Starting phenix.real_space_refine on Thu Jul 25 18:53:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/07_2024/8psa_17848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/07_2024/8psa_17848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/07_2024/8psa_17848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/07_2024/8psa_17848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/07_2024/8psa_17848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8psa_17848/07_2024/8psa_17848.cif" } resolution = 3.6 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 107 5.16 5 C 18912 2.51 5 N 4967 2.21 5 O 5694 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 93": "OD1" <-> "OD2" Residue "A PHE 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 514": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ASP 648": "OD1" <-> "OD2" Residue "A ASP 652": "OD1" <-> "OD2" Residue "A ASP 675": "OD1" <-> "OD2" Residue "A GLU 746": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A GLU 938": "OE1" <-> "OE2" Residue "A ASP 991": "OD1" <-> "OD2" Residue "A GLU 1048": "OE1" <-> "OE2" Residue "A TYR 1072": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1094": "OE1" <-> "OE2" Residue "A GLU 1132": "OE1" <-> "OE2" Residue "A PHE 1134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1139": "OE1" <-> "OE2" Residue "A TYR 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A GLU 1268": "OE1" <-> "OE2" Residue "A GLU 1317": "OE1" <-> "OE2" Residue "A TYR 1332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1333": "OD1" <-> "OD2" Residue "A GLU 1354": "OE1" <-> "OE2" Residue "A GLU 1357": "OE1" <-> "OE2" Residue "A TYR 1438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1475": "OE1" <-> "OE2" Residue "A PHE 1512": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1513": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1576": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1579": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1612": "OD1" <-> "OD2" Residue "A PHE 1687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1712": "OE1" <-> "OE2" Residue "A ASP 1713": "OD1" <-> "OD2" Residue "A ASP 1742": "OD1" <-> "OD2" Residue "A ASP 1784": "OD1" <-> "OD2" Residue "B ASP 142": "OD1" <-> "OD2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 207": "OE1" <-> "OE2" Residue "B PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 111": "OE1" <-> "OE2" Residue "G PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 262": "OE1" <-> "OE2" Residue "G ASP 287": "OD1" <-> "OD2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 347": "OE1" <-> "OE2" Residue "G ASP 351": "OD1" <-> "OD2" Residue "G ASP 437": "OD1" <-> "OD2" Residue "G ASP 534": "OD1" <-> "OD2" Residue "G ASP 538": "OD1" <-> "OD2" Residue "G PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 689": "OE1" <-> "OE2" Residue "G GLU 693": "OE1" <-> "OE2" Residue "G TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 790": "OD1" <-> "OD2" Residue "G PHE 799": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 801": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 870": "OE1" <-> "OE2" Residue "G GLU 885": "OE1" <-> "OE2" Residue "G GLU 981": "OE1" <-> "OE2" Residue "G GLU 992": "OE1" <-> "OE2" Residue "G GLU 1038": "OE1" <-> "OE2" Residue "G PHE 1174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 1266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1299": "OD1" <-> "OD2" Residue "G PHE 1300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 1310": "OD1" <-> "OD2" Residue "G PHE 1339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1419": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1420": "OE1" <-> "OE2" Residue "G GLU 1448": "OE1" <-> "OE2" Residue "G PHE 1450": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1467": "OE1" <-> "OE2" Residue "G GLU 1469": "OE1" <-> "OE2" Residue "G PHE 1486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1656": "OE1" <-> "OE2" Residue "G GLU 1658": "OE1" <-> "OE2" Residue "G PHE 1704": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 1738": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1749": "OE1" <-> "OE2" Residue "G PHE 1752": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1757": "OE1" <-> "OE2" Residue "G ASP 1820": "OD1" <-> "OD2" Residue "G TYR 1833": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 1846": "OE1" <-> "OE2" Residue "G PHE 1916": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29681 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12409 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 3 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 16018 Classifications: {'peptide': 2036} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} Chain breaks: 1 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 14.78, per 1000 atoms: 0.50 Number of scatterers: 29681 At special positions: 0 Unit cell: (183.57, 181.46, 176.185, 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 107 16.00 P 1 15.00 O 5694 8.00 N 4967 7.00 C 18912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.15 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: 10.71 Conformation dependent library (CDL) restraints added in 5.4 seconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 34 sheets defined 50.7% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.76 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 27 through 32 Processing helix chain 'A' and resid 52 through 65 removed outlier: 3.527A pdb=" N MET A 56 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 70 removed outlier: 3.528A pdb=" N ALA A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 90 removed outlier: 7.752A pdb=" N LYS A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N GLU A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.723A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.008A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 3.952A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.789A pdb=" N GLN A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.758A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 removed outlier: 3.559A pdb=" N ALA A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE A 749 " --> pdb=" O VAL A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.153A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.205A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.736A pdb=" N PHE A 932 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 969 removed outlier: 3.560A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 976 removed outlier: 3.531A pdb=" N ALA A 976 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.728A pdb=" N VAL A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.751A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1086 through 1100 removed outlier: 4.331A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1112 removed outlier: 3.718A pdb=" N ASN A1112 " --> pdb=" O GLU A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.596A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1263 Processing helix chain 'A' and resid 1275 through 1280 removed outlier: 3.732A pdb=" N PHE A1279 " --> pdb=" O GLN A1276 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A1280 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1361 through 1366 removed outlier: 4.199A pdb=" N SER A1366 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1424 through 1429 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1477 removed outlier: 3.542A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1509 Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.523A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 removed outlier: 3.686A pdb=" N LEU A1536 " --> pdb=" O ILE A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1546 through 1565 removed outlier: 4.153A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.577A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1603 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 3.607A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 3.947A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 removed outlier: 3.672A pdb=" N TYR A1694 " --> pdb=" O ASN A1690 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1734 through 1738 removed outlier: 3.795A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.954A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 Processing helix chain 'A' and resid 1783 through 1791 removed outlier: 3.501A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1802 Processing helix chain 'A' and resid 1804 through 1824 removed outlier: 3.685A pdb=" N GLY A1824 " --> pdb=" O PHE A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.628A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 removed outlier: 4.354A pdb=" N HIS B 152 " --> pdb=" O SER B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.690A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.747A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 4.357A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.517A pdb=" N TRP B 254 " --> pdb=" O LEU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 removed outlier: 4.126A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 removed outlier: 3.718A pdb=" N TYR B 294 " --> pdb=" O MET B 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.770A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 49 removed outlier: 4.375A pdb=" N ALA G 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 Processing helix chain 'G' and resid 80 through 96 Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 169 through 202 removed outlier: 3.678A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N VAL G 182 " --> pdb=" O GLN G 178 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU G 183 " --> pdb=" O THR G 179 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 3.795A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 222 through 225 Processing helix chain 'G' and resid 227 through 232 Processing helix chain 'G' and resid 233 through 257 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 275 through 286 removed outlier: 4.242A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 291 No H-bonds generated for 'chain 'G' and resid 289 through 291' Processing helix chain 'G' and resid 292 through 314 Processing helix chain 'G' and resid 320 through 329 Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.857A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.892A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 removed outlier: 3.577A pdb=" N ARG G 412 " --> pdb=" O PHE G 409 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 433 Processing helix chain 'G' and resid 434 through 446 removed outlier: 4.207A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 511 through 520 removed outlier: 4.030A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.591A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 612 Processing helix chain 'G' and resid 626 through 641 removed outlier: 3.877A pdb=" N GLN G 640 " --> pdb=" O SER G 636 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 673 removed outlier: 3.789A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.708A pdb=" N GLY G 699 " --> pdb=" O ILE G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 752 Processing helix chain 'G' and resid 753 through 759 Processing helix chain 'G' and resid 777 through 783 Processing helix chain 'G' and resid 784 through 790 removed outlier: 4.045A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 808 removed outlier: 3.821A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 823 Processing helix chain 'G' and resid 831 through 835 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 899 removed outlier: 4.706A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 3.524A pdb=" N ALA G 886 " --> pdb=" O PRO G 882 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1036 through 1043 removed outlier: 3.930A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1057 through 1062 removed outlier: 3.569A pdb=" N PHE G1062 " --> pdb=" O ALA G1059 " (cutoff:3.500A) Processing helix chain 'G' and resid 1069 through 1091 removed outlier: 3.764A pdb=" N LYS G1084 " --> pdb=" O GLY G1080 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY G1091 " --> pdb=" O HIS G1087 " (cutoff:3.500A) Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1174 Processing helix chain 'G' and resid 1189 through 1193 Processing helix chain 'G' and resid 1257 through 1270 Processing helix chain 'G' and resid 1293 through 1304 removed outlier: 3.921A pdb=" N VAL G1297 " --> pdb=" O THR G1293 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N HIS G1302 " --> pdb=" O TYR G1298 " (cutoff:3.500A) Processing helix chain 'G' and resid 1308 through 1312 removed outlier: 3.718A pdb=" N PHE G1311 " --> pdb=" O CYS G1308 " (cutoff:3.500A) Processing helix chain 'G' and resid 1322 through 1324 No H-bonds generated for 'chain 'G' and resid 1322 through 1324' Processing helix chain 'G' and resid 1325 through 1336 removed outlier: 3.685A pdb=" N VAL G1329 " --> pdb=" O PHE G1325 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.591A pdb=" N VAL G1443 " --> pdb=" O LYS G1439 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1523 removed outlier: 3.652A pdb=" N ARG G1522 " --> pdb=" O ASP G1518 " (cutoff:3.500A) Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.753A pdb=" N ALA G1554 " --> pdb=" O ASN G1550 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG G1555 " --> pdb=" O GLU G1551 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY G1558 " --> pdb=" O ALA G1554 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 removed outlier: 3.647A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 removed outlier: 3.656A pdb=" N VAL G1690 " --> pdb=" O ALA G1686 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 removed outlier: 3.954A pdb=" N GLY G1726 " --> pdb=" O GLY G1722 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA G1735 " --> pdb=" O GLU G1731 " (cutoff:3.500A) Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1820 removed outlier: 3.859A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1840 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.843A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) Processing helix chain 'G' and resid 1868 through 1882 removed outlier: 3.555A pdb=" N ARG G1881 " --> pdb=" O ARG G1877 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 4.069A pdb=" N VAL G1910 " --> pdb=" O ALA G1906 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1923 through 1928 removed outlier: 4.069A pdb=" N LEU G1927 " --> pdb=" O ASP G1923 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1948 removed outlier: 3.753A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.726A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) Processing helix chain 'G' and resid 2022 through 2033 removed outlier: 3.631A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2035 through 2044 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.389A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 9.090A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.713A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 9.586A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N LEU A 926 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.713A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 499 Processing sheet with id=AA6, first strand: chain 'A' and resid 502 through 503 Processing sheet with id=AA7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA8, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.841A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR A1642 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL A1572 " --> pdb=" O LEU A1625 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AB2, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.955A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1119 through 1126 removed outlier: 3.577A pdb=" N MET A1121 " --> pdb=" O LYS A1177 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB5, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB6, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB7, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB8, first strand: chain 'A' and resid 1837 through 1842 removed outlier: 5.545A pdb=" N VAL A1842 " --> pdb=" O ALA A1846 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ALA A1846 " --> pdb=" O VAL A1842 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.688A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 269 through 270 removed outlier: 3.718A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL G 157 " --> pdb=" O LEU G 502 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.122A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC4, first strand: chain 'G' and resid 592 through 594 removed outlier: 4.149A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE G 728 " --> pdb=" O MET G 764 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY G 768 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TRP G 732 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.800A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC7, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC8, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.559A pdb=" N VAL G1195 " --> pdb=" O ILE G1210 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE G1210 " --> pdb=" O VAL G1195 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU G1197 " --> pdb=" O THR G1208 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU G1204 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N MET G1221 " --> pdb=" O LEU G1238 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1158 through 1161 Processing sheet with id=AD1, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 4.002A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL G1629 " --> pdb=" O LEU G1637 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1358 through 1359 removed outlier: 6.510A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1424 through 1426 removed outlier: 3.768A pdb=" N PHE G1486 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA G1508 " --> pdb=" O VAL G1483 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 1424 through 1426 removed outlier: 3.768A pdb=" N PHE G1486 " --> pdb=" O GLU G1469 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G1464 " --> pdb=" O MET G1433 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N TYR G1431 " --> pdb=" O PHE G1466 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD6, first strand: chain 'G' and resid 1737 through 1741 removed outlier: 3.747A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 1886 through 1893 removed outlier: 6.810A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY G1902 " --> pdb=" O GLY G1853 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLY G1853 " --> pdb=" O GLY G1902 " (cutoff:3.500A) 1461 hydrogen bonds defined for protein. 4089 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: 19.65 Time building geometry restraints manager: 11.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.32: 5215 1.32 - 1.47: 7890 1.47 - 1.62: 17006 1.62 - 1.76: 0 1.76 - 1.91: 189 Bond restraints: 30300 Sorted by residual: bond pdb=" C PRO A1399 " pdb=" O PRO A1399 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.10e-02 8.26e+03 2.97e+01 bond pdb=" N GLU G1199 " pdb=" CA GLU G1199 " ideal model delta sigma weight residual 1.453 1.496 -0.043 8.30e-03 1.45e+04 2.66e+01 bond pdb=" C7 FMN G2101 " pdb=" C8 FMN G2101 " ideal model delta sigma weight residual 1.390 1.488 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.60e-03 1.35e+04 1.97e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.14e-02 7.69e+03 1.92e+01 ... (remaining 30295 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.67: 590 104.67 - 112.29: 13173 112.29 - 119.91: 15658 119.91 - 127.53: 11419 127.53 - 135.15: 201 Bond angle restraints: 41041 Sorted by residual: angle pdb=" CB GLU A 841 " pdb=" CG GLU A 841 " pdb=" CD GLU A 841 " ideal model delta sigma weight residual 112.60 125.67 -13.07 1.70e+00 3.46e-01 5.91e+01 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 125.00 -12.40 1.70e+00 3.46e-01 5.32e+01 angle pdb=" CB GLU A 364 " pdb=" CG GLU A 364 " pdb=" CD GLU A 364 " ideal model delta sigma weight residual 112.60 124.41 -11.81 1.70e+00 3.46e-01 4.82e+01 angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.33 125.87 -5.54 8.00e-01 1.56e+00 4.80e+01 angle pdb=" C SER G 233 " pdb=" N ILE G 234 " pdb=" CA ILE G 234 " ideal model delta sigma weight residual 120.24 124.54 -4.30 6.30e-01 2.52e+00 4.67e+01 ... (remaining 41036 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 16356 17.84 - 35.67: 1522 35.67 - 53.51: 300 53.51 - 71.34: 79 71.34 - 89.18: 36 Dihedral angle restraints: 18293 sinusoidal: 7353 harmonic: 10940 Sorted by residual: dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PHE G1411 " pdb=" C PHE G1411 " pdb=" N TYR G1412 " pdb=" CA TYR G1412 " ideal model delta harmonic sigma weight residual 180.00 154.27 25.73 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 -43.85 -42.15 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 18290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1933 0.055 - 0.110: 1649 0.110 - 0.165: 800 0.165 - 0.219: 206 0.219 - 0.274: 25 Chirality restraints: 4613 Sorted by residual: chirality pdb=" CA ILE G 652 " pdb=" N ILE G 652 " pdb=" C ILE G 652 " pdb=" CB ILE G 652 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA ILE A1384 " pdb=" N ILE A1384 " pdb=" C ILE A1384 " pdb=" CB ILE A1384 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 4610 not shown) Planarity restraints: 5299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1660 " -0.045 2.00e-02 2.50e+03 2.59e-02 1.34e+01 pdb=" CG TYR A1660 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR A1660 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A1660 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A1660 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A1660 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR A1660 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1660 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 624 " -0.042 2.00e-02 2.50e+03 2.21e-02 9.74e+00 pdb=" CG TYR G 624 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR G 624 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR G 624 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR G 624 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR G 624 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR G 624 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR G 624 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " -0.005 2.00e-02 2.50e+03 1.43e-02 9.74e+00 pdb=" C10 FMN G2101 " -0.017 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.001 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " -0.001 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.006 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " 0.008 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " 0.001 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " 0.003 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.006 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.005 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " 0.003 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " 0.015 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " 0.008 2.00e-02 2.50e+03 ... (remaining 5296 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1044 2.72 - 3.26: 30342 3.26 - 3.81: 46902 3.81 - 4.35: 64343 4.35 - 4.90: 104227 Nonbonded interactions: 246858 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OD2 ASP G1791 " model vdw 2.170 2.440 nonbonded pdb=" OG1 THR G1470 " pdb=" ND2 ASN G1514 " model vdw 2.215 2.520 nonbonded pdb=" OH TYR G1266 " pdb=" OD1 ASN G1561 " model vdw 2.235 2.440 nonbonded pdb=" O GLY A 389 " pdb=" ND2 ASN A 738 " model vdw 2.245 2.520 nonbonded pdb=" O VAL G1381 " pdb=" OG1 THR G1422 " model vdw 2.268 2.440 ... (remaining 246853 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 1.190 Check model and map are aligned: 0.230 Set scattering table: 0.290 Process input model: 83.720 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.014 0.109 30300 Z= 0.908 Angle : 1.911 13.073 41041 Z= 1.394 Chirality : 0.088 0.274 4613 Planarity : 0.006 0.028 5299 Dihedral : 15.238 89.176 11246 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.58 % Allowed : 7.87 % Favored : 91.55 % Rotamer: Outliers : 0.74 % Allowed : 5.14 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % 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: -3.68 (0.11), residues: 3774 helix: -2.80 (0.09), residues: 1658 sheet: -2.25 (0.22), residues: 415 loop : -1.92 (0.14), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.006 TRP G 865 HIS 0.014 0.003 HIS A1689 PHE 0.042 0.005 PHE G 939 TYR 0.053 0.005 TYR A1660 ARG 0.010 0.001 ARG A1036 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 337 time to evaluate : 3.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.9108 (mtm-85) cc_final: 0.8278 (mmt180) REVERT: A 431 GLU cc_start: 0.9151 (tp30) cc_final: 0.8852 (tp30) REVERT: A 708 SER cc_start: 0.8708 (OUTLIER) cc_final: 0.8462 (m) REVERT: A 713 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8617 (tm-30) REVERT: A 754 ASP cc_start: 0.9451 (t0) cc_final: 0.9182 (t0) REVERT: A 925 ASP cc_start: 0.9264 (t0) cc_final: 0.8946 (t70) REVERT: A 1124 GLU cc_start: 0.8766 (pp20) cc_final: 0.8353 (pp20) REVERT: A 1267 ASP cc_start: 0.8864 (t0) cc_final: 0.8649 (t70) REVERT: A 1268 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8669 (mm-30) REVERT: A 1332 TYR cc_start: 0.8924 (p90) cc_final: 0.8705 (p90) REVERT: B 185 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8333 (mt-10) REVERT: B 277 LEU cc_start: 0.7769 (OUTLIER) cc_final: 0.7452 (mm) REVERT: G 229 ASP cc_start: 0.9056 (m-30) cc_final: 0.8586 (t0) REVERT: G 268 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8550 (mmmm) REVERT: G 425 SER cc_start: 0.9385 (t) cc_final: 0.9100 (p) REVERT: G 564 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8392 (tp30) REVERT: G 630 MET cc_start: 0.8812 (tpp) cc_final: 0.8307 (tpp) REVERT: G 750 MET cc_start: 0.8975 (mmt) cc_final: 0.8590 (mmt) REVERT: G 1011 MET cc_start: 0.9308 (mtt) cc_final: 0.8633 (tmm) REVERT: G 1067 ASP cc_start: 0.8912 (OUTLIER) cc_final: 0.8530 (t70) REVERT: G 1136 GLU cc_start: 0.9107 (tp30) cc_final: 0.8860 (pp20) REVERT: G 1299 ASP cc_start: 0.9216 (t0) cc_final: 0.9008 (t0) REVERT: G 1405 GLU cc_start: 0.7370 (pt0) cc_final: 0.6925 (tm-30) REVERT: G 1631 MET cc_start: 0.5418 (tpt) cc_final: 0.4720 (tpp) REVERT: G 1676 MET cc_start: 0.7813 (ptm) cc_final: 0.7076 (ptm) REVERT: G 1784 MET cc_start: 0.8100 (tmm) cc_final: 0.7669 (tmm) outliers start: 24 outliers final: 10 residues processed: 354 average time/residue: 0.3917 time to fit residues: 228.3549 Evaluate side-chains 265 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 252 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 708 SER Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1308 SER Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 191 SER Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1511 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.9980 chunk 285 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 114 optimal weight: 8.9990 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 7.9990 chunk 342 optimal weight: 5.9990 overall best weight: 4.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 388 ASN A 422 HIS A 438 ASN A 524 GLN A 758 ASN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 829 ASN A 881 ASN A 882 ASN A 987 ASN A 989 GLN A1000 GLN A1063 HIS A1239 HIS A1271 GLN A1385 GLN A1432 HIS A1482 GLN A1549 ASN A1563 HIS A1570 ASN A1610 ASN A1689 HIS A1703 HIS A1766 ASN A1783 ASN A1845 ASN B 271 ASN G 36 GLN G 85 ASN G 181 HIS G 245 GLN G 248 HIS G 350 GLN G 440 ASN G 640 GLN G 715 GLN G 747 HIS G 910 GLN G 993 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1241 ASN G1302 HIS ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1383 ASN G1399 ASN G1424 GLN G1451 GLN G1476 ASN ** G1514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1890 ASN G1995 ASN ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2044 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30300 Z= 0.292 Angle : 0.613 7.875 41041 Z= 0.326 Chirality : 0.044 0.213 4613 Planarity : 0.004 0.062 5299 Dihedral : 5.751 71.340 4061 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.37 % Favored : 96.56 % Rotamer: Outliers : 1.51 % Allowed : 9.66 % Favored : 88.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.13), residues: 3774 helix: -0.21 (0.12), residues: 1668 sheet: -1.57 (0.21), residues: 494 loop : -0.89 (0.15), residues: 1612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G1449 HIS 0.007 0.001 HIS G1352 PHE 0.024 0.002 PHE A 450 TYR 0.019 0.002 TYR A1513 ARG 0.006 0.001 ARG G1881 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 279 time to evaluate : 3.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.8994 (mtm-85) cc_final: 0.8192 (mmt180) REVERT: A 358 GLU cc_start: 0.8775 (tp30) cc_final: 0.8461 (tp30) REVERT: A 431 GLU cc_start: 0.8972 (tp30) cc_final: 0.8736 (tp30) REVERT: A 925 ASP cc_start: 0.9326 (t0) cc_final: 0.9116 (t70) REVERT: A 1124 GLU cc_start: 0.8836 (pp20) cc_final: 0.8487 (pp20) REVERT: A 1268 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8506 (mm-30) REVERT: A 1484 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7783 (tm-30) REVERT: A 1496 GLU cc_start: 0.9243 (OUTLIER) cc_final: 0.8928 (mp0) REVERT: A 1702 GLU cc_start: 0.8804 (pm20) cc_final: 0.8571 (pm20) REVERT: B 185 GLU cc_start: 0.8448 (mt-10) cc_final: 0.8029 (mt-10) REVERT: B 277 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7249 (mm) REVERT: G 229 ASP cc_start: 0.8955 (m-30) cc_final: 0.8668 (t0) REVERT: G 630 MET cc_start: 0.8638 (tpp) cc_final: 0.8185 (tpp) REVERT: G 750 MET cc_start: 0.8923 (mmt) cc_final: 0.8573 (mmt) REVERT: G 850 MET cc_start: 0.8175 (mtm) cc_final: 0.7207 (tpt) REVERT: G 1011 MET cc_start: 0.9248 (mtt) cc_final: 0.8727 (tmm) REVERT: G 1067 ASP cc_start: 0.9002 (OUTLIER) cc_final: 0.8749 (t70) REVERT: G 1604 ARG cc_start: 0.6703 (ptp90) cc_final: 0.6408 (mtm110) REVERT: G 1645 GLU cc_start: 0.3804 (OUTLIER) cc_final: 0.3485 (pm20) REVERT: G 1676 MET cc_start: 0.7791 (ptm) cc_final: 0.7176 (ptm) REVERT: G 1784 MET cc_start: 0.8095 (tmm) cc_final: 0.7773 (tmm) REVERT: G 1822 MET cc_start: 0.6475 (mpp) cc_final: 0.5724 (mpp) outliers start: 49 outliers final: 26 residues processed: 313 average time/residue: 0.3818 time to fit residues: 200.1532 Evaluate side-chains 274 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 3.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1061 SER Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 448 VAL Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1645 GLU Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1871 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 284 optimal weight: 30.0000 chunk 233 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 342 optimal weight: 2.9990 chunk 370 optimal weight: 40.0000 chunk 305 optimal weight: 6.9990 chunk 340 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 275 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1444 ASN A1552 ASN A1758 ASN B 271 ASN G 163 GLN G 500 HIS G1088 GLN ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1514 ASN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 30300 Z= 0.254 Angle : 0.566 8.492 41041 Z= 0.294 Chirality : 0.043 0.215 4613 Planarity : 0.004 0.071 5299 Dihedral : 5.339 69.492 4056 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.82 % Favored : 96.13 % Rotamer: Outliers : 1.75 % Allowed : 11.84 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3774 helix: 0.64 (0.12), residues: 1671 sheet: -1.32 (0.22), residues: 500 loop : -0.60 (0.16), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G1449 HIS 0.006 0.001 HIS A 454 PHE 0.030 0.002 PHE G1423 TYR 0.024 0.002 TYR G1608 ARG 0.004 0.000 ARG G1881 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 261 time to evaluate : 3.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4301 (ttt) cc_final: 0.4098 (ttt) REVERT: A 358 GLU cc_start: 0.8774 (tp30) cc_final: 0.8458 (tp30) REVERT: A 529 MET cc_start: 0.9165 (mmm) cc_final: 0.8953 (mmm) REVERT: A 611 LYS cc_start: 0.9110 (tmmt) cc_final: 0.8813 (mmtm) REVERT: A 847 GLU cc_start: 0.8984 (tt0) cc_final: 0.8513 (tm-30) REVERT: A 925 ASP cc_start: 0.9279 (t0) cc_final: 0.9044 (t70) REVERT: A 1124 GLU cc_start: 0.8826 (pp20) cc_final: 0.8478 (pp20) REVERT: A 1484 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: A 1496 GLU cc_start: 0.9114 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: B 185 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8150 (mt-10) REVERT: G 229 ASP cc_start: 0.8851 (m-30) cc_final: 0.8647 (t0) REVERT: G 630 MET cc_start: 0.8612 (tpp) cc_final: 0.8181 (tpp) REVERT: G 750 MET cc_start: 0.8915 (OUTLIER) cc_final: 0.8558 (mmt) REVERT: G 1011 MET cc_start: 0.9260 (mtt) cc_final: 0.8699 (tmm) REVERT: G 1067 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8835 (t70) REVERT: G 1323 MET cc_start: 0.4885 (tpt) cc_final: 0.3871 (tpt) REVERT: G 1404 MET cc_start: 0.6806 (ppp) cc_final: 0.5157 (ptp) REVERT: G 1405 GLU cc_start: 0.7748 (tm-30) cc_final: 0.6651 (tm-30) REVERT: G 1520 LEU cc_start: 0.6377 (mp) cc_final: 0.5652 (mt) REVERT: G 1604 ARG cc_start: 0.6740 (ptp90) cc_final: 0.6279 (mtm110) REVERT: G 1676 MET cc_start: 0.7871 (ptm) cc_final: 0.7424 (ptm) REVERT: G 1763 THR cc_start: 0.9298 (m) cc_final: 0.8883 (p) REVERT: G 1784 MET cc_start: 0.8114 (tmm) cc_final: 0.7786 (tmm) REVERT: G 1822 MET cc_start: 0.6504 (mpp) cc_final: 0.6072 (mpp) outliers start: 57 outliers final: 37 residues processed: 299 average time/residue: 0.3693 time to fit residues: 184.2018 Evaluate side-chains 285 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 244 time to evaluate : 3.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1209 VAL Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1409 SER Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1611 GLN Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 10.0000 chunk 257 optimal weight: 0.0070 chunk 177 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 163 optimal weight: 0.0980 chunk 230 optimal weight: 10.0000 chunk 344 optimal weight: 6.9990 chunk 364 optimal weight: 6.9990 chunk 179 optimal weight: 4.9990 chunk 326 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.8204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 475 GLN ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 163 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30300 Z= 0.162 Angle : 0.518 8.808 41041 Z= 0.266 Chirality : 0.041 0.331 4613 Planarity : 0.004 0.070 5299 Dihedral : 4.904 68.890 4051 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.85 % Allowed : 12.70 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.14), residues: 3774 helix: 1.05 (0.13), residues: 1681 sheet: -1.22 (0.22), residues: 514 loop : -0.30 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G1449 HIS 0.008 0.001 HIS G1568 PHE 0.020 0.001 PHE G1423 TYR 0.023 0.001 TYR A1513 ARG 0.003 0.000 ARG G1881 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 275 time to evaluate : 3.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 435 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8994 (mm-30) REVERT: A 841 GLU cc_start: 0.6056 (tp30) cc_final: 0.5242 (tp30) REVERT: A 847 GLU cc_start: 0.8981 (tt0) cc_final: 0.8507 (tm-30) REVERT: A 925 ASP cc_start: 0.9235 (t0) cc_final: 0.8970 (t70) REVERT: A 1124 GLU cc_start: 0.8829 (pp20) cc_final: 0.8311 (tm-30) REVERT: A 1484 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7821 (tm-30) REVERT: A 1496 GLU cc_start: 0.9087 (OUTLIER) cc_final: 0.8775 (mp0) REVERT: A 1702 GLU cc_start: 0.8870 (pm20) cc_final: 0.8623 (pm20) REVERT: B 179 LYS cc_start: 0.7279 (OUTLIER) cc_final: 0.6442 (mmtt) REVERT: B 185 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 194 PHE cc_start: 0.8145 (m-10) cc_final: 0.7935 (m-10) REVERT: B 247 ARG cc_start: 0.8289 (mmm160) cc_final: 0.7944 (mmt180) REVERT: G 163 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7664 (mm-40) REVERT: G 213 LEU cc_start: 0.8689 (mt) cc_final: 0.8459 (mt) REVERT: G 528 ILE cc_start: 0.8626 (OUTLIER) cc_final: 0.8400 (mm) REVERT: G 630 MET cc_start: 0.8558 (tpp) cc_final: 0.8143 (tpp) REVERT: G 750 MET cc_start: 0.8836 (OUTLIER) cc_final: 0.8442 (mmt) REVERT: G 1011 MET cc_start: 0.9249 (mtt) cc_final: 0.8676 (tmm) REVERT: G 1038 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8227 (mp0) REVERT: G 1067 ASP cc_start: 0.9045 (OUTLIER) cc_final: 0.8791 (t70) REVERT: G 1106 GLU cc_start: 0.8256 (mp0) cc_final: 0.7694 (mp0) REVERT: G 1223 MET cc_start: 0.5567 (tpt) cc_final: 0.5293 (tpt) REVERT: G 1323 MET cc_start: 0.4573 (tpt) cc_final: 0.4099 (tpt) REVERT: G 1332 ARG cc_start: 0.8044 (tpt-90) cc_final: 0.7760 (ttm170) REVERT: G 1404 MET cc_start: 0.6680 (ppp) cc_final: 0.5149 (ptp) REVERT: G 1405 GLU cc_start: 0.7559 (tm-30) cc_final: 0.6402 (tm-30) REVERT: G 1412 TYR cc_start: 0.7092 (m-10) cc_final: 0.6501 (m-10) REVERT: G 1604 ARG cc_start: 0.6813 (ptp90) cc_final: 0.6366 (mtm110) REVERT: G 1676 MET cc_start: 0.7959 (ptm) cc_final: 0.7352 (ptm) REVERT: G 1763 THR cc_start: 0.9302 (m) cc_final: 0.8688 (p) REVERT: G 1784 MET cc_start: 0.8040 (tmm) cc_final: 0.7305 (tmm) outliers start: 60 outliers final: 36 residues processed: 315 average time/residue: 0.3816 time to fit residues: 198.4740 Evaluate side-chains 294 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 251 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1234 MET Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 163 GLN Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 528 ILE Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 5 optimal weight: 9.9990 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 9.9990 chunk 310 optimal weight: 6.9990 chunk 251 optimal weight: 10.0000 chunk 0 optimal weight: 30.0000 chunk 186 optimal weight: 6.9990 chunk 327 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN A 527 GLN A1146 HIS B 157 HIS B 271 ASN G 163 GLN G 224 ASN G1512 HIS G1523 ASN G1529 GLN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 30300 Z= 0.365 Angle : 0.613 8.648 41041 Z= 0.319 Chirality : 0.044 0.307 4613 Planarity : 0.004 0.072 5299 Dihedral : 5.254 67.415 4048 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.66 % Favored : 95.28 % Rotamer: Outliers : 2.58 % Allowed : 13.99 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3774 helix: 0.80 (0.12), residues: 1696 sheet: -1.19 (0.22), residues: 492 loop : -0.51 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G1449 HIS 0.007 0.001 HIS A 11 PHE 0.025 0.002 PHE A 450 TYR 0.026 0.002 TYR G1608 ARG 0.005 0.001 ARG G 200 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 244 time to evaluate : 3.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5325 (mmm) cc_final: 0.5090 (mmt) REVERT: A 847 GLU cc_start: 0.8979 (tt0) cc_final: 0.8505 (tm-30) REVERT: A 925 ASP cc_start: 0.9268 (t0) cc_final: 0.9012 (t0) REVERT: A 1496 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8858 (mp0) REVERT: B 160 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8638 (mmmm) REVERT: B 168 MET cc_start: 0.6718 (tpp) cc_final: 0.6370 (tpp) REVERT: B 179 LYS cc_start: 0.7441 (OUTLIER) cc_final: 0.6555 (mmtt) REVERT: B 185 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 247 ARG cc_start: 0.8182 (mmm160) cc_final: 0.7630 (mtp85) REVERT: G 213 LEU cc_start: 0.8666 (mt) cc_final: 0.8425 (mt) REVERT: G 630 MET cc_start: 0.8680 (tpp) cc_final: 0.8191 (tpp) REVERT: G 750 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8554 (mmt) REVERT: G 1011 MET cc_start: 0.9257 (mtt) cc_final: 0.8710 (tmm) REVERT: G 1067 ASP cc_start: 0.9111 (OUTLIER) cc_final: 0.8904 (t70) REVERT: G 1223 MET cc_start: 0.5676 (tpt) cc_final: 0.5475 (tpt) REVERT: G 1332 ARG cc_start: 0.8085 (tpt-90) cc_final: 0.7747 (mmt-90) REVERT: G 1404 MET cc_start: 0.6637 (ppp) cc_final: 0.4788 (ptp) REVERT: G 1405 GLU cc_start: 0.7818 (tm-30) cc_final: 0.6733 (tm-30) REVERT: G 1543 ASP cc_start: 0.5340 (OUTLIER) cc_final: 0.5034 (t0) REVERT: G 1604 ARG cc_start: 0.6849 (ptp90) cc_final: 0.6564 (mtm110) REVERT: G 1656 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: G 1673 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8176 (pm20) REVERT: G 1676 MET cc_start: 0.7919 (ptm) cc_final: 0.7584 (ptm) REVERT: G 1763 THR cc_start: 0.9230 (m) cc_final: 0.8843 (p) REVERT: G 1784 MET cc_start: 0.8051 (tmm) cc_final: 0.7289 (tmm) REVERT: G 1822 MET cc_start: 0.6460 (mpp) cc_final: 0.5769 (mpp) REVERT: G 2049 GLU cc_start: 0.4871 (OUTLIER) cc_final: 0.4640 (mm-30) outliers start: 84 outliers final: 55 residues processed: 308 average time/residue: 0.4061 time to fit residues: 207.3291 Evaluate side-chains 300 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 238 time to evaluate : 3.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 581 THR Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1285 ILE Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1440 ASP Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1656 GLU Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Chi-restraints excluded: chain G residue 2049 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 2.9990 chunk 328 optimal weight: 20.0000 chunk 72 optimal weight: 3.9990 chunk 213 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 364 optimal weight: 9.9990 chunk 302 optimal weight: 5.9990 chunk 168 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 ASN B 292 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30300 Z= 0.203 Angle : 0.537 9.934 41041 Z= 0.275 Chirality : 0.042 0.297 4613 Planarity : 0.004 0.072 5299 Dihedral : 4.993 67.976 4048 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.37 % Favored : 96.58 % Rotamer: Outliers : 2.31 % Allowed : 14.98 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.14), residues: 3774 helix: 1.04 (0.13), residues: 1687 sheet: -1.21 (0.22), residues: 502 loop : -0.33 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G2045 HIS 0.006 0.001 HIS A 454 PHE 0.015 0.001 PHE A 450 TYR 0.024 0.001 TYR A1513 ARG 0.003 0.000 ARG G1522 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 266 time to evaluate : 3.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5124 (mmm) cc_final: 0.4851 (mmt) REVERT: A 841 GLU cc_start: 0.6073 (tp30) cc_final: 0.5188 (tp30) REVERT: A 847 GLU cc_start: 0.8989 (tt0) cc_final: 0.8472 (tm-30) REVERT: A 925 ASP cc_start: 0.9218 (t0) cc_final: 0.8952 (t0) REVERT: A 1496 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8820 (mp0) REVERT: A 1702 GLU cc_start: 0.8875 (pm20) cc_final: 0.8653 (pm20) REVERT: B 179 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6514 (mmtm) REVERT: B 185 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8065 (mt-10) REVERT: B 241 PHE cc_start: 0.7808 (OUTLIER) cc_final: 0.6716 (m-80) REVERT: G 213 LEU cc_start: 0.8708 (mt) cc_final: 0.8435 (mt) REVERT: G 482 CYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8658 (p) REVERT: G 630 MET cc_start: 0.8596 (tpp) cc_final: 0.8158 (tpp) REVERT: G 750 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8514 (mmt) REVERT: G 1011 MET cc_start: 0.9257 (mtt) cc_final: 0.8682 (tmm) REVERT: G 1038 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8148 (mp0) REVERT: G 1067 ASP cc_start: 0.9118 (OUTLIER) cc_final: 0.8887 (t70) REVERT: G 1332 ARG cc_start: 0.8017 (tpt-90) cc_final: 0.7816 (mmt-90) REVERT: G 1404 MET cc_start: 0.6761 (ppp) cc_final: 0.4877 (ptp) REVERT: G 1405 GLU cc_start: 0.7637 (tm-30) cc_final: 0.6591 (tm-30) REVERT: G 1470 THR cc_start: 0.5254 (OUTLIER) cc_final: 0.4859 (p) REVERT: G 1604 ARG cc_start: 0.6764 (ptp90) cc_final: 0.6471 (mtm110) REVERT: G 1656 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7611 (pt0) REVERT: G 1673 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8229 (pm20) REVERT: G 1676 MET cc_start: 0.7948 (ptm) cc_final: 0.7665 (ptm) REVERT: G 1763 THR cc_start: 0.9198 (m) cc_final: 0.8861 (p) REVERT: G 1784 MET cc_start: 0.8075 (tmm) cc_final: 0.7285 (tmm) REVERT: G 1822 MET cc_start: 0.6403 (mpp) cc_final: 0.5737 (mpp) REVERT: G 2049 GLU cc_start: 0.4796 (OUTLIER) cc_final: 0.4513 (mm-30) outliers start: 75 outliers final: 50 residues processed: 319 average time/residue: 0.4131 time to fit residues: 217.5301 Evaluate side-chains 306 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 247 time to evaluate : 3.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1365 MET Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 638 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1489 ILE Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1656 GLU Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2049 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 266 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 307 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 227 optimal weight: 3.9990 chunk 221 optimal weight: 1.9990 chunk 167 optimal weight: 20.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G2000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30300 Z= 0.211 Angle : 0.538 8.253 41041 Z= 0.277 Chirality : 0.042 0.229 4613 Planarity : 0.004 0.071 5299 Dihedral : 4.916 66.941 4048 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.00 % Favored : 95.95 % Rotamer: Outliers : 2.37 % Allowed : 15.44 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3774 helix: 1.13 (0.13), residues: 1680 sheet: -1.17 (0.22), residues: 519 loop : -0.27 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G2045 HIS 0.005 0.001 HIS G1568 PHE 0.019 0.001 PHE A 450 TYR 0.023 0.001 TYR A1513 ARG 0.008 0.000 ARG G 200 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 266 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5314 (mmm) cc_final: 0.4993 (mmm) REVERT: A 841 GLU cc_start: 0.6040 (tp30) cc_final: 0.5185 (tp30) REVERT: A 847 GLU cc_start: 0.8960 (tt0) cc_final: 0.8465 (tm-30) REVERT: A 923 MET cc_start: 0.9137 (tpt) cc_final: 0.8895 (tpt) REVERT: A 925 ASP cc_start: 0.9204 (t0) cc_final: 0.8937 (t0) REVERT: B 179 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6472 (mmtm) REVERT: B 185 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8100 (mt-10) REVERT: B 247 ARG cc_start: 0.8454 (mmm160) cc_final: 0.7783 (mmt180) REVERT: G 55 THR cc_start: 0.7965 (OUTLIER) cc_final: 0.7698 (t) REVERT: G 213 LEU cc_start: 0.8690 (mt) cc_final: 0.8402 (mt) REVERT: G 630 MET cc_start: 0.8606 (tpp) cc_final: 0.8182 (tpp) REVERT: G 750 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8519 (mmt) REVERT: G 1011 MET cc_start: 0.9266 (mtt) cc_final: 0.8749 (tmm) REVERT: G 1038 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8132 (mp0) REVERT: G 1067 ASP cc_start: 0.9156 (OUTLIER) cc_final: 0.8906 (t70) REVERT: G 1323 MET cc_start: 0.4980 (tpt) cc_final: 0.4286 (mmm) REVERT: G 1404 MET cc_start: 0.6741 (ppp) cc_final: 0.4878 (ptp) REVERT: G 1405 GLU cc_start: 0.7681 (tm-30) cc_final: 0.6652 (tm-30) REVERT: G 1470 THR cc_start: 0.5249 (OUTLIER) cc_final: 0.4790 (p) REVERT: G 1604 ARG cc_start: 0.6834 (ptp90) cc_final: 0.6556 (mtm110) REVERT: G 1656 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7595 (pt0) REVERT: G 1673 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8214 (pm20) REVERT: G 1676 MET cc_start: 0.7895 (ptm) cc_final: 0.7659 (ptm) REVERT: G 1784 MET cc_start: 0.8057 (tmm) cc_final: 0.7231 (tmm) REVERT: G 1822 MET cc_start: 0.6348 (mpp) cc_final: 0.5799 (mpp) REVERT: G 2049 GLU cc_start: 0.4848 (OUTLIER) cc_final: 0.4606 (mm-30) outliers start: 77 outliers final: 59 residues processed: 323 average time/residue: 0.3920 time to fit residues: 209.0380 Evaluate side-chains 315 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 249 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 968 VAL Chi-restraints excluded: chain A residue 971 ASN Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain A residue 1866 ASP Chi-restraints excluded: chain A residue 1875 ASP Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 282 ASP Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 439 ILE Chi-restraints excluded: chain G residue 482 CYS Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 638 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 755 SER Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1293 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1656 GLU Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1718 THR Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1871 LEU Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2035 SER Chi-restraints excluded: chain G residue 2049 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 217 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 0.0270 chunk 70 optimal weight: 0.7980 chunk 231 optimal weight: 9.9990 chunk 247 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 285 optimal weight: 0.0570 overall best weight: 0.9758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1780 ASN B 271 ASN G 224 ASN G 446 ASN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30300 Z= 0.144 Angle : 0.522 9.926 41041 Z= 0.265 Chirality : 0.042 0.291 4613 Planarity : 0.004 0.071 5299 Dihedral : 4.458 65.026 4045 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.10 % Favored : 96.85 % Rotamer: Outliers : 1.69 % Allowed : 16.42 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.14), residues: 3774 helix: 1.30 (0.13), residues: 1692 sheet: -0.88 (0.22), residues: 516 loop : -0.12 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G2045 HIS 0.008 0.001 HIS A 454 PHE 0.027 0.001 PHE G1423 TYR 0.023 0.001 TYR G1506 ARG 0.004 0.000 ARG G 200 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 3.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5220 (mmm) cc_final: 0.4965 (mmm) REVERT: A 841 GLU cc_start: 0.5932 (tp30) cc_final: 0.4837 (tp30) REVERT: A 847 GLU cc_start: 0.8961 (tt0) cc_final: 0.8492 (tm-30) REVERT: A 925 ASP cc_start: 0.9171 (t0) cc_final: 0.8895 (t0) REVERT: A 1124 GLU cc_start: 0.8753 (pp20) cc_final: 0.8243 (tm-30) REVERT: A 1496 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8795 (mp0) REVERT: A 1681 GLU cc_start: 0.9099 (tm-30) cc_final: 0.8564 (tm-30) REVERT: B 160 LYS cc_start: 0.8903 (mmmm) cc_final: 0.8645 (mmmm) REVERT: B 179 LYS cc_start: 0.7344 (OUTLIER) cc_final: 0.6315 (mmtm) REVERT: B 185 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 207 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8110 (mm-30) REVERT: G 55 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7322 (t) REVERT: G 213 LEU cc_start: 0.8716 (mt) cc_final: 0.8484 (mt) REVERT: G 630 MET cc_start: 0.8525 (tpp) cc_final: 0.8139 (tpp) REVERT: G 750 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8442 (mmt) REVERT: G 1011 MET cc_start: 0.9273 (mtt) cc_final: 0.8730 (tmm) REVERT: G 1038 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8157 (mp0) REVERT: G 1067 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8884 (t70) REVERT: G 1323 MET cc_start: 0.4659 (tpt) cc_final: 0.4104 (mmm) REVERT: G 1359 MET cc_start: 0.3826 (mtp) cc_final: 0.3532 (mtp) REVERT: G 1404 MET cc_start: 0.6412 (ppp) cc_final: 0.5123 (ptp) REVERT: G 1405 GLU cc_start: 0.7540 (tm-30) cc_final: 0.6501 (tm-30) REVERT: G 1412 TYR cc_start: 0.7076 (m-10) cc_final: 0.6460 (m-10) REVERT: G 1484 LYS cc_start: 0.8913 (tppt) cc_final: 0.8469 (tptp) REVERT: G 1543 ASP cc_start: 0.5316 (OUTLIER) cc_final: 0.5097 (t0) REVERT: G 1604 ARG cc_start: 0.6802 (ptp90) cc_final: 0.6090 (ptm160) REVERT: G 1673 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8276 (pm20) REVERT: G 1676 MET cc_start: 0.7920 (ptm) cc_final: 0.7696 (ptm) REVERT: G 1763 THR cc_start: 0.9093 (m) cc_final: 0.8649 (p) REVERT: G 1784 MET cc_start: 0.8016 (tmm) cc_final: 0.7232 (tmm) REVERT: G 1995 ASN cc_start: 0.7323 (m110) cc_final: 0.6382 (m-40) REVERT: G 2006 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7247 (mt) REVERT: G 2049 GLU cc_start: 0.4860 (OUTLIER) cc_final: 0.4571 (mm-30) outliers start: 55 outliers final: 38 residues processed: 332 average time/residue: 0.3949 time to fit residues: 218.1336 Evaluate side-chains 304 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 258 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain B residue 271 ASN Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 446 ASN Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1213 LEU Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1583 MET Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Chi-restraints excluded: chain G residue 2049 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 30.0000 chunk 348 optimal weight: 0.9990 chunk 317 optimal weight: 5.9990 chunk 338 optimal weight: 30.0000 chunk 203 optimal weight: 1.9990 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 0.1980 chunk 103 optimal weight: 9.9990 chunk 305 optimal weight: 7.9990 chunk 320 optimal weight: 1.9990 chunk 337 optimal weight: 7.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 GLN ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 446 ASN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 30300 Z= 0.183 Angle : 0.544 13.304 41041 Z= 0.273 Chirality : 0.042 0.385 4613 Planarity : 0.004 0.071 5299 Dihedral : 4.444 63.386 4044 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.44 % Favored : 96.50 % Rotamer: Outliers : 1.66 % Allowed : 16.91 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.14), residues: 3774 helix: 1.37 (0.13), residues: 1687 sheet: -0.91 (0.22), residues: 528 loop : -0.07 (0.17), residues: 1559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1813 HIS 0.009 0.001 HIS G1568 PHE 0.029 0.001 PHE G1423 TYR 0.031 0.001 TYR G1506 ARG 0.004 0.000 ARG G 469 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 259 time to evaluate : 3.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5256 (mmm) cc_final: 0.4971 (mmm) REVERT: A 841 GLU cc_start: 0.6003 (tp30) cc_final: 0.5101 (tp30) REVERT: A 847 GLU cc_start: 0.8933 (tt0) cc_final: 0.8476 (tm-30) REVERT: A 925 ASP cc_start: 0.9168 (t0) cc_final: 0.8900 (t0) REVERT: A 1124 GLU cc_start: 0.8756 (pp20) cc_final: 0.8228 (tm-30) REVERT: A 1496 GLU cc_start: 0.9091 (OUTLIER) cc_final: 0.8762 (mp0) REVERT: B 160 LYS cc_start: 0.8894 (mmmm) cc_final: 0.8641 (mmmm) REVERT: B 179 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6454 (mmtm) REVERT: B 185 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8165 (mt-10) REVERT: G 55 THR cc_start: 0.7656 (OUTLIER) cc_final: 0.7333 (t) REVERT: G 630 MET cc_start: 0.8547 (tpp) cc_final: 0.8191 (tpp) REVERT: G 750 MET cc_start: 0.8866 (OUTLIER) cc_final: 0.8449 (mmt) REVERT: G 1011 MET cc_start: 0.9273 (mtt) cc_final: 0.8835 (tmm) REVERT: G 1038 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8130 (mp0) REVERT: G 1067 ASP cc_start: 0.9152 (OUTLIER) cc_final: 0.8899 (t70) REVERT: G 1319 MET cc_start: 0.5017 (ppp) cc_final: 0.4700 (ttp) REVERT: G 1323 MET cc_start: 0.4885 (tpt) cc_final: 0.4268 (mmm) REVERT: G 1404 MET cc_start: 0.6726 (ppp) cc_final: 0.4998 (ptp) REVERT: G 1405 GLU cc_start: 0.7625 (tm-30) cc_final: 0.6595 (tm-30) REVERT: G 1412 TYR cc_start: 0.6978 (m-10) cc_final: 0.6372 (m-10) REVERT: G 1543 ASP cc_start: 0.5291 (OUTLIER) cc_final: 0.5015 (t0) REVERT: G 1604 ARG cc_start: 0.6772 (ptp90) cc_final: 0.6233 (ptm160) REVERT: G 1673 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8236 (pm20) REVERT: G 1676 MET cc_start: 0.7904 (ptm) cc_final: 0.7653 (ptm) REVERT: G 1763 THR cc_start: 0.9053 (m) cc_final: 0.8696 (p) REVERT: G 1784 MET cc_start: 0.8014 (tmm) cc_final: 0.7224 (tmm) REVERT: G 1822 MET cc_start: 0.6057 (mpp) cc_final: 0.5184 (mpp) REVERT: G 1995 ASN cc_start: 0.7204 (m110) cc_final: 0.6322 (m-40) REVERT: G 2006 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7066 (mt) outliers start: 54 outliers final: 42 residues processed: 301 average time/residue: 0.4061 time to fit residues: 202.6863 Evaluate side-chains 302 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 241 PHE Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 446 ASN Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 1067 ASP Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1543 ASP Chi-restraints excluded: chain G residue 1583 MET Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 chunk 218 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 248 optimal weight: 9.9990 chunk 375 optimal weight: 5.9990 chunk 345 optimal weight: 0.9980 chunk 299 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 231 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 224 ASN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30300 Z= 0.310 Angle : 0.606 12.596 41041 Z= 0.308 Chirality : 0.044 0.357 4613 Planarity : 0.004 0.081 5299 Dihedral : 4.747 64.043 4044 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.19 % Favored : 95.79 % Rotamer: Outliers : 1.91 % Allowed : 16.88 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3774 helix: 1.13 (0.13), residues: 1693 sheet: -1.07 (0.22), residues: 517 loop : -0.20 (0.16), residues: 1564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1813 HIS 0.006 0.001 HIS A 454 PHE 0.028 0.002 PHE G1423 TYR 0.026 0.002 TYR G1506 ARG 0.009 0.000 ARG G 200 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 251 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 599 MET cc_start: 0.5178 (mmm) cc_final: 0.4697 (mmm) REVERT: A 841 GLU cc_start: 0.6087 (tp30) cc_final: 0.5663 (tp30) REVERT: A 847 GLU cc_start: 0.9025 (tt0) cc_final: 0.8514 (tm-30) REVERT: A 925 ASP cc_start: 0.9188 (t0) cc_final: 0.8930 (t0) REVERT: A 1124 GLU cc_start: 0.8689 (pp20) cc_final: 0.8338 (pp20) REVERT: A 1406 MET cc_start: 0.9059 (ttp) cc_final: 0.8788 (ppp) REVERT: A 1496 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8766 (mp0) REVERT: B 160 LYS cc_start: 0.8941 (mmmm) cc_final: 0.8671 (mmmm) REVERT: B 179 LYS cc_start: 0.7388 (OUTLIER) cc_final: 0.6548 (mmtm) REVERT: B 185 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8121 (mt-10) REVERT: G 55 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7593 (t) REVERT: G 630 MET cc_start: 0.8663 (tpp) cc_final: 0.8232 (tpp) REVERT: G 750 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8527 (mmt) REVERT: G 1011 MET cc_start: 0.9263 (mtt) cc_final: 0.8837 (tmm) REVERT: G 1038 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8079 (mp0) REVERT: G 1319 MET cc_start: 0.4968 (ppp) cc_final: 0.4050 (ttp) REVERT: G 1323 MET cc_start: 0.4836 (tpt) cc_final: 0.3968 (mmm) REVERT: G 1404 MET cc_start: 0.6731 (ppp) cc_final: 0.4559 (ptp) REVERT: G 1405 GLU cc_start: 0.7688 (tm-30) cc_final: 0.6591 (tm-30) REVERT: G 1484 LYS cc_start: 0.8956 (tppt) cc_final: 0.8481 (tptp) REVERT: G 1604 ARG cc_start: 0.6769 (ptp90) cc_final: 0.6287 (ptp-110) REVERT: G 1673 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8258 (pm20) REVERT: G 1676 MET cc_start: 0.7876 (ptm) cc_final: 0.7567 (ptm) REVERT: G 1763 THR cc_start: 0.9012 (m) cc_final: 0.8688 (p) REVERT: G 1784 MET cc_start: 0.8002 (tmm) cc_final: 0.7387 (tmm) REVERT: G 1822 MET cc_start: 0.6226 (mpp) cc_final: 0.5429 (mpp) REVERT: G 2006 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7450 (mm) REVERT: G 2049 GLU cc_start: 0.4845 (OUTLIER) cc_final: 0.4620 (mm-30) outliers start: 62 outliers final: 51 residues processed: 298 average time/residue: 0.4018 time to fit residues: 197.2848 Evaluate side-chains 305 residues out of total 3253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 248 time to evaluate : 3.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 607 LYS Chi-restraints excluded: chain A residue 611 LYS Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 838 MET Chi-restraints excluded: chain A residue 881 ASN Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 1085 ASP Chi-restraints excluded: chain A residue 1150 ASP Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1295 SER Chi-restraints excluded: chain A residue 1484 GLU Chi-restraints excluded: chain A residue 1496 GLU Chi-restraints excluded: chain A residue 1633 THR Chi-restraints excluded: chain A residue 1666 THR Chi-restraints excluded: chain A residue 1708 ASP Chi-restraints excluded: chain A residue 1726 LYS Chi-restraints excluded: chain A residue 1779 ILE Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain A residue 1850 GLU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 265 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 81 ASP Chi-restraints excluded: chain G residue 112 ASN Chi-restraints excluded: chain G residue 115 THR Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 318 SER Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 581 THR Chi-restraints excluded: chain G residue 602 VAL Chi-restraints excluded: chain G residue 750 MET Chi-restraints excluded: chain G residue 840 THR Chi-restraints excluded: chain G residue 967 ILE Chi-restraints excluded: chain G residue 1133 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1421 ASN Chi-restraints excluded: chain G residue 1430 VAL Chi-restraints excluded: chain G residue 1434 HIS Chi-restraints excluded: chain G residue 1491 VAL Chi-restraints excluded: chain G residue 1511 SER Chi-restraints excluded: chain G residue 1531 VAL Chi-restraints excluded: chain G residue 1579 ILE Chi-restraints excluded: chain G residue 1583 MET Chi-restraints excluded: chain G residue 1648 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1821 VAL Chi-restraints excluded: chain G residue 1845 ASP Chi-restraints excluded: chain G residue 1881 ARG Chi-restraints excluded: chain G residue 1885 LEU Chi-restraints excluded: chain G residue 1966 CYS Chi-restraints excluded: chain G residue 2006 LEU Chi-restraints excluded: chain G residue 2035 SER Chi-restraints excluded: chain G residue 2049 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 7.9990 chunk 318 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 299 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 307 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 821 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 165 ASN G 224 ASN G 446 ASN ** G1581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.088440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.068123 restraints weight = 110224.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.069941 restraints weight = 51935.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.070225 restraints weight = 26625.589| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30300 Z= 0.156 Angle : 0.541 12.788 41041 Z= 0.271 Chirality : 0.042 0.332 4613 Planarity : 0.004 0.083 5299 Dihedral : 4.393 64.352 4042 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 1.81 % Allowed : 16.94 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.14), residues: 3774 helix: 1.34 (0.13), residues: 1692 sheet: -0.97 (0.22), residues: 536 loop : -0.03 (0.17), residues: 1546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1813 HIS 0.008 0.001 HIS A 454 PHE 0.028 0.001 PHE G1423 TYR 0.028 0.001 TYR G1506 ARG 0.007 0.000 ARG G 200 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5533.08 seconds wall clock time: 100 minutes 54.13 seconds (6054.13 seconds total)