Starting phenix.real_space_refine on Sun Jul 5 19:53:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psj_17853/07_2026/8psj_17853.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.008 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 2 5.49 5 S 108 5.16 5 C 18920 2.51 5 N 4969 2.21 5 O 5696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29695 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 12402 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 2 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: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 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: 5.74, per 1000 atoms: 0.19 Number of scatterers: 29695 At special positions: 0 Unit cell: (179.35, 185.68, 173.02, 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 108 16.00 P 2 15.00 O 5696 8.00 N 4969 7.00 C 18920 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=2.12 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.11 Conformation dependent library (CDL) restraints added in 927.8 milliseconds 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7042 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 29 sheets defined 51.7% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 removed outlier: 3.822A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 84 through 90 removed outlier: 3.906A pdb=" N ILE A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 351 removed outlier: 3.901A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 383 removed outlier: 3.505A pdb=" N ALA A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.455A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 444 through 457 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 463 through 484 Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.656A pdb=" N GLN A 527 " --> pdb=" O SER A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.511A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 615 " --> pdb=" O LYS A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.593A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 725 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 755 through 759 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 removed outlier: 3.591A pdb=" N ARG A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 847 through 856 removed outlier: 4.311A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 883 removed outlier: 6.013A pdb=" N ILE A 883 " --> pdb=" O ALA A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 891 removed outlier: 3.944A pdb=" N MET A 891 " --> pdb=" O GLY A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.705A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 935 through 969 removed outlier: 3.637A pdb=" N GLU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.507A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 4.024A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1046 through 1058 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.200A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1108 through 1112 removed outlier: 3.667A 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 1194 through 1199 removed outlier: 4.021A pdb=" N TYR A1198 " --> pdb=" O ASN A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 removed outlier: 3.868A pdb=" N GLN A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.631A 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 1262 Processing helix chain 'A' and resid 1273 through 1279 removed outlier: 4.158A pdb=" N GLU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1306 through 1321 removed outlier: 3.639A pdb=" N VAL A1312 " --> pdb=" O SER A1308 " (cutoff:3.500A) 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 1365 Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1424 through 1430 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1474 removed outlier: 3.623A pdb=" N ARG A1455 " --> pdb=" O GLN A1451 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLU A1473 " --> pdb=" O ALA A1469 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1510 removed outlier: 3.509A pdb=" N PHE A1485 " --> pdb=" O ASP A1481 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU A1496 " --> pdb=" O GLU A1492 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TRP A1508 " --> pdb=" O ALA A1504 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.613A pdb=" N ASP A1550 " --> pdb=" O THR A1546 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.826A 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 1601 removed outlier: 3.615A pdb=" N ASN A1594 " --> pdb=" O ALA A1590 " (cutoff:3.500A) Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 4.025A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.790A 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 Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.793A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1760 removed outlier: 3.573A pdb=" N THR A1760 " --> pdb=" O ILE A1756 " (cutoff:3.500A) Processing helix chain 'A' and resid 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 Processing helix chain 'A' and resid 1792 through 1802 removed outlier: 3.553A pdb=" N TYR A1798 " --> pdb=" O GLN A1794 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 removed outlier: 3.612A pdb=" N GLY A1824 " --> pdb=" O PHE A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1833 through 1835 No H-bonds generated for 'chain 'A' and resid 1833 through 1835' Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.810A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.784A pdb=" N LEU B 151 " --> pdb=" O ALA B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 179 through 194 removed outlier: 3.996A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.848A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 229 Processing helix chain 'B' and resid 229 through 237 removed outlier: 3.530A pdb=" N SER B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 253 removed outlier: 3.555A pdb=" N ALA B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 removed outlier: 4.454A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 removed outlier: 3.590A pdb=" N ALA B 291 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 27 No H-bonds generated for 'chain 'G' and resid 25 through 27' Processing helix chain 'G' and resid 29 through 41 removed outlier: 3.618A pdb=" N GLN G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 78 through 82 removed outlier: 3.894A pdb=" N ASP G 81 " --> pdb=" O GLY G 78 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLN G 82 " --> pdb=" O GLN G 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 78 through 82' Processing helix chain 'G' and resid 86 through 95 removed outlier: 3.580A pdb=" N GLU G 90 " --> pdb=" O LEU G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.951A pdb=" N LEU G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 169 through 180 Processing helix chain 'G' and resid 180 through 202 removed outlier: 3.522A pdb=" N GLY G 185 " --> pdb=" O HIS G 181 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS G 189 " --> pdb=" O GLY G 185 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 Processing helix chain 'G' and resid 214 through 221 removed outlier: 3.986A pdb=" N TRP G 218 " --> pdb=" O ASN G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 257 Proline residue: G 239 - end of helix removed outlier: 3.552A pdb=" N LEU G 246 " --> pdb=" O GLY G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.924A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 314 Processing helix chain 'G' and resid 320 through 330 removed outlier: 3.546A pdb=" N LEU G 324 " --> pdb=" O PRO G 320 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ASP G 326 " --> pdb=" O SER G 322 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 359 removed outlier: 3.560A pdb=" N VAL G 349 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 removed outlier: 3.526A pdb=" N GLN G 365 " --> pdb=" O ALA G 362 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 395 removed outlier: 3.720A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 429 through 434 Proline residue: G 434 - end of helix Processing helix chain 'G' and resid 435 through 446 removed outlier: 3.525A pdb=" N ASN G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 removed outlier: 3.542A pdb=" N VAL G 480 " --> pdb=" O SER G 476 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 507 through 510 removed outlier: 3.583A pdb=" N SER G 510 " --> pdb=" O GLY G 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 507 through 510' Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.883A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 4.250A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 565 removed outlier: 3.584A pdb=" N GLU G 564 " --> pdb=" O ASN G 560 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 588 Processing helix chain 'G' and resid 603 through 612 removed outlier: 3.500A pdb=" N ALA G 608 " --> pdb=" O PRO G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 622 through 624 No H-bonds generated for 'chain 'G' and resid 622 through 624' Processing helix chain 'G' and resid 626 through 641 removed outlier: 3.659A pdb=" N ALA G 633 " --> pdb=" O GLY G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 672 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.639A pdb=" N LEU G 698 " --> pdb=" O TYR G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 759 removed outlier: 6.362A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 783 removed outlier: 3.685A pdb=" N THR G 777 " --> pdb=" O SER G 773 " (cutoff:3.500A) Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 787 Processing helix chain 'G' and resid 802 through 808 removed outlier: 4.248A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 removed outlier: 3.635A pdb=" N LYS G 819 " --> pdb=" O PRO G 815 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N CYS G 824 " --> pdb=" O CYS G 820 " (cutoff:3.500A) Processing helix chain 'G' and resid 828 through 837 removed outlier: 4.564A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 887 removed outlier: 4.203A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 887 through 898 Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 941 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 1008 removed outlier: 3.545A pdb=" N GLN G1008 " --> pdb=" O LEU G1004 " (cutoff:3.500A) Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1034 through 1051 removed outlier: 3.584A pdb=" N SER G1037 " --> pdb=" O LEU G1034 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA G1042 " --> pdb=" O HIS G1039 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL G1044 " --> pdb=" O GLU G1041 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ASP G1045 " --> pdb=" O ALA G1042 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN G1046 " --> pdb=" O VAL G1043 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL G1048 " --> pdb=" O ASP G1045 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N GLN G1049 " --> pdb=" O GLN G1046 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG G1050 " --> pdb=" O ASP G1047 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 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 1175 Processing helix chain 'G' and resid 1189 through 1192 removed outlier: 3.600A pdb=" N LYS G1192 " --> pdb=" O THR G1189 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1189 through 1192' Processing helix chain 'G' and resid 1257 through 1271 removed outlier: 3.528A pdb=" N LYS G1268 " --> pdb=" O GLU G1264 " (cutoff:3.500A) Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1324 through 1336 removed outlier: 4.177A pdb=" N VAL G1328 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1337 through 1339 No H-bonds generated for 'chain 'G' and resid 1337 through 1339' Processing helix chain 'G' and resid 1340 through 1344 Processing helix chain 'G' and resid 1418 through 1422 Processing helix chain 'G' and resid 1438 through 1447 removed outlier: 3.579A pdb=" N ALA G1442 " --> pdb=" O SER G1438 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 Processing helix chain 'G' and resid 1550 through 1557 Processing helix chain 'G' and resid 1561 through 1566 removed outlier: 3.941A pdb=" N VAL G1565 " --> pdb=" O ASN G1561 " (cutoff:3.500A) Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 removed outlier: 5.080A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN G1595 " --> pdb=" O ALA G1591 " (cutoff:3.500A) Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.695A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 removed outlier: 3.563A pdb=" N GLN G1688 " --> pdb=" O SER G1684 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1734 removed outlier: 3.669A pdb=" N GLY G1726 " --> pdb=" O GLY G1722 " (cutoff:3.500A) Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1796 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1819 removed outlier: 4.072A 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: 3.805A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1883 Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 3.844A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1924 through 1931 removed outlier: 4.022A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU G1931 " --> pdb=" O LEU G1927 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1952 removed outlier: 3.569A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU G1946 " --> pdb=" O GLU G1942 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1983 removed outlier: 4.476A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.567A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS G1993 " --> pdb=" O LYS G1989 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 Processing helix chain 'G' and resid 2002 through 2007 Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2035 through 2044 removed outlier: 4.374A pdb=" N ILE G2041 " --> pdb=" O PRO G2037 " (cutoff:3.500A) Processing helix chain 'G' and resid 2044 through 2050 removed outlier: 3.514A pdb=" N GLN G2050 " --> pdb=" O GLU G2046 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.678A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 8.158A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 5.915A pdb=" N VAL A 44 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.649A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 400 through 402 current: chain 'A' and resid 649 through 651 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 649 through 651 current: chain 'A' and resid 702 through 707 removed outlier: 6.551A pdb=" N VAL A 703 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N VAL A 735 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL A 705 " --> pdb=" O VAL A 735 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 732 through 736 current: chain 'A' and resid 820 through 822 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 820 through 822 current: chain 'A' and resid 862 through 869 removed outlier: 9.876A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N LEU A 926 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA6, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA7, first strand: chain 'A' and resid 1243 through 1244 removed outlier: 3.787A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AA9, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB1, first strand: chain 'A' and resid 1123 through 1126 Processing sheet with id=AB2, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB3, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB4, first strand: chain 'A' and resid 1723 through 1724 removed outlier: 3.617A pdb=" N THR A1732 " --> pdb=" O SER A1723 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB6, first strand: chain 'A' and resid 1837 through 1842 removed outlier: 5.325A pdb=" N VAL A1842 " --> pdb=" O ALA A1846 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ALA A1846 " --> pdb=" O VAL A1842 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.710A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 459 through 460 removed outlier: 7.341A pdb=" N ALA G 270 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ALA G 158 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL G 157 " --> pdb=" O LEU G 502 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 418 through 420 removed outlier: 3.611A pdb=" N LEU G 377 " --> pdb=" O ILE G 341 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN G 376 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL G 371 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC2, first strand: chain 'G' and resid 728 through 730 removed outlier: 4.105A pdb=" N TYR G 702 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU G 679 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE G 617 " --> pdb=" O GLY G 648 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ASN G 650 " --> pdb=" O ILE G 617 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N LEU G 619 " --> pdb=" O ASN G 650 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N ILE G 652 " --> pdb=" O LEU G 619 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 739 through 740 Processing sheet with id=AC4, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC5, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC6, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.290A pdb=" N VAL G1195 " --> pdb=" O ILE G1210 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE G1210 " --> pdb=" O VAL G1195 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G1197 " --> pdb=" O THR G1208 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N PHE G1158 " --> pdb=" O ILE G1251 " (cutoff:3.500A) removed outlier: 8.664A pdb=" N GLU G1253 " --> pdb=" O PHE G1158 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N THR G1160 " --> pdb=" O GLU G1253 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 1285 through 1291 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1285 through 1291 current: chain 'G' and resid 1387 through 1398 removed outlier: 3.624A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1401 through 1413 current: chain 'G' and resid 1635 through 1643 Processing sheet with id=AC8, first strand: chain 'G' and resid 1431 through 1435 removed outlier: 3.748A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY G1502 " --> pdb=" O ILE G1489 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1471 through 1474 removed outlier: 7.172A pdb=" N GLU G1471 " --> pdb=" O VAL G1483 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL G1483 " --> pdb=" O GLU G1471 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR G1473 " --> pdb=" O SER G1481 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD2, first strand: chain 'G' and resid 1740 through 1741 1350 hydrogen bonds defined for protein. 3777 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: 7.13 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5080 1.31 - 1.45: 7664 1.45 - 1.58: 17377 1.58 - 1.72: 3 1.72 - 1.85: 190 Bond restraints: 30314 Sorted by residual: bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.305 -0.069 1.14e-02 7.69e+03 3.63e+01 bond pdb=" C7 FMN G2101 " pdb=" C8 FMN G2101 " ideal model delta sigma weight residual 1.390 1.491 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" N ILE G1537 " pdb=" CA ILE G1537 " ideal model delta sigma weight residual 1.458 1.496 -0.038 7.70e-03 1.69e+04 2.47e+01 bond pdb=" C4 FMN G2101 " pdb=" C4A FMN G2101 " ideal model delta sigma weight residual 1.390 1.489 -0.099 2.00e-02 2.50e+03 2.45e+01 bond pdb=" C PRO A1658 " pdb=" O PRO A1658 " ideal model delta sigma weight residual 1.237 1.175 0.063 1.28e-02 6.10e+03 2.39e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 30021 2.11 - 4.21: 9754 4.21 - 6.32: 1198 6.32 - 8.43: 82 8.43 - 10.54: 5 Bond angle restraints: 41060 Sorted by residual: angle pdb=" C GLY G 662 " pdb=" N ILE G 663 " pdb=" CA ILE G 663 " ideal model delta sigma weight residual 120.33 126.10 -5.77 8.00e-01 1.56e+00 5.21e+01 angle pdb=" CB GLU A 381 " pdb=" CG GLU A 381 " pdb=" CD GLU A 381 " ideal model delta sigma weight residual 112.60 123.14 -10.54 1.70e+00 3.46e-01 3.84e+01 angle pdb=" CA ASP G 186 " pdb=" CB ASP G 186 " pdb=" CG ASP G 186 " ideal model delta sigma weight residual 112.60 118.67 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" N ARG A1502 " pdb=" CA ARG A1502 " pdb=" C ARG A1502 " ideal model delta sigma weight residual 111.07 104.65 6.42 1.07e+00 8.73e-01 3.60e+01 angle pdb=" CB GLU A1378 " pdb=" CG GLU A1378 " pdb=" CD GLU A1378 " ideal model delta sigma weight residual 112.60 122.73 -10.13 1.70e+00 3.46e-01 3.55e+01 ... (remaining 41055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 16457 17.98 - 35.95: 1468 35.95 - 53.93: 256 53.93 - 71.91: 75 71.91 - 89.89: 39 Dihedral angle restraints: 18295 sinusoidal: 7356 harmonic: 10939 Sorted by residual: dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ASP G 974 " pdb=" C ASP G 974 " pdb=" N LYS G 975 " pdb=" CA LYS G 975 " ideal model delta harmonic sigma weight residual 180.00 156.73 23.27 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU G 370 " pdb=" C LEU G 370 " pdb=" N VAL G 371 " pdb=" CA VAL G 371 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 18292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1973 0.056 - 0.112: 1610 0.112 - 0.167: 830 0.167 - 0.223: 178 0.223 - 0.279: 23 Chirality restraints: 4614 Sorted by residual: chirality pdb=" CA VAL A 893 " pdb=" N VAL A 893 " pdb=" C VAL A 893 " pdb=" CB VAL A 893 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE A1328 " pdb=" N ILE A1328 " pdb=" C ILE A1328 " pdb=" CB ILE A1328 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.70 -0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4611 not shown) Planarity restraints: 5299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1401 " -0.065 2.00e-02 2.50e+03 3.40e-02 2.31e+01 pdb=" CG TYR A1401 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A1401 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A1401 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR A1401 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A1401 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR A1401 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1401 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP G1449 " -0.050 2.00e-02 2.50e+03 2.51e-02 1.57e+01 pdb=" CG TRP G1449 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP G1449 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP G1449 " 0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP G1449 " -0.017 2.00e-02 2.50e+03 pdb=" CE2 TRP G1449 " -0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP G1449 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP G1449 " -0.010 2.00e-02 2.50e+03 pdb=" CZ3 TRP G1449 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP G1449 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.045 2.00e-02 2.50e+03 2.39e-02 1.14e+01 pdb=" CG TYR A1529 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.012 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.018 2.00e-02 2.50e+03 ... (remaining 5296 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 359 2.64 - 3.20: 27120 3.20 - 3.77: 46441 3.77 - 4.33: 65874 4.33 - 4.90: 107710 Nonbonded interactions: 247504 Sorted by model distance: nonbonded pdb=" OH TYR B 249 " pdb=" OD1 ASP B 288 " model vdw 2.072 3.040 nonbonded pdb=" OH TYR G 177 " pdb=" OE2 GLU G 220 " model vdw 2.113 3.040 nonbonded pdb=" OG1 THR A1812 " pdb=" NH1 ARG A1841 " model vdw 2.227 3.120 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.227 3.040 nonbonded pdb=" OG1 THR G1663 " pdb=" O THR G1803 " model vdw 2.227 3.040 ... (remaining 247499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.040 Extract box with map and model: 0.570 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.370 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 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 0.101 30316 Z= 1.044 Angle : 1.912 15.307 41062 Z= 1.394 Chirality : 0.088 0.279 4614 Planarity : 0.007 0.034 5299 Dihedral : 14.910 89.885 11250 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.68 % Favored : 92.00 % Rotamer: Outliers : 0.62 % Allowed : 5.29 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.68 (0.11), residues: 3776 helix: -2.84 (0.09), residues: 1667 sheet: -2.34 (0.21), residues: 459 loop : -1.82 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1017 TYR 0.065 0.006 TYR A1401 PHE 0.037 0.005 PHE G 799 TRP 0.050 0.007 TRP G1449 HIS 0.015 0.003 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.01389 / 1.04 (30314) covalent geometry : angle 1.91064 / 1.39 (41060) SS BOND : bond 0.08772 / 4.62 ( 1) SS BOND : angle 11.40983 / 6.64 ( 2) hydrogen bonds : bond 0.22200 / 14.51 ( 1350) hydrogen bonds : angle 9.57112 / 6.79 ( 3777) Misc. bond : bond 0.05267 / 2.77 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 291 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 841 GLU cc_start: 0.9233 (mp0) cc_final: 0.8509 (tp30) REVERT: A 923 MET cc_start: 0.9304 (tpp) cc_final: 0.9049 (tpp) REVERT: A 981 GLU cc_start: 0.9027 (mp0) cc_final: 0.8818 (mm-30) REVERT: A 1123 GLN cc_start: 0.9298 (tm-30) cc_final: 0.8719 (tm-30) REVERT: A 1124 GLU cc_start: 0.8942 (tp30) cc_final: 0.8495 (tp30) REVERT: A 1130 ASP cc_start: 0.9042 (m-30) cc_final: 0.8722 (m-30) REVERT: A 1396 MET cc_start: 0.9490 (mtp) cc_final: 0.9187 (mtp) REVERT: A 1461 ASP cc_start: 0.9418 (m-30) cc_final: 0.9178 (m-30) REVERT: A 1751 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8388 (mp0) REVERT: A 1776 ILE cc_start: 0.8677 (pt) cc_final: 0.8414 (mp) REVERT: A 1789 ARG cc_start: 0.8406 (tmt170) cc_final: 0.7837 (tpt90) REVERT: A 1794 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 1797 GLU cc_start: 0.8747 (tm-30) cc_final: 0.8347 (pp20) REVERT: B 149 LEU cc_start: 0.9267 (mp) cc_final: 0.8907 (pp) REVERT: B 174 ASP cc_start: 0.8865 (t70) cc_final: 0.8435 (t0) REVERT: B 202 GLU cc_start: 0.8304 (tt0) cc_final: 0.8102 (tt0) REVERT: B 211 GLU cc_start: 0.7522 (tm-30) cc_final: 0.6951 (tp30) REVERT: B 277 LEU cc_start: 0.5008 (OUTLIER) cc_final: 0.4633 (mt) REVERT: G 169 TYR cc_start: 0.8037 (p90) cc_final: 0.7609 (p90) REVERT: G 174 ARG cc_start: 0.7720 (mtt180) cc_final: 0.6918 (mmm-85) REVERT: G 209 PHE cc_start: 0.7335 (m-80) cc_final: 0.7062 (m-80) REVERT: G 311 TYR cc_start: 0.8379 (t80) cc_final: 0.8157 (t80) REVERT: G 553 ASN cc_start: 0.7811 (p0) cc_final: 0.7368 (p0) REVERT: G 618 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8411 (mt-10) REVERT: G 765 LEU cc_start: 0.9436 (tp) cc_final: 0.9023 (tp) REVERT: G 1180 MET cc_start: 0.8383 (mtp) cc_final: 0.8033 (mtm) REVERT: G 1265 MET cc_start: 0.9344 (ttp) cc_final: 0.9045 (ttp) REVERT: G 1359 MET cc_start: 0.8250 (tpt) cc_final: 0.7544 (tpp) REVERT: G 1456 ASP cc_start: 0.9215 (m-30) cc_final: 0.8632 (p0) REVERT: G 1633 ASN cc_start: 0.9028 (t0) cc_final: 0.8787 (t0) REVERT: G 1658 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9012 (mt-10) REVERT: G 1784 MET cc_start: 0.9322 (tmm) cc_final: 0.8952 (tmm) REVERT: G 1822 MET cc_start: 0.8992 (mtm) cc_final: 0.8768 (mtm) REVERT: G 1982 MET cc_start: 0.9057 (mmp) cc_final: 0.8732 (mmm) outliers start: 20 outliers final: 3 residues processed: 309 average time/residue: 0.1898 time to fit residues: 96.3450 Evaluate side-chains 213 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 208 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1751 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain G residue 626 SER Chi-restraints excluded: chain G residue 1641 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 5.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN A 379 ASN A 527 GLN A 829 ASN A1188 GLN A1239 HIS A1458 GLN A1549 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 224 ASN G 248 HIS G 275 GLN G 330 ASN G 440 ASN G 495 GLN G 640 GLN G 718 ASN G1055 HIS G1078 HIS G1186 ASN G1355 ASN G1451 GLN G1595 ASN G1674 GLN G1697 HIS G1872 GLN G1912 ASN G1983 ASN G2044 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.082678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.059379 restraints weight = 109864.105| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.01 r_work: 0.2908 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30316 Z= 0.142 Angle : 0.576 8.697 41062 Z= 0.305 Chirality : 0.043 0.195 4614 Planarity : 0.005 0.221 5299 Dihedral : 5.455 65.000 4059 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.49 % Favored : 97.48 % Rotamer: Outliers : 0.55 % Allowed : 8.43 % Favored : 91.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.13), residues: 3776 helix: -0.19 (0.12), residues: 1699 sheet: -1.67 (0.21), residues: 527 loop : -0.60 (0.16), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 231 TYR 0.019 0.001 TYR B 294 PHE 0.023 0.002 PHE A 35 TRP 0.017 0.001 TRP G 661 HIS 0.007 0.001 HIS G1697 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (30314) covalent geometry : angle 0.57468 / 0.30 (41060) SS BOND : bond 0.00521 / 0.27 ( 1) SS BOND : angle 4.72551 / 2.68 ( 2) hydrogen bonds : bond 0.04278 / 2.78 ( 1350) hydrogen bonds : angle 5.24543 / 3.71 ( 3777) Misc. bond : bond 0.00017 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 242 time to evaluate : 1.080 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9147 (mttm) cc_final: 0.8774 (mmtt) REVERT: A 342 GLN cc_start: 0.9211 (mt0) cc_final: 0.8689 (mp10) REVERT: A 529 MET cc_start: 0.9135 (mmp) cc_final: 0.8843 (mmp) REVERT: A 1017 ARG cc_start: 0.8861 (mmm-85) cc_final: 0.8544 (ttm-80) REVERT: A 1123 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8265 (tm-30) REVERT: A 1130 ASP cc_start: 0.8326 (m-30) cc_final: 0.7892 (m-30) REVERT: A 1167 LEU cc_start: 0.9147 (mt) cc_final: 0.8818 (mt) REVERT: A 1789 ARG cc_start: 0.8145 (tmt170) cc_final: 0.7891 (tpt90) REVERT: B 149 LEU cc_start: 0.9020 (mp) cc_final: 0.8702 (pp) REVERT: B 174 ASP cc_start: 0.8512 (t70) cc_final: 0.8178 (t70) REVERT: G 174 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6733 (mmm-85) REVERT: G 630 MET cc_start: 0.8928 (ttt) cc_final: 0.8709 (ttt) REVERT: G 765 LEU cc_start: 0.9235 (tp) cc_final: 0.8971 (tp) REVERT: G 1136 GLU cc_start: 0.8724 (tp30) cc_final: 0.8437 (tp30) REVERT: G 1265 MET cc_start: 0.9036 (ttp) cc_final: 0.8553 (ttp) REVERT: G 1456 ASP cc_start: 0.9036 (m-30) cc_final: 0.8409 (p0) REVERT: G 1658 GLU cc_start: 0.8852 (mt-10) cc_final: 0.8602 (mt-10) REVERT: G 1854 MET cc_start: 0.8093 (mmm) cc_final: 0.7769 (mmm) REVERT: G 1982 MET cc_start: 0.8669 (mmp) cc_final: 0.8303 (mmp) outliers start: 18 outliers final: 8 residues processed: 255 average time/residue: 0.1942 time to fit residues: 80.9589 Evaluate side-chains 215 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 207 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 626 SER Chi-restraints excluded: chain G residue 1641 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 40 optimal weight: 5.9990 chunk 276 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 58 optimal weight: 0.9990 chunk 253 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 283 optimal weight: 20.0000 chunk 153 optimal weight: 0.0470 overall best weight: 2.2484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 829 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 251 GLN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061998 restraints weight = 110657.523| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.85 r_work: 0.2943 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30316 Z= 0.124 Angle : 0.520 10.124 41062 Z= 0.270 Chirality : 0.042 0.223 4614 Planarity : 0.003 0.038 5299 Dihedral : 4.927 62.846 4054 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 0.58 % Allowed : 10.00 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.14), residues: 3776 helix: 0.79 (0.13), residues: 1710 sheet: -1.27 (0.22), residues: 521 loop : -0.32 (0.16), residues: 1545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 247 TYR 0.021 0.001 TYR G1298 PHE 0.022 0.001 PHE A 35 TRP 0.014 0.001 TRP G 661 HIS 0.010 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (30314) covalent geometry : angle 0.51910 / 0.27 (41060) SS BOND : bond 0.00330 / 0.17 ( 1) SS BOND : angle 3.97331 / 2.27 ( 2) hydrogen bonds : bond 0.03562 / 2.33 ( 1350) hydrogen bonds : angle 4.78338 / 3.38 ( 3777) Misc. bond : bond 0.00050 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8585 (mm-30) REVERT: A 336 LYS cc_start: 0.9066 (mttm) cc_final: 0.8697 (mmtt) REVERT: A 342 GLN cc_start: 0.9241 (mt0) cc_final: 0.8702 (mp10) REVERT: A 529 MET cc_start: 0.9122 (mmp) cc_final: 0.8805 (mmp) REVERT: A 1123 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 1124 GLU cc_start: 0.8454 (tp30) cc_final: 0.7982 (tp30) REVERT: A 1130 ASP cc_start: 0.8395 (m-30) cc_final: 0.7940 (m-30) REVERT: A 1167 LEU cc_start: 0.9139 (mt) cc_final: 0.8812 (mt) REVERT: A 1789 ARG cc_start: 0.8189 (tmt170) cc_final: 0.7971 (tpt90) REVERT: B 237 MET cc_start: 0.7237 (mmt) cc_final: 0.6848 (mmm) REVERT: G 171 GLU cc_start: 0.8437 (mm-30) cc_final: 0.8083 (mm-30) REVERT: G 174 ARG cc_start: 0.7439 (mtt180) cc_final: 0.6854 (mmm-85) REVERT: G 518 ARG cc_start: 0.8901 (mpp80) cc_final: 0.8165 (mpp80) REVERT: G 1456 ASP cc_start: 0.8969 (m-30) cc_final: 0.8426 (p0) REVERT: G 1658 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8455 (mt-10) REVERT: G 1768 LYS cc_start: 0.8922 (pttm) cc_final: 0.8424 (mtmt) REVERT: G 1854 MET cc_start: 0.8243 (mmm) cc_final: 0.7883 (mmm) REVERT: G 1982 MET cc_start: 0.8620 (mmp) cc_final: 0.8359 (mmm) outliers start: 19 outliers final: 7 residues processed: 253 average time/residue: 0.1771 time to fit residues: 72.2106 Evaluate side-chains 213 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 206 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 135 optimal weight: 8.9990 chunk 357 optimal weight: 20.0000 chunk 153 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 277 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 chunk 186 optimal weight: 20.0000 chunk 95 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 ASN A 829 ASN A1689 HIS B 251 GLN B 261 GLN G 275 GLN G1226 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.082184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059625 restraints weight = 110936.407| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.17 r_work: 0.2905 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30316 Z= 0.183 Angle : 0.542 10.504 41062 Z= 0.279 Chirality : 0.043 0.228 4614 Planarity : 0.004 0.043 5299 Dihedral : 4.813 61.304 4050 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.02 % Allowed : 11.53 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.14), residues: 3776 helix: 0.96 (0.13), residues: 1713 sheet: -1.09 (0.22), residues: 534 loop : -0.21 (0.16), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 852 TYR 0.045 0.002 TYR G1298 PHE 0.020 0.002 PHE A 35 TRP 0.012 0.001 TRP G 661 HIS 0.006 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.18 (30314) covalent geometry : angle 0.54080 / 0.28 (41060) SS BOND : bond 0.00212 / 0.11 ( 1) SS BOND : angle 4.30100 / 2.48 ( 2) hydrogen bonds : bond 0.03633 / 2.38 ( 1350) hydrogen bonds : angle 4.71785 / 3.33 ( 3777) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9103 (mttm) cc_final: 0.8719 (mmtt) REVERT: A 342 GLN cc_start: 0.9237 (mt0) cc_final: 0.8689 (mp10) REVERT: A 529 MET cc_start: 0.9112 (mmp) cc_final: 0.8777 (mmp) REVERT: A 923 MET cc_start: 0.9014 (ttm) cc_final: 0.8812 (ttm) REVERT: A 1123 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8381 (tm-30) REVERT: A 1124 GLU cc_start: 0.8490 (tp30) cc_final: 0.8047 (tp30) REVERT: A 1130 ASP cc_start: 0.8443 (m-30) cc_final: 0.7975 (m-30) REVERT: A 1167 LEU cc_start: 0.9070 (mt) cc_final: 0.8626 (mt) REVERT: A 1821 LYS cc_start: 0.8449 (mppt) cc_final: 0.8214 (mttt) REVERT: B 211 GLU cc_start: 0.7370 (tm-30) cc_final: 0.7008 (tp30) REVERT: B 237 MET cc_start: 0.7452 (mmt) cc_final: 0.7209 (mmt) REVERT: B 251 GLN cc_start: 0.7222 (pt0) cc_final: 0.6771 (tp-100) REVERT: G 171 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8057 (mm-30) REVERT: G 174 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6639 (mmm-85) REVERT: G 551 THR cc_start: 0.7098 (OUTLIER) cc_final: 0.6759 (p) REVERT: G 1456 ASP cc_start: 0.8978 (m-30) cc_final: 0.8424 (p0) REVERT: G 1982 MET cc_start: 0.8748 (mmp) cc_final: 0.8503 (mmp) outliers start: 33 outliers final: 20 residues processed: 238 average time/residue: 0.1939 time to fit residues: 75.9281 Evaluate side-chains 213 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 468 LEU Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1156 CYS Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 37 optimal weight: 5.9990 chunk 279 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 353 optimal weight: 20.0000 chunk 124 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 329 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 280 optimal weight: 0.0870 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN G 38 ASN G 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.082941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059966 restraints weight = 110926.416| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.99 r_work: 0.2933 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30316 Z= 0.124 Angle : 0.503 8.748 41062 Z= 0.258 Chirality : 0.042 0.260 4614 Planarity : 0.003 0.043 5299 Dihedral : 4.621 59.314 4050 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.14 % Allowed : 12.27 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.14), residues: 3776 helix: 1.14 (0.13), residues: 1715 sheet: -0.93 (0.22), residues: 543 loop : -0.09 (0.16), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 340 TYR 0.024 0.001 TYR B 294 PHE 0.021 0.001 PHE A 35 TRP 0.013 0.001 TRP G1138 HIS 0.005 0.001 HIS G 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (30314) covalent geometry : angle 0.50202 / 0.26 (41060) SS BOND : bond 0.00162 / 0.09 ( 1) SS BOND : angle 3.68724 / 2.12 ( 2) hydrogen bonds : bond 0.03318 / 2.17 ( 1350) hydrogen bonds : angle 4.56647 / 3.23 ( 3777) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9092 (mttm) cc_final: 0.8673 (mmtt) REVERT: A 342 GLN cc_start: 0.9243 (mt0) cc_final: 0.8687 (mp10) REVERT: A 529 MET cc_start: 0.9135 (mmp) cc_final: 0.8812 (mmp) REVERT: A 1123 GLN cc_start: 0.9062 (tm-30) cc_final: 0.8350 (tm-30) REVERT: A 1124 GLU cc_start: 0.8539 (tp30) cc_final: 0.8038 (tp30) REVERT: A 1130 ASP cc_start: 0.8383 (m-30) cc_final: 0.7941 (m-30) REVERT: A 1167 LEU cc_start: 0.9050 (mt) cc_final: 0.8637 (mt) REVERT: A 1396 MET cc_start: 0.9419 (mtm) cc_final: 0.9199 (mtp) REVERT: A 1773 VAL cc_start: 0.7423 (OUTLIER) cc_final: 0.6973 (t) REVERT: A 1813 TRP cc_start: 0.8278 (t-100) cc_final: 0.7863 (t-100) REVERT: A 1821 LYS cc_start: 0.8554 (mppt) cc_final: 0.8315 (mttt) REVERT: B 211 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6950 (tp30) REVERT: B 237 MET cc_start: 0.7429 (mmt) cc_final: 0.7179 (mmt) REVERT: G 171 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8068 (mm-30) REVERT: G 174 ARG cc_start: 0.7267 (mtt180) cc_final: 0.6614 (mmm-85) REVERT: G 551 THR cc_start: 0.6994 (OUTLIER) cc_final: 0.6692 (p) REVERT: G 1175 LYS cc_start: 0.9091 (tttm) cc_final: 0.8882 (mmtm) REVERT: G 1456 ASP cc_start: 0.8988 (m-30) cc_final: 0.8453 (p0) REVERT: G 1669 GLN cc_start: 0.8579 (pm20) cc_final: 0.8197 (pt0) REVERT: G 1982 MET cc_start: 0.8794 (mmp) cc_final: 0.8539 (mmp) REVERT: G 2026 PHE cc_start: 0.9142 (m-80) cc_final: 0.8915 (m-80) outliers start: 37 outliers final: 16 residues processed: 238 average time/residue: 0.1798 time to fit residues: 71.3420 Evaluate side-chains 212 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 801 PHE Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1777 THR Chi-restraints excluded: chain G residue 1886 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 342 optimal weight: 3.9990 chunk 154 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 278 optimal weight: 6.9990 chunk 189 optimal weight: 6.9990 chunk 291 optimal weight: 6.9990 chunk 267 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 205 optimal weight: 0.1980 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN ** A1689 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN G 723 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.083291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.060336 restraints weight = 109837.339| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 2.98 r_work: 0.2945 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30316 Z= 0.116 Angle : 0.496 8.710 41062 Z= 0.253 Chirality : 0.041 0.262 4614 Planarity : 0.003 0.044 5299 Dihedral : 4.488 57.244 4048 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.17 % Allowed : 12.67 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3776 helix: 1.28 (0.13), residues: 1718 sheet: -0.78 (0.22), residues: 541 loop : -0.03 (0.16), residues: 1517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 340 TYR 0.014 0.001 TYR B 294 PHE 0.021 0.001 PHE A 35 TRP 0.012 0.001 TRP G 661 HIS 0.005 0.001 HIS G 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (30314) covalent geometry : angle 0.49553 / 0.25 (41060) SS BOND : bond 0.00103 / 0.05 ( 1) SS BOND : angle 3.44320 / 1.98 ( 2) hydrogen bonds : bond 0.03187 / 2.09 ( 1350) hydrogen bonds : angle 4.47526 / 3.16 ( 3777) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 206 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9025 (mttm) cc_final: 0.8616 (mmtt) REVERT: A 342 GLN cc_start: 0.9254 (mt0) cc_final: 0.8703 (mp10) REVERT: A 529 MET cc_start: 0.9126 (mmp) cc_final: 0.8801 (mmp) REVERT: A 1123 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8321 (tm-30) REVERT: A 1124 GLU cc_start: 0.8554 (tp30) cc_final: 0.8048 (tp30) REVERT: A 1130 ASP cc_start: 0.8465 (m-30) cc_final: 0.8038 (m-30) REVERT: A 1167 LEU cc_start: 0.9044 (mt) cc_final: 0.8629 (mt) REVERT: A 1396 MET cc_start: 0.9411 (mtm) cc_final: 0.9132 (mtp) REVERT: A 1773 VAL cc_start: 0.7451 (OUTLIER) cc_final: 0.7036 (t) REVERT: A 1813 TRP cc_start: 0.8337 (t-100) cc_final: 0.7922 (t-100) REVERT: A 1821 LYS cc_start: 0.8515 (mppt) cc_final: 0.8159 (mttt) REVERT: B 211 GLU cc_start: 0.7350 (tm-30) cc_final: 0.6960 (tp30) REVERT: B 237 MET cc_start: 0.7419 (mmt) cc_final: 0.7162 (mmt) REVERT: B 290 MET cc_start: 0.2987 (tmm) cc_final: 0.2038 (tmm) REVERT: G 171 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8027 (mm-30) REVERT: G 174 ARG cc_start: 0.7243 (mtt180) cc_final: 0.6584 (mmm-85) REVERT: G 534 ASP cc_start: 0.6762 (OUTLIER) cc_final: 0.6110 (m-30) REVERT: G 551 THR cc_start: 0.7091 (OUTLIER) cc_final: 0.6802 (p) REVERT: G 800 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8637 (pp) REVERT: G 1669 GLN cc_start: 0.8539 (pm20) cc_final: 0.8178 (pt0) REVERT: G 1982 MET cc_start: 0.8822 (mmp) cc_final: 0.8584 (mmp) REVERT: G 2026 PHE cc_start: 0.9121 (m-80) cc_final: 0.8885 (m-80) outliers start: 38 outliers final: 24 residues processed: 238 average time/residue: 0.1887 time to fit residues: 74.4387 Evaluate side-chains 224 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 196 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 965 HIS Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 800 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1777 THR Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1886 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 342 optimal weight: 3.9990 chunk 332 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 chunk 174 optimal weight: 9.9990 chunk 319 optimal weight: 9.9990 chunk 228 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 184 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN ** A1188 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1433 HIS A1689 HIS G 275 GLN G1535 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.082161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.059656 restraints weight = 111188.591| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.15 r_work: 0.2908 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30316 Z= 0.193 Angle : 0.542 9.861 41062 Z= 0.276 Chirality : 0.042 0.263 4614 Planarity : 0.004 0.043 5299 Dihedral : 4.622 57.387 4048 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.11 % Allowed : 13.41 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3776 helix: 1.27 (0.13), residues: 1720 sheet: -0.77 (0.23), residues: 529 loop : -0.03 (0.17), residues: 1527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1171 TYR 0.025 0.001 TYR G 126 PHE 0.019 0.001 PHE A 35 TRP 0.017 0.001 TRP G1138 HIS 0.005 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (30314) covalent geometry : angle 0.54160 / 0.28 (41060) SS BOND : bond 0.00220 / 0.12 ( 1) SS BOND : angle 4.05431 / 2.35 ( 2) hydrogen bonds : bond 0.03466 / 2.27 ( 1350) hydrogen bonds : angle 4.58066 / 3.24 ( 3777) Misc. bond : bond 0.00015 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 203 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9102 (mttm) cc_final: 0.8707 (mmtt) REVERT: A 342 GLN cc_start: 0.9223 (mt0) cc_final: 0.8673 (mp10) REVERT: A 529 MET cc_start: 0.9106 (mmp) cc_final: 0.8756 (mmp) REVERT: A 1123 GLN cc_start: 0.9130 (tm-30) cc_final: 0.8387 (tm-30) REVERT: A 1124 GLU cc_start: 0.8529 (tp30) cc_final: 0.8050 (tp30) REVERT: A 1130 ASP cc_start: 0.8553 (m-30) cc_final: 0.8088 (m-30) REVERT: A 1167 LEU cc_start: 0.9050 (mt) cc_final: 0.8585 (mt) REVERT: A 1396 MET cc_start: 0.9452 (mtm) cc_final: 0.9175 (mtp) REVERT: A 1773 VAL cc_start: 0.7431 (OUTLIER) cc_final: 0.6989 (t) REVERT: A 1813 TRP cc_start: 0.8303 (t-100) cc_final: 0.7860 (t-100) REVERT: A 1821 LYS cc_start: 0.8401 (mppt) cc_final: 0.8123 (mttt) REVERT: B 211 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7030 (tp30) REVERT: B 237 MET cc_start: 0.7377 (mmt) cc_final: 0.7116 (mmt) REVERT: G 81 ASP cc_start: 0.7333 (m-30) cc_final: 0.6782 (m-30) REVERT: G 171 GLU cc_start: 0.8288 (mm-30) cc_final: 0.7798 (mm-30) REVERT: G 174 ARG cc_start: 0.7281 (mtt180) cc_final: 0.6541 (mmm-85) REVERT: G 534 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6533 (m-30) REVERT: G 551 THR cc_start: 0.7144 (OUTLIER) cc_final: 0.6866 (p) REVERT: G 764 MET cc_start: 0.8791 (mpp) cc_final: 0.8398 (mpp) REVERT: G 800 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8705 (pp) REVERT: G 1580 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8690 (p) REVERT: G 1982 MET cc_start: 0.8824 (mmp) cc_final: 0.8546 (mmp) outliers start: 36 outliers final: 26 residues processed: 234 average time/residue: 0.1751 time to fit residues: 68.8765 Evaluate side-chains 231 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 200 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 965 HIS Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 547 ILE Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 800 LEU Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1156 CYS Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1886 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 72 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 221 optimal weight: 20.0000 chunk 281 optimal weight: 20.0000 chunk 226 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 321 optimal weight: 8.9990 chunk 285 optimal weight: 20.0000 chunk 200 optimal weight: 30.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN A1188 GLN A1671 ASN ** G 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 275 GLN ** G1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1352 HIS ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.081371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.060405 restraints weight = 111552.839| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.74 r_work: 0.2903 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 30316 Z= 0.251 Angle : 0.605 10.906 41062 Z= 0.309 Chirality : 0.044 0.248 4614 Planarity : 0.004 0.092 5299 Dihedral : 4.863 58.784 4048 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 1.32 % Allowed : 13.81 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3776 helix: 1.13 (0.13), residues: 1715 sheet: -0.81 (0.23), residues: 523 loop : -0.11 (0.16), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 852 TYR 0.017 0.002 TYR A 417 PHE 0.020 0.002 PHE A 450 TRP 0.015 0.001 TRP G1138 HIS 0.005 0.001 HIS A1063 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (30314) covalent geometry : angle 0.60376 / 0.31 (41060) SS BOND : bond 0.00317 / 0.17 ( 1) SS BOND : angle 4.49248 / 2.61 ( 2) hydrogen bonds : bond 0.03757 / 2.45 ( 1350) hydrogen bonds : angle 4.74501 / 3.35 ( 3777) Misc. bond : bond 0.00006 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9136 (mttm) cc_final: 0.8685 (mmtt) REVERT: A 338 LEU cc_start: 0.9015 (tp) cc_final: 0.8581 (tp) REVERT: A 342 GLN cc_start: 0.9202 (mt0) cc_final: 0.8643 (mp10) REVERT: A 529 MET cc_start: 0.9088 (mmp) cc_final: 0.8730 (mmp) REVERT: A 1130 ASP cc_start: 0.8449 (m-30) cc_final: 0.7969 (m-30) REVERT: A 1167 LEU cc_start: 0.9040 (mt) cc_final: 0.8580 (mt) REVERT: A 1283 MET cc_start: 0.8918 (mpp) cc_final: 0.8577 (mpp) REVERT: A 1773 VAL cc_start: 0.7521 (OUTLIER) cc_final: 0.7108 (t) REVERT: A 1785 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7676 (p) REVERT: A 1813 TRP cc_start: 0.8376 (t-100) cc_final: 0.8004 (t-100) REVERT: A 1821 LYS cc_start: 0.8351 (mppt) cc_final: 0.7955 (mttt) REVERT: B 199 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7419 (tm-30) REVERT: B 237 MET cc_start: 0.7461 (mmt) cc_final: 0.7211 (mmt) REVERT: G 534 ASP cc_start: 0.6883 (OUTLIER) cc_final: 0.6584 (m-30) REVERT: G 551 THR cc_start: 0.7054 (OUTLIER) cc_final: 0.6779 (p) REVERT: G 764 MET cc_start: 0.8832 (mpp) cc_final: 0.8442 (mpp) REVERT: G 801 PHE cc_start: 0.8694 (OUTLIER) cc_final: 0.8267 (m-80) REVERT: G 1580 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8624 (p) REVERT: G 1982 MET cc_start: 0.8737 (mmp) cc_final: 0.8525 (mmp) outliers start: 43 outliers final: 32 residues processed: 235 average time/residue: 0.1650 time to fit residues: 65.3372 Evaluate side-chains 228 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 965 HIS Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1388 MET Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 176 LEU Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 773 SER Chi-restraints excluded: chain G residue 777 THR Chi-restraints excluded: chain G residue 801 PHE Chi-restraints excluded: chain G residue 898 ASP Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1156 CYS Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1580 THR Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1886 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 116 optimal weight: 2.9990 chunk 162 optimal weight: 6.9990 chunk 156 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 283 optimal weight: 0.0050 chunk 124 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 224 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 210 optimal weight: 8.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN A1148 HIS A1671 ASN B 251 GLN G 275 GLN ** G1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1839 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.083631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.061999 restraints weight = 109769.094| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.90 r_work: 0.2964 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 30316 Z= 0.105 Angle : 0.524 10.221 41062 Z= 0.266 Chirality : 0.042 0.264 4614 Planarity : 0.003 0.044 5299 Dihedral : 4.528 58.480 4048 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.05 % Allowed : 14.21 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3776 helix: 1.32 (0.13), residues: 1725 sheet: -0.69 (0.23), residues: 526 loop : -0.00 (0.17), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1881 TYR 0.031 0.001 TYR G 67 PHE 0.021 0.001 PHE A 35 TRP 0.015 0.001 TRP G1138 HIS 0.003 0.001 HIS G 760 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (30314) covalent geometry : angle 0.52349 / 0.27 (41060) SS BOND : bond 0.00057 / 0.03 ( 1) SS BOND : angle 3.19528 / 1.83 ( 2) hydrogen bonds : bond 0.03151 / 2.07 ( 1350) hydrogen bonds : angle 4.47068 / 3.16 ( 3777) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 216 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9024 (mttm) cc_final: 0.8605 (mmtt) REVERT: A 338 LEU cc_start: 0.8991 (tp) cc_final: 0.8571 (tp) REVERT: A 342 GLN cc_start: 0.9248 (mt0) cc_final: 0.8715 (mp10) REVERT: A 529 MET cc_start: 0.9104 (mmp) cc_final: 0.8799 (mmp) REVERT: A 1121 MET cc_start: 0.7709 (mmm) cc_final: 0.7486 (ttm) REVERT: A 1123 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8436 (tm-30) REVERT: A 1124 GLU cc_start: 0.8223 (tp30) cc_final: 0.7975 (tp30) REVERT: A 1130 ASP cc_start: 0.8543 (m-30) cc_final: 0.8162 (m-30) REVERT: A 1167 LEU cc_start: 0.9059 (mt) cc_final: 0.8663 (mt) REVERT: A 1773 VAL cc_start: 0.7436 (OUTLIER) cc_final: 0.7068 (t) REVERT: A 1785 THR cc_start: 0.7814 (OUTLIER) cc_final: 0.7598 (p) REVERT: A 1813 TRP cc_start: 0.8255 (t-100) cc_final: 0.7903 (t-100) REVERT: A 1821 LYS cc_start: 0.8409 (mppt) cc_final: 0.8083 (mttt) REVERT: B 237 MET cc_start: 0.7304 (mmt) cc_final: 0.7057 (mmt) REVERT: B 290 MET cc_start: 0.2527 (tmm) cc_final: 0.1916 (tmm) REVERT: G 551 THR cc_start: 0.6925 (OUTLIER) cc_final: 0.6645 (p) REVERT: G 764 MET cc_start: 0.8757 (mpp) cc_final: 0.8408 (mpp) REVERT: G 800 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8634 (pp) REVERT: G 1426 THR cc_start: 0.7872 (OUTLIER) cc_final: 0.7305 (t) REVERT: G 1580 THR cc_start: 0.8911 (m) cc_final: 0.8604 (p) REVERT: G 1656 GLU cc_start: 0.8248 (mp0) cc_final: 0.7984 (mp0) REVERT: G 1982 MET cc_start: 0.8816 (mmp) cc_final: 0.8600 (mmm) outliers start: 34 outliers final: 20 residues processed: 245 average time/residue: 0.1763 time to fit residues: 72.4667 Evaluate side-chains 225 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 965 HIS Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 773 SER Chi-restraints excluded: chain G residue 800 LEU Chi-restraints excluded: chain G residue 898 ASP Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1426 THR Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1886 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 246 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 287 optimal weight: 0.5980 chunk 230 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 255 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 274 optimal weight: 9.9990 chunk 359 optimal weight: 6.9990 chunk 312 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN A1845 ASN G 275 GLN ** G1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.082825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061662 restraints weight = 110393.127| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.83 r_work: 0.2944 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30316 Z= 0.151 Angle : 0.551 10.731 41062 Z= 0.278 Chirality : 0.042 0.270 4614 Planarity : 0.004 0.048 5299 Dihedral : 4.537 58.497 4048 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.08 % Allowed : 14.36 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3776 helix: 1.33 (0.13), residues: 1719 sheet: -0.65 (0.23), residues: 524 loop : 0.00 (0.17), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 759 TYR 0.027 0.001 TYR G 67 PHE 0.020 0.001 PHE A 35 TRP 0.016 0.001 TRP G1138 HIS 0.010 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (30314) covalent geometry : angle 0.55057 / 0.28 (41060) SS BOND : bond 0.00178 / 0.09 ( 1) SS BOND : angle 3.62536 / 2.10 ( 2) hydrogen bonds : bond 0.03304 / 2.16 ( 1350) hydrogen bonds : angle 4.50883 / 3.19 ( 3777) Misc. bond : bond 0.00001 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7552 Ramachandran restraints generated. 3776 Oldfield, 0 Emsley, 3776 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 LYS cc_start: 0.9077 (mttm) cc_final: 0.8612 (mmtt) REVERT: A 338 LEU cc_start: 0.8997 (tp) cc_final: 0.8575 (tp) REVERT: A 342 GLN cc_start: 0.9221 (mt0) cc_final: 0.8645 (mp10) REVERT: A 529 MET cc_start: 0.9131 (mmp) cc_final: 0.8802 (mmp) REVERT: A 803 MET cc_start: 0.9300 (mmm) cc_final: 0.9034 (mtp) REVERT: A 1121 MET cc_start: 0.7625 (mmm) cc_final: 0.7350 (ttm) REVERT: A 1123 GLN cc_start: 0.9168 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 1124 GLU cc_start: 0.8256 (tp30) cc_final: 0.8006 (tp30) REVERT: A 1130 ASP cc_start: 0.8487 (m-30) cc_final: 0.8088 (m-30) REVERT: A 1167 LEU cc_start: 0.9056 (mt) cc_final: 0.8615 (mt) REVERT: A 1773 VAL cc_start: 0.7487 (OUTLIER) cc_final: 0.7108 (t) REVERT: A 1785 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7686 (p) REVERT: A 1813 TRP cc_start: 0.8307 (t-100) cc_final: 0.7943 (t-100) REVERT: A 1821 LYS cc_start: 0.8392 (mppt) cc_final: 0.7982 (mttt) REVERT: B 174 ASP cc_start: 0.8617 (t70) cc_final: 0.8199 (t0) REVERT: B 199 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7092 (tm-30) REVERT: B 237 MET cc_start: 0.7450 (mmt) cc_final: 0.7209 (mmt) REVERT: G 132 MET cc_start: 0.2817 (tpt) cc_final: 0.2543 (tpt) REVERT: G 551 THR cc_start: 0.7032 (OUTLIER) cc_final: 0.6789 (p) REVERT: G 764 MET cc_start: 0.8733 (mpp) cc_final: 0.8376 (mpp) REVERT: G 800 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8640 (pp) REVERT: G 1180 MET cc_start: 0.6661 (ptt) cc_final: 0.5969 (ptt) REVERT: G 1426 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7217 (t) REVERT: G 1580 THR cc_start: 0.8954 (m) cc_final: 0.8646 (p) REVERT: G 1656 GLU cc_start: 0.8261 (mp0) cc_final: 0.7983 (mp0) REVERT: G 1982 MET cc_start: 0.8847 (mmp) cc_final: 0.8561 (mmp) outliers start: 35 outliers final: 27 residues processed: 230 average time/residue: 0.1793 time to fit residues: 69.8969 Evaluate side-chains 225 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 193 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 965 HIS Chi-restraints excluded: chain A residue 1038 GLU Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1773 VAL Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain A residue 1872 SER Chi-restraints excluded: chain A residue 1879 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 534 ASP Chi-restraints excluded: chain G residue 551 THR Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 773 SER Chi-restraints excluded: chain G residue 800 LEU Chi-restraints excluded: chain G residue 801 PHE Chi-restraints excluded: chain G residue 898 ASP Chi-restraints excluded: chain G residue 941 VAL Chi-restraints excluded: chain G residue 1130 THR Chi-restraints excluded: chain G residue 1343 VAL Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1426 THR Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1629 VAL Chi-restraints excluded: chain G residue 1698 PHE Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 1886 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 31 optimal weight: 0.4980 chunk 85 optimal weight: 20.0000 chunk 220 optimal weight: 20.0000 chunk 238 optimal weight: 6.9990 chunk 340 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 chunk 242 optimal weight: 10.0000 chunk 234 optimal weight: 0.7980 chunk 157 optimal weight: 8.9990 chunk 141 optimal weight: 0.5980 chunk 257 optimal weight: 0.5980 overall best weight: 1.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 829 ASN G 275 GLN ** G1178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1892 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.083817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062278 restraints weight = 110065.442| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.85 r_work: 0.2972 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 30316 Z= 0.107 Angle : 0.527 11.058 41062 Z= 0.266 Chirality : 0.041 0.260 4614 Planarity : 0.003 0.045 5299 Dihedral : 4.404 57.785 4048 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.11 % Allowed : 14.43 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3776 helix: 1.43 (0.13), residues: 1720 sheet: -0.57 (0.23), residues: 527 loop : 0.02 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 759 TYR 0.027 0.001 TYR G 67 PHE 0.021 0.001 PHE A 35 TRP 0.015 0.001 TRP G1138 HIS 0.008 0.001 HIS B 152 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (30314) covalent geometry : angle 0.52632 / 0.27 (41060) SS BOND : bond 0.00043 / 0.02 ( 1) SS BOND : angle 3.07324 / 1.77 ( 2) hydrogen bonds : bond 0.03095 / 2.03 ( 1350) hydrogen bonds : angle 4.40888 / 3.12 ( 3777) Misc. bond : bond 0.00000 / 0.00 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6872.53 seconds wall clock time: 119 minutes 2.70 seconds (7142.70 seconds total)