2" Residue "A PHE 1689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1700": "OE1" <-> "OE2" Residue "A ARG 1712": "NH1" <-> "NH2" Residue "A PHE 1736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 41": "NH1" <-> "NH2" Residue "B GLU 49": "OE1" <-> "OE2" Residue "B TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 92": "OE1" <-> "OE2" Residue "B GLU 94": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 125": "OE1" <-> "OE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 135": "NH1" <-> "NH2" Residue "B ARG 144": "NH1" <-> "NH2" Residue "B TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 175": "OD1" <-> "OD2" Residue "B TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "B TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 208": "NH1" <-> "NH2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 235": "OD1" <-> "OD2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 350": "NH1" <-> "NH2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 423": "NH1" <-> "NH2" Residue "B PHE 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B TYR 471": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 495": "NH1" <-> "NH2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 511": "OD1" <-> "OD2" Residue "B GLU 544": "OE1" <-> "OE2" Residue "B ASP 547": "OD1" <-> "OD2" Residue "B GLU 555": "OE1" <-> "OE2" Residue "B PHE 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 589": "OD1" <-> "OD2" Residue "B ARG 594": "NH1" <-> "NH2" Residue "B ASP 614": "OD1" <-> "OD2" Residue "B PHE 615": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 645": "NH1" <-> "NH2" Residue "B ASP 648": "OD1" <-> "OD2" Residue "B ARG 666": "NH1" <-> "NH2" Residue "B GLU 680": "OE1" <-> "OE2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B GLU 702": "OE1" <-> "OE2" Residue "B GLU 705": "OE1" <-> "OE2" Residue "B ARG 745": "NH1" <-> "NH2" Residue "B GLU 753": "OE1" <-> "OE2" Residue "B ASP 785": "OD1" <-> "OD2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 789": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 798": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 800": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 832": "OD1" <-> "OD2" Residue "B TYR 845": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 861": "OE1" <-> "OE2" Residue "B ASP 907": "OD1" <-> "OD2" Residue "B GLU 937": "OE1" <-> "OE2" Residue "B ARG 942": "NH1" <-> "NH2" Residue "B ARG 946": "NH1" <-> "NH2" Residue "B GLU 965": "OE1" <-> "OE2" Residue "B PHE 967": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 984": "OE1" <-> "OE2" Residue "B GLU 985": "OE1" <-> "OE2" Residue "B PHE 1013": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1016": "OE1" <-> "OE2" Residue "B PHE 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1036": "OE1" <-> "OE2" Residue "B ASP 1042": "OD1" <-> "OD2" Residue "B ASP 1049": "OD1" <-> "OD2" Residue "B PHE 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1103": "OD1" <-> "OD2" Residue "B GLU 1104": "OE1" <-> "OE2" Residue "B ASP 1121": "OD1" <-> "OD2" Residue "B GLU 1136": "OE1" <-> "OE2" Residue "B ASP 1146": "OD1" <-> "OD2" Residue "B GLU 1158": "OE1" <-> "OE2" Residue "B ARG 1162": "NH1" <-> "NH2" Residue "B ARG 1163": "NH1" <-> "NH2" Residue "B ARG 1170": "NH1" <-> "NH2" Residue "B ASP 1201": "OD1" <-> "OD2" Residue "B PHE 1210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1212": "NH1" <-> "NH2" Residue "B ARG 1214": "NH1" <-> "NH2" Residue "B TYR 1252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1290": "OD1" <-> "OD2" Residue "B ASP 1292": "OD1" <-> "OD2" Residue "B GLU 1303": "OE1" <-> "OE2" Residue "B ARG 1331": "NH1" <-> "NH2" Residue "B ASP 1384": "OD1" <-> "OD2" Residue "B PHE 1425": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1462": "OE1" <-> "OE2" Residue "B GLU 1467": "OE1" <-> "OE2" Residue "B PHE 1479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1480": "NH1" <-> "NH2" Residue "B PHE 1487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1505": "OE1" <-> "OE2" Residue "B GLU 1516": "OE1" <-> "OE2" Residue "B TYR 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1531": "OD1" <-> "OD2" Residue "B PHE 1546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1557": "OE1" <-> "OE2" Residue "B PHE 1585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1622": "NH1" <-> "NH2" Residue "B ASP 1627": "OD1" <-> "OD2" Residue "B ARG 1651": "NH1" <-> "NH2" Residue "B GLU 1673": "OE1" <-> "OE2" Residue "B PHE 1683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1696": "OD1" <-> "OD2" Residue "B GLU 1702": "OE1" <-> "OE2" Residue "B ARG 1710": "NH1" <-> "NH2" Residue "B PHE 1721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1733": "OE1" <-> "OE2" Residue "B ARG 1744": "NH1" <-> "NH2" Residue "B TYR 1750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1761": "OD1" <-> "OD2" Residue "B GLU 1772": "OE1" <-> "OE2" Residue "B GLU 1775": "OE1" <-> "OE2" Residue "B PHE 1807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1829": "OE1" <-> "OE2" Residue "B ASP 1838": "OD1" <-> "OD2" Residue "B ARG 1867": "NH1" <-> "NH2" Residue "B TYR 1870": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1886": "OD1" <-> "OD2" Residue "B ARG 1890": "NH1" <-> "NH2" Residue "B GLU 1894": "OE1" <-> "OE2" Residue "B TYR 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1923": "NH1" <-> "NH2" Residue "B PHE 1935": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1941": "OD1" <-> "OD2" Residue "B ASP 1963": "OD1" <-> "OD2" Residue "B GLU 1979": "OE1" <-> "OE2" Residue "B ARG 2000": "NH1" <-> "NH2" Residue "B PHE 2037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 2045": "OE1" <-> "OE2" Residue "B GLU 2054": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 27610 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 11486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1460, 11486 Classifications: {'peptide': 1460} Link IDs: {'PTRANS': 61, 'TRANS': 1398} Chain breaks: 2 Chain: "B" Number of atoms: 16124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2055, 16124 Unusual residues: {'FMN': 1} Classifications: {'peptide': 2054, 'undetermined': 1} Link IDs: {'PTRANS': 102, 'TRANS': 1951, None: 1} Not linked: pdbres="TRP B2063 " pdbres="FMN B2101 " Time building chain proxies: 14.81, per 1000 atoms: 0.54 Number of scatterers: 27610 At special positions: 0 Unit cell: (204.48, 129.93, 178.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 95 16.00 P 1 15.00 O 5279 8.00 N 4640 7.00 C 17595 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.33 Conformation dependent library (CDL) restraints added in 5.5 seconds 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6524 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 148 helices and 25 sheets defined 38.1% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.10 Creating SS restraints... Processing helix chain 'A' and resid 3 through 19 removed outlier: 4.218A pdb=" N GLN A 7 " --> pdb=" O PRO A 3 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 9 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 35 removed outlier: 4.427A pdb=" N VAL A 34 " --> pdb=" O GLU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 85 through 88 No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 324 through 345 removed outlier: 4.354A pdb=" N ASP A 329 " --> pdb=" O GLU A 325 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG A 331 " --> pdb=" O THR A 327 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 340 " --> pdb=" O GLN A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 367 through 376 removed outlier: 3.712A pdb=" N LEU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 384 Processing helix chain 'A' and resid 400 through 416 removed outlier: 4.008A pdb=" N ARG A 405 " --> pdb=" O TRP A 401 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A 416 " --> pdb=" O TYR A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 436 removed outlier: 3.886A pdb=" N GLN A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 451 removed outlier: 3.551A pdb=" N HIS A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE A 450 " --> pdb=" O MET A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 457 No H-bonds generated for 'chain 'A' and resid 455 through 457' Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.706A pdb=" N GLN A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 526 Processing helix chain 'A' and resid 641 through 656 removed outlier: 3.580A pdb=" N LEU A 646 " --> pdb=" O ASP A 642 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN A 652 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 687 removed outlier: 3.503A pdb=" N GLN A 682 " --> pdb=" O ALA A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 713 Processing helix chain 'A' and resid 730 through 741 removed outlier: 4.008A pdb=" N ILE A 737 " --> pdb=" O VAL A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 783 Processing helix chain 'A' and resid 785 through 800 Processing helix chain 'A' and resid 827 through 843 removed outlier: 3.571A pdb=" N LEU A 834 " --> pdb=" O SER A 830 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 835 " --> pdb=" O LYS A 831 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N THR A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A 837 " --> pdb=" O GLY A 833 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N PHE A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ASN A 839 " --> pdb=" O GLU A 835 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N TYR A 842 " --> pdb=" O PHE A 838 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 871 No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 873 through 876 No H-bonds generated for 'chain 'A' and resid 873 through 876' Processing helix chain 'A' and resid 886 through 896 removed outlier: 3.506A pdb=" N LEU A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 904 No H-bonds generated for 'chain 'A' and resid 901 through 904' Processing helix chain 'A' and resid 918 through 920 No H-bonds generated for 'chain 'A' and resid 918 through 920' Processing helix chain 'A' and resid 924 through 956 removed outlier: 3.552A pdb=" N THR A 938 " --> pdb=" O GLU A 934 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A 943 " --> pdb=" O SER A 939 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL A 945 " --> pdb=" O VAL A 941 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 953 " --> pdb=" O THR A 949 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ARG A 954 " --> pdb=" O GLY A 950 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 956 " --> pdb=" O GLU A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 961 No H-bonds generated for 'chain 'A' and resid 959 through 961' Processing helix chain 'A' and resid 986 through 992 Processing helix chain 'A' and resid 1002 through 1004 No H-bonds generated for 'chain 'A' and resid 1002 through 1004' Processing helix chain 'A' and resid 1022 through 1027 Processing helix chain 'A' and resid 1034 through 1043 Processing helix chain 'A' and resid 1073 through 1079 removed outlier: 3.586A pdb=" N ILE A1076 " --> pdb=" O ASP A1073 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N LYS A1077 " --> pdb=" O LYS A1074 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS A1078 " --> pdb=" O ASP A1075 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1086 Processing helix chain 'A' and resid 1095 through 1097 No H-bonds generated for 'chain 'A' and resid 1095 through 1097' Processing helix chain 'A' and resid 1125 through 1134 Processing helix chain 'A' and resid 1182 through 1185 Processing helix chain 'A' and resid 1189 through 1192 No H-bonds generated for 'chain 'A' and resid 1189 through 1192' Processing helix chain 'A' and resid 1197 through 1211 removed outlier: 3.518A pdb=" N TYR A1201 " --> pdb=" O PRO A1197 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A1208 " --> pdb=" O VAL A1204 " (cutoff:3.500A) Processing helix chain 'A' and resid 1218 through 1223 Processing helix chain 'A' and resid 1241 through 1248 removed outlier: 3.714A pdb=" N GLY A1246 " --> pdb=" O SER A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1267 through 1277 removed outlier: 3.862A pdb=" N MET A1270 " --> pdb=" O ILE A1267 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A1271 " --> pdb=" O ASN A1268 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TRP A1273 " --> pdb=" O MET A1270 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A1274 " --> pdb=" O SER A1271 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A1276 " --> pdb=" O TRP A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1308 Processing helix chain 'A' and resid 1324 through 1332 removed outlier: 3.511A pdb=" N ALA A1331 " --> pdb=" O SER A1327 " (cutoff:3.500A) Processing helix chain 'A' and resid 1341 through 1344 No H-bonds generated for 'chain 'A' and resid 1341 through 1344' Processing helix chain 'A' and resid 1349 through 1351 No H-bonds generated for 'chain 'A' and resid 1349 through 1351' Processing helix chain 'A' and resid 1377 through 1383 Processing helix chain 'A' and resid 1411 through 1415 removed outlier: 3.584A pdb=" N THR A1414 " --> pdb=" O GLY A1411 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1430 No H-bonds generated for 'chain 'A' and resid 1428 through 1430' Processing helix chain 'A' and resid 1432 through 1461 removed outlier: 3.527A pdb=" N GLN A1445 " --> pdb=" O LYS A1441 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A1447 " --> pdb=" O LYS A1443 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1451 " --> pdb=" O LYS A1447 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A1455 " --> pdb=" O GLU A1451 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TYR A1456 " --> pdb=" O ASP A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1479 No H-bonds generated for 'chain 'A' and resid 1476 through 1479' Processing helix chain 'A' and resid 1482 through 1498 removed outlier: 3.727A pdb=" N GLN A1497 " --> pdb=" O LYS A1493 " (cutoff:3.500A) Processing helix chain 'A' and resid 1512 through 1520 removed outlier: 3.898A pdb=" N LEU A1517 " --> pdb=" O LEU A1513 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE A1520 " --> pdb=" O ALA A1516 " (cutoff:3.500A) Processing helix chain 'A' and resid 1524 through 1526 No H-bonds generated for 'chain 'A' and resid 1524 through 1526' Processing helix chain 'A' and resid 1538 through 1554 removed outlier: 4.043A pdb=" N LYS A1542 " --> pdb=" O LYS A1538 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A1545 " --> pdb=" O ASP A1541 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1570 No H-bonds generated for 'chain 'A' and resid 1568 through 1570' Processing helix chain 'A' and resid 1579 through 1593 removed outlier: 3.561A pdb=" N LEU A1591 " --> pdb=" O ALA A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1610 removed outlier: 3.585A pdb=" N GLU A1610 " --> pdb=" O LYS A1607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1607 through 1610' Processing helix chain 'A' and resid 1649 through 1653 removed outlier: 3.660A pdb=" N PHE A1653 " --> pdb=" O ASP A1650 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1685 removed outlier: 3.503A pdb=" N LYS A1667 " --> pdb=" O GLU A1663 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1673 " --> pdb=" O GLU A1669 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A1674 " --> pdb=" O ALA A1670 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE A1684 " --> pdb=" O HIS A1680 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1706 removed outlier: 5.793A pdb=" N GLN A1703 " --> pdb=" O GLU A1700 " (cutoff:3.500A) Proline residue: A1704 - end of helix Processing helix chain 'A' and resid 1727 through 1729 No H-bonds generated for 'chain 'A' and resid 1727 through 1729' Processing helix chain 'B' and resid 31 through 43 removed outlier: 4.526A pdb=" N GLY B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 73 removed outlier: 3.706A pdb=" N LEU B 64 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 96 removed outlier: 3.591A pdb=" N ALA B 84 " --> pdb=" O GLN B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.653A pdb=" N ILE B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'B' and resid 128 through 137 removed outlier: 3.639A pdb=" N TYR B 132 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 178 through 187 Processing helix chain 'B' and resid 196 through 206 removed outlier: 4.164A pdb=" N GLU B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 removed outlier: 3.535A pdb=" N GLU B 228 " --> pdb=" O ILE B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 244 No H-bonds generated for 'chain 'B' and resid 242 through 244' Processing helix chain 'B' and resid 246 through 263 removed outlier: 3.623A pdb=" N CYS B 250 " --> pdb=" O CYS B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.545A pdb=" N VAL B 290 " --> pdb=" O VAL B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 320 removed outlier: 3.854A pdb=" N GLU B 301 " --> pdb=" O TRP B 297 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.602A pdb=" N ASP B 334 " --> pdb=" O SER B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 367 removed outlier: 4.301A pdb=" N LYS B 359 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 361 " --> pdb=" O LEU B 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR B 364 " --> pdb=" O PHE B 360 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N HIS B 367 " --> pdb=" O GLU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 404 removed outlier: 3.786A pdb=" N LEU B 397 " --> pdb=" O SER B 393 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA B 404 " --> pdb=" O ASN B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 445 through 451 Processing helix chain 'B' and resid 483 through 492 removed outlier: 3.643A pdb=" N GLU B 489 " --> pdb=" O ALA B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 No H-bonds generated for 'chain 'B' and resid 498 through 501' Processing helix chain 'B' and resid 516 through 518 No H-bonds generated for 'chain 'B' and resid 516 through 518' Processing helix chain 'B' and resid 520 through 523 No H-bonds generated for 'chain 'B' and resid 520 through 523' Processing helix chain 'B' and resid 526 through 531 removed outlier: 3.868A pdb=" N GLU B 529 " --> pdb=" O ARG B 526 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLY B 530 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 531 " --> pdb=" O LYS B 528 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 526 through 531' Processing helix chain 'B' and resid 553 through 555 No H-bonds generated for 'chain 'B' and resid 553 through 555' Processing helix chain 'B' and resid 561 through 563 No H-bonds generated for 'chain 'B' and resid 561 through 563' Processing helix chain 'B' and resid 570 through 573 No H-bonds generated for 'chain 'B' and resid 570 through 573' Processing helix chain 'B' and resid 591 through 596 removed outlier: 3.629A pdb=" N LEU B 595 " --> pdb=" O LYS B 591 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 3.626A pdb=" N ALA B 618 " --> pdb=" O ASP B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 648 Processing helix chain 'B' and resid 665 through 680 removed outlier: 3.901A pdb=" N TRP B 670 " --> pdb=" O ARG B 666 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE B 672 " --> pdb=" O LEU B 668 " (cutoff:3.500A) Proline residue: B 673 - end of helix Processing helix chain 'B' and resid 697 through 704 removed outlier: 3.822A pdb=" N GLU B 702 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TYR B 703 " --> pdb=" O VAL B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 719 through 729 removed outlier: 3.568A pdb=" N ASN B 723 " --> pdb=" O ILE B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 768 removed outlier: 6.158A pdb=" N SER B 764 " --> pdb=" O LEU B 760 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N LYS B 765 " --> pdb=" O GLN B 761 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS B 768 " --> pdb=" O SER B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 791 Proline residue: B 788 - end of helix Processing helix chain 'B' and resid 795 through 798 Processing helix chain 'B' and resid 812 through 814 No H-bonds generated for 'chain 'B' and resid 812 through 814' Processing helix chain 'B' and resid 824 through 831 removed outlier: 3.576A pdb=" N GLN B 828 " --> pdb=" O PRO B 824 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 829 " --> pdb=" O ALA B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 842 through 844 No H-bonds generated for 'chain 'B' and resid 842 through 844' Processing helix chain 'B' and resid 869 through 878 Processing helix chain 'B' and resid 886 through 895 removed outlier: 4.383A pdb=" N LEU B 890 " --> pdb=" O LYS B 886 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 891 " --> pdb=" O ASN B 887 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA B 892 " --> pdb=" O LYS B 888 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 907 removed outlier: 3.730A pdb=" N LYS B 902 " --> pdb=" O ASP B 898 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 925 No H-bonds generated for 'chain 'B' and resid 923 through 925' Processing helix chain 'B' and resid 928 through 939 removed outlier: 3.859A pdb=" N VAL B 936 " --> pdb=" O ALA B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 966 Processing helix chain 'B' and resid 980 through 983 Processing helix chain 'B' and resid 986 through 996 removed outlier: 3.596A pdb=" N SER B 992 " --> pdb=" O LYS B 988 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA B 996 " --> pdb=" O SER B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 998 through 1001 Processing helix chain 'B' and resid 1007 through 1017 Processing helix chain 'B' and resid 1033 through 1039 removed outlier: 4.278A pdb=" N GLU B1036 " --> pdb=" O GLU B1033 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N PHE B1039 " --> pdb=" O GLU B1036 " (cutoff:3.500A) Processing helix chain 'B' and resid 1045 through 1047 No H-bonds generated for 'chain 'B' and resid 1045 through 1047' Processing helix chain 'B' and resid 1054 through 1056 No H-bonds generated for 'chain 'B' and resid 1054 through 1056' Processing helix chain 'B' and resid 1058 through 1060 No H-bonds generated for 'chain 'B' and resid 1058 through 1060' Processing helix chain 'B' and resid 1080 through 1083 No H-bonds generated for 'chain 'B' and resid 1080 through 1083' Processing helix chain 'B' and resid 1085 through 1099 removed outlier: 3.860A pdb=" N LYS B1097 " --> pdb=" O LYS B1093 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1104 through 1106 No H-bonds generated for 'chain 'B' and resid 1104 through 1106' Processing helix chain 'B' and resid 1147 through 1154 removed outlier: 3.634A pdb=" N ASP B1152 " --> pdb=" O GLN B1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 1161 through 1166 Processing helix chain 'B' and resid 1181 through 1185 removed outlier: 4.216A pdb=" N VAL B1185 " --> pdb=" O ALA B1182 " (cutoff:3.500A) Processing helix chain 'B' and resid 1270 through 1282 removed outlier: 3.614A pdb=" N LYS B1280 " --> pdb=" O ASN B1276 " (cutoff:3.500A) Processing helix chain 'B' and resid 1308 through 1318 Processing helix chain 'B' and resid 1323 through 1325 No H-bonds generated for 'chain 'B' and resid 1323 through 1325' Processing helix chain 'B' and resid 1337 through 1343 removed outlier: 3.542A pdb=" N ILE B1341 " --> pdb=" O ASP B1338 " (cutoff:3.500A) Processing helix chain 'B' and resid 1345 through 1351 removed outlier: 3.764A pdb=" N LYS B1350 " --> pdb=" O LYS B1346 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B1351 " --> pdb=" O ALA B1347 " (cutoff:3.500A) Processing helix chain 'B' and resid 1361 through 1363 No H-bonds generated for 'chain 'B' and resid 1361 through 1363' Processing helix chain 'B' and resid 1452 through 1460 removed outlier: 3.597A pdb=" N ALA B1456 " --> pdb=" O ALA B1452 " (cutoff:3.500A) Processing helix chain 'B' and resid 1528 through 1536 removed outlier: 3.536A pdb=" N ARG B1535 " --> pdb=" O ASP B1531 " (cutoff:3.500A) Processing helix chain 'B' and resid 1569 through 1573 Processing helix chain 'B' and resid 1583 through 1588 Processing helix chain 'B' and resid 1598 through 1612 removed outlier: 3.674A pdb=" N ALA B1607 " --> pdb=" O ALA B1603 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU B1608 " --> pdb=" O ALA B1604 " (cutoff:3.500A) Processing helix chain 'B' and resid 1618 through 1620 No H-bonds generated for 'chain 'B' and resid 1618 through 1620' Processing helix chain 'B' and resid 1695 through 1700 Processing helix chain 'B' and resid 1702 through 1719 removed outlier: 3.741A pdb=" N VAL B1707 " --> pdb=" O VAL B1703 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TRP B1708 " --> pdb=" O ALA B1704 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG B1710 " --> pdb=" O SER B1706 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS B1714 " --> pdb=" O ARG B1710 " (cutoff:3.500A) Processing helix chain 'B' and resid 1723 through 1728 Processing helix chain 'B' and resid 1741 through 1751 removed outlier: 3.581A pdb=" N SER B1745 " --> pdb=" O ALA B1741 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B1746 " --> pdb=" O LYS B1742 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B1749 " --> pdb=" O SER B1745 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR B1750 " --> pdb=" O ILE B1746 " (cutoff:3.500A) Processing helix chain 'B' and resid 1788 through 1790 No H-bonds generated for 'chain 'B' and resid 1788 through 1790' Processing helix chain 'B' and resid 1792 through 1812 Proline residue: B1797 - end of helix removed outlier: 3.664A pdb=" N LEU B1801 " --> pdb=" O PRO B1797 " (cutoff:3.500A) Processing helix chain 'B' and resid 1828 through 1833 removed outlier: 3.825A pdb=" N LEU B1833 " --> pdb=" O GLU B1829 " (cutoff:3.500A) Processing helix chain 'B' and resid 1842 through 1855 Processing helix chain 'B' and resid 1886 through 1898 removed outlier: 4.231A pdb=" N VAL B1892 " --> pdb=" O ALA B1888 " (cutoff:3.500A) Processing helix chain 'B' and resid 1925 through 1930 Processing helix chain 'B' and resid 1959 through 1971 removed outlier: 3.539A pdb=" N VAL B1965 " --> pdb=" O ILE B1961 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N LYS B1968 " --> pdb=" O GLU B1964 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B1970 " --> pdb=" O SER B1966 " (cutoff:3.500A) Processing helix chain 'B' and resid 2001 through 2013 removed outlier: 3.910A pdb=" N LYS B2004 " --> pdb=" O SER B2001 " (cutoff:3.500A) Proline residue: B2005 - end of helix removed outlier: 3.656A pdb=" N THR B2008 " --> pdb=" O PRO B2005 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE B2009 " --> pdb=" O PHE B2006 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N CYS B2011 " --> pdb=" O THR B2008 " (cutoff:3.500A) Processing helix chain 'B' and resid 2043 through 2051 removed outlier: 3.513A pdb=" N VAL B2047 " --> pdb=" O TYR B2043 " (cutoff:3.500A) Processing helix chain 'B' and resid 2054 through 2060 removed outlier: 3.516A pdb=" N HIS B2058 " --> pdb=" O GLU B2054 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ILE B2059 " --> pdb=" O LYS B2055 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 43 through 46 removed outlier: 6.051A pdb=" N GLN A 77 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLU A 46 " --> pdb=" O GLN A 77 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU A 79 " --> pdb=" O GLU A 46 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.444A pdb=" N ALA A 755 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 8.089A pdb=" N THR A 669 " --> pdb=" O ALA A 755 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A 757 " --> pdb=" O THR A 669 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 492 through 498 Processing sheet with id= D, first strand: chain 'A' and resid 637 through 640 removed outlier: 4.759A pdb=" N LEU A 628 " --> pdb=" O ASP A 640 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL A 911 " --> pdb=" O LYS A 629 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 808 through 810 Processing sheet with id= F, first strand: chain 'A' and resid 1047 through 1049 Processing sheet with id= G, first strand: chain 'A' and resid 1106 through 1113 Processing sheet with id= H, first strand: chain 'A' and resid 1121 through 1123 Processing sheet with id= I, first strand: chain 'A' and resid 1230 through 1232 removed outlier: 6.738A pdb=" N ILE A1313 " --> pdb=" O GLY A1231 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1010 " --> pdb=" O VAL A1373 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N MET A1375 " --> pdb=" O VAL A1008 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL A1008 " --> pdb=" O MET A1375 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 1529 through 1531 removed outlier: 5.830A pdb=" N PHE A1564 " --> pdb=" O ALA A1530 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'A' and resid 1629 through 1634 removed outlier: 3.776A pdb=" N LEU A1393 " --> pdb=" O ILE A1645 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A1647 " --> pdb=" O VAL A1391 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N VAL A1391 " --> pdb=" O VAL A1647 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 164 through 167 removed outlier: 6.693A pdb=" N HIS B 508 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE B 167 " --> pdb=" O HIS B 508 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU B 510 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG B 534 " --> pdb=" O VAL B 509 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N ASP B 511 " --> pdb=" O ARG B 534 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE B 536 " --> pdb=" O ASP B 511 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 425 through 428 removed outlier: 3.712A pdb=" N LEU B 378 " --> pdb=" O VAL B 386 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 388 " --> pdb=" O ILE B 376 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE B 376 " --> pdb=" O THR B 388 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 577 through 580 Processing sheet with id= O, first strand: chain 'B' and resid 659 through 661 removed outlier: 7.814A pdb=" N LEU B 660 " --> pdb=" O SER B 687 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N SER B 689 " --> pdb=" O LEU B 660 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS B 711 " --> pdb=" O LEU B 688 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ILE B 690 " --> pdb=" O HIS B 711 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N GLY B 713 " --> pdb=" O ILE B 690 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU B 714 " --> pdb=" O PRO B 736 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL B 738 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE B 773 " --> pdb=" O LEU B 739 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP B 741 " --> pdb=" O ILE B 773 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 775 " --> pdb=" O TRP B 741 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 852 through 855 Processing sheet with id= Q, first strand: chain 'B' and resid 1129 through 1131 Processing sheet with id= R, first strand: chain 'B' and resid 1193 through 1196 Processing sheet with id= S, first strand: chain 'B' and resid 1211 through 1213 Processing sheet with id= T, first strand: chain 'B' and resid 1303 through 1305 removed outlier: 6.611A pdb=" N GLU B1405 " --> pdb=" O ARG B1393 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL B1395 " --> pdb=" O THR B1403 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N THR B1403 " --> pdb=" O VAL B1395 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B1418 " --> pdb=" O ILE B1410 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG B1412 " --> pdb=" O PRO B1416 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N PHE B1425 " --> pdb=" O HIS B1366 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N HIS B1366 " --> pdb=" O PHE B1425 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LEU B1367 " --> pdb=" O PHE B1628 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ALA B1623 " --> pdb=" O GLU B1673 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N THR B1658 " --> pdb=" O VAL B1667 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ILE B1669 " --> pdb=" O VAL B1656 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL B1656 " --> pdb=" O ILE B1669 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU B1671 " --> pdb=" O ILE B1654 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE B1654 " --> pdb=" O GLU B1671 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU B1673 " --> pdb=" O LYS B1652 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS B1652 " --> pdb=" O GLU B1673 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B1646 " --> pdb=" O ILE B1653 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LYS B1655 " --> pdb=" O HIS B1644 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N HIS B1644 " --> pdb=" O LYS B1655 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 1437 through 1441 removed outlier: 3.864A pdb=" N SER B1495 " --> pdb=" O LYS B1486 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'B' and resid 1445 through 1449 removed outlier: 3.553A pdb=" N VAL B1445 " --> pdb=" O PHE B1479 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN B1475 " --> pdb=" O PHE B1449 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N THR B1476 " --> pdb=" O GLU B1505 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU B1505 " --> pdb=" O THR B1476 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ALA B1502 " --> pdb=" O ALA B1515 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B1515 " --> pdb=" O ALA B1502 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU B1504 " --> pdb=" O GLN B1513 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B1513 " --> pdb=" O LEU B1504 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU B1506 " --> pdb=" O ILE B1511 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ILE B1511 " --> pdb=" O LEU B1506 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'B' and resid 1680 through 1683 removed outlier: 6.949A pdb=" N MET B1821 " --> pdb=" O PHE B1681 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N PHE B1683 " --> pdb=" O MET B1821 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N ALA B1823 " --> pdb=" O PHE B1683 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'B' and resid 1733 through 1737 Processing sheet with id= Y, first strand: chain 'B' and resid 1870 through 1875 removed outlier: 6.137A pdb=" N ALA B1919 " --> pdb=" O ILE B1906 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ILE B1906 " --> pdb=" O ALA B1919 " (cutoff:3.500A) removed outlier: 7.774A pdb=" N ASP B1921 " --> pdb=" O LEU B1904 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N LEU B1904 " --> pdb=" O ASP B1921 " (cutoff:3.500A) 812 hydrogen bonds defined for protein. 2310 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: 12.68 Time building geometry restraints manager: 12.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8395 1.33 - 1.45: 4418 1.45 - 1.57: 15221 1.57 - 1.69: 2 1.69 - 1.81: 163 Bond restraints: 28199 Sorted by residual: bond pdb=" CA THR A1359 " pdb=" CB THR A1359 " ideal model delta sigma weight residual 1.526 1.488 0.038 1.51e-02 4.39e+03 6.34e+00 bond pdb=" C LYS B2004 " pdb=" N PRO B2005 " ideal model delta sigma weight residual 1.337 1.368 -0.031 1.24e-02 6.50e+03 6.20e+00 bond pdb=" C ASP A1254 " pdb=" N LYS A1255 " ideal model delta sigma weight residual 1.331 1.262 0.069 2.83e-02 1.25e+03 5.87e+00 bond pdb=" CB VAL A1316 " pdb=" CG2 VAL A1316 " ideal model delta sigma weight residual 1.521 1.444 0.077 3.30e-02 9.18e+02 5.49e+00 bond pdb=" N GLU B 49 " pdb=" CA GLU B 49 " ideal model delta sigma weight residual 1.457 1.486 -0.028 1.29e-02 6.01e+03 4.81e+00 ... (remaining 28194 not shown) Histogram of bond angle deviations from ideal: 97.56 - 104.93: 521 104.93 - 112.29: 13719 112.29 - 119.66: 10409 119.66 - 127.03: 13239 127.03 - 134.39: 311 Bond angle restraints: 38199 Sorted by residual: angle pdb=" C SER B 241 " pdb=" N ILE B 242 " pdb=" CA ILE B 242 " ideal model delta sigma weight residual 120.24 125.35 -5.11 6.30e-01 2.52e+00 6.59e+01 angle pdb=" N PHE B1353 " pdb=" CA PHE B1353 " pdb=" C PHE B1353 " ideal model delta sigma weight residual 109.81 122.50 -12.69 2.21e+00 2.05e-01 3.30e+01 angle pdb=" C GLN B1899 " pdb=" N THR B1900 " pdb=" CA THR B1900 " ideal model delta sigma weight residual 121.54 132.16 -10.62 1.91e+00 2.74e-01 3.09e+01 angle pdb=" CA ASN A 439 " pdb=" C ASN A 439 " pdb=" N PRO A 440 " ideal model delta sigma weight residual 117.68 121.09 -3.41 7.10e-01 1.98e+00 2.31e+01 angle pdb=" C SER B 751 " pdb=" N PHE B 752 " pdb=" CA PHE B 752 " ideal model delta sigma weight residual 121.54 129.57 -8.03 1.91e+00 2.74e-01 1.77e+01 ... (remaining 38194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.98: 15893 23.98 - 47.97: 940 47.97 - 71.95: 111 71.95 - 95.93: 46 95.93 - 119.91: 1 Dihedral angle restraints: 16991 sinusoidal: 6833 harmonic: 10158 Sorted by residual: dihedral pdb=" CA ASP B 235 " pdb=" C ASP B 235 " pdb=" N GLN B 236 " pdb=" CA GLN B 236 " ideal model delta harmonic sigma weight residual 180.00 145.69 34.31 0 5.00e+00 4.00e-02 4.71e+01 dihedral pdb=" C5' FMN B2101 " pdb=" O5' FMN B2101 " pdb=" P FMN B2101 " pdb=" O1P FMN B2101 " ideal model delta sinusoidal sigma weight residual 75.26 -44.66 119.91 1 2.00e+01 2.50e-03 3.60e+01 dihedral pdb=" CA LEU A 53 " pdb=" C LEU A 53 " pdb=" N ALA A 54 " pdb=" CA ALA A 54 " ideal model delta harmonic sigma weight residual 180.00 150.08 29.92 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 16988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 3238 0.062 - 0.125: 890 0.125 - 0.187: 118 0.187 - 0.249: 14 0.249 - 0.311: 6 Chirality restraints: 4266 Sorted by residual: chirality pdb=" CB VAL B 386 " pdb=" CA VAL B 386 " pdb=" CG1 VAL B 386 " pdb=" CG2 VAL B 386 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA PHE B1353 " pdb=" N PHE B1353 " pdb=" C PHE B1353 " pdb=" CB PHE B1353 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" CB ILE B 628 " pdb=" CA ILE B 628 " pdb=" CG1 ILE B 628 " pdb=" CG2 ILE B 628 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 4263 not shown) Planarity restraints: 4926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 963 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 964 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 964 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 964 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 441 " 0.049 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO B 442 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO B 442 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 442 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A1015 " -0.048 5.00e-02 4.00e+02 7.19e-02 8.27e+00 pdb=" N PRO A1016 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO A1016 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1016 " -0.040 5.00e-02 4.00e+02 ... (remaining 4923 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8409 2.81 - 3.33: 24089 3.33 - 3.85: 46181 3.85 - 4.38: 56105 4.38 - 4.90: 95043 Nonbonded interactions: 229827 Sorted by model distance: nonbonded pdb=" OD1 ASP A1064 " pdb=" OH TYR A1080 " model vdw 2.285 2.440 nonbonded pdb=" O VAL B1962 " pdb=" OG SER B1966 " model vdw 2.289 2.440 nonbonded pdb=" O GLU B 702 " pdb=" OG1 THR B 706 " model vdw 2.295 2.440 nonbonded pdb=" O SER B 506 " pdb=" OG SER B 533 " model vdw 2.297 2.440 nonbonded pdb=" O SER A 73 " pdb=" OG SER A 73 " model vdw 2.297 2.440 ... (remaining 229822 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 20.520 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 78.240 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 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 : 0.008 0.081 28199 Z= 0.511 Angle : 0.877 14.093 38199 Z= 0.475 Chirality : 0.057 0.311 4266 Planarity : 0.007 0.073 4926 Dihedral : 15.489 119.914 10467 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 1.19 % Allowed : 8.22 % Favored : 90.59 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -5.07 (0.10), residues: 3506 helix: -4.39 (0.05), residues: 1458 sheet: -2.27 (0.21), residues: 474 loop : -2.49 (0.13), residues: 1574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 28 HIS 0.019 0.002 HIS A1135 PHE 0.040 0.003 PHE A1363 TYR 0.025 0.002 TYR B 30 ARG 0.010 0.001 ARG A 932 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 348 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 14 residues processed: 375 average time/residue: 0.4745 time to fit residues: 269.6441 Evaluate side-chains 229 residues out of total 3017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 215 time to evaluate : 3.492 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.2548 time to fit residues: 11.3201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 296 optimal weight: 6.9990 chunk 266 optimal weight: 3.9990 chunk 147 optimal weight: 9.9990 chunk 90 optimal weight: 5.9990 chunk 179 optimal weight: 5.9990 chunk 142 optimal weight: 0.0980 chunk 275 optimal weight: 9.9990 chunk 106 optimal weight: 0.6980 chunk 167 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 318 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 436 ASN A 449 HIS A 452 HIS A 780 HIS A 975 ASN A1175 GLN A1226 HIS A1323 GLN A1332 ASN A1491 GLN A1501 ASN A1561 ASN A1727 ASN B 80 GLN B 91 ASN B 171 GLN B 236 GLN B 237 GLN B 400 ASN ** B 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 HIS ** B 525 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 732 HIS B 796 HIS B 979 ASN B1006 ASN B1018 GLN B1180 ASN B1366 HIS B1518 ASN B1536 HIS B1548 ASN B1611 GLN B1644 HIS B1676 GLN B1717 ASN B1729 ASN B1730 ASN B1913 ASN ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1938 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1995 HIS B2038 GLN B2062 HIS Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28199 Z= 0.219 Angle : 0.581 10.823 38199 Z= 0.305 Chirality : 0.044 0.183 4266 Planarity : 0.005 0.055 4926 Dihedral : 5.602 104.793 3778 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.76 % Allowed : 11.10 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.12), residues: 3506 helix: -2.49 (0.11), residues: 1448 sheet: -1.77 (0.22), residues: 487 loop : -1.95 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1017 HIS 0.010 0.001 HIS A1135 PHE 0.024 0.001 PHE A 35 TYR 0.019 0.001 TYR A 347 ARG 0.006 0.000 ARG A1354 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 256 time to evaluate : 3.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 31 residues processed: 299 average time/residue: 0.4637 time to fit residues: 214.5420 Evaluate side-chains 252 residues out of total 3017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 221 time to evaluate : 3.233 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2749 time to fit residues: 19.8181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 351 random chunks: chunk 177 optimal weight: 0.0970 chunk 98 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 87 optimal weight: 0.0470 chunk 319 optimal weight: 0.9980 chunk 344 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 316 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 overall best weight: 1.0280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 817 ASN A 892 ASN A 933 ASN A1501 ASN A1727 ASN A1742 ASN B 460 GLN B 525 HIS B 724 GLN B1366 HIS B1729 ASN B1730 ASN B1899 GLN ** B1933 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28199 Z= 0.168 Angle : 0.524 8.897 38199 Z= 0.271 Chirality : 0.043 0.168 4266 Planarity : 0.004 0.057 4926 Dihedral : 4.974 61.352 3778 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.36 % Allowed : 13.03 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.13), residues: 3506 helix: -1.36 (0.13), residues: 1450 sheet: -1.49 (0.22), residues: 493 loop : -1.69 (0.15), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1017 HIS 0.010 0.001 HIS A1135 PHE 0.023 0.001 PHE A 35 TYR 0.016 0.001 TYR A 347 ARG 0.005 0.000 ARG A 954 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7012 Ramachandran restraints generated. 3506 Oldfield, 0 Emsley, 3506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 247 time to evaluate : 3.380 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 22 residues processed: 283 average time/residue: 0.4515 time to fit residues: 201.3336 Evaluate side-chains 244 residues out of total 3017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 222 time to evaluate : 3.295 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.2681 time to fit residues: 15.7484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 62.8451 > 50: distance: 5 - 32: 3.776 distance: 11 - 40: 4.829 distance: 33 - 36: 5.774 distance: 34 - 35: 4.174 distance: 34 - 40: 4.386 distance: 36 - 37: 5.223 distance: 37 - 38: 3.635 distance: 37 - 39: 4.219 distance: 40 - 41: 7.866 distance: 41 - 42: 4.985 distance: 41 - 44: 7.881 distance: 42 - 43: 4.376 distance: 42 - 46: 12.457 distance: 44 - 45: 16.393 distance: 46 - 47: 6.146 distance: 47 - 48: 3.447 distance: 47 - 50: 3.067 distance: 48 - 52: 4.465 distance: 50 - 51: 17.710 distance: 53 - 54: 6.266 distance: 53 - 56: 10.308 distance: 54 - 55: 14.818 distance: 54 - 61: 12.519 distance: 55 - 82: 21.513 distance: 56 - 57: 8.596 distance: 57 - 58: 10.416 distance: 58 - 59: 13.972 distance: 58 - 60: 10.731 distance: 61 - 62: 10.433 distance: 62 - 63: 9.809 distance: 62 - 65: 12.110 distance: 63 - 64: 23.748 distance: 63 - 68: 12.583 distance: 65 - 66: 12.925 distance: 65 - 67: 19.779 distance: 68 - 69: 7.527 distance: 69 - 70: 16.265 distance: 69 - 72: 26.783 distance: 70 - 71: 41.063 distance: 70 - 73: 15.561 distance: 73 - 74: 6.636 distance: 74 - 75: 8.437 distance: 74 - 77: 6.046 distance: 75 - 76: 8.939 distance: 75 - 82: 7.637 distance: 76 - 109: 3.419 distance: 77 - 78: 15.695 distance: 78 - 79: 9.330 distance: 79 - 80: 5.261 distance: 80 - 81: 11.059 distance: 82 - 83: 6.602 distance: 83 - 84: 9.257 distance: 83 - 86: 4.783 distance: 84 - 85: 11.987 distance: 84 - 88: 6.954 distance: 86 - 87: 20.115 distance: 88 - 89: 4.667 distance: 89 - 90: 9.279 distance: 89 - 92: 3.428 distance: 90 - 91: 5.442 distance: 90 - 95: 10.228 distance: 91 - 124: 18.633 distance: 92 - 93: 7.623 distance: 92 - 94: 7.252 distance: 95 - 96: 4.385 distance: 96 - 97: 3.147 distance: 96 - 99: 4.747 distance: 97 - 98: 7.136 distance: 97 - 109: 4.012 distance: 98 - 129: 8.331 distance: 99 - 100: 5.803 distance: 100 - 102: 5.567 distance: 102 - 104: 5.244 distance: 102 - 105: 5.640 distance: 103 - 104: 5.313 distance: 104 - 106: 5.142 distance: 105 - 107: 4.960 distance: 106 - 108: 4.619 distance: 107 - 108: 3.960