Starting phenix.real_space_refine on Sun Jul 5 18:57:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.cif" model { file = "/net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psp_17859/07_2026/8psp_17859.cif" } resolution = 2.9 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= -0.002 sd= 0.013 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 75 residue(s): 0.03s 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: 6.33, per 1000 atoms: 0.21 Number of scatterers: 29695 At special positions: 0 Unit cell: (180.405, 184.625, 174.075, 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=2.19 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: 2.65 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 170 helices and 28 sheets defined 51.5% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 4.353A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 37 Processing helix chain 'A' and resid 51 through 65 removed outlier: 3.573A pdb=" N ASN A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 73 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 329 through 350 Processing helix chain 'A' and resid 355 through 383 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.089A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.663A 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 483 Processing helix chain 'A' and resid 521 through 531 removed outlier: 3.501A pdb=" N TYR A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.663A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 670 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.612A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 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: 3.503A pdb=" N ARG A 813 " --> pdb=" O GLN A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.615A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.745A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 882 Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 897 through 907 Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.656A pdb=" N VAL A 933 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 970 removed outlier: 3.981A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 removed outlier: 4.101A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.347A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1198 Processing helix chain 'A' and resid 1201 through 1206 Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.751A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (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: 3.661A pdb=" N GLU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.744A 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 1320 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1362 through 1366 removed outlier: 4.268A pdb=" N SER A1366 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1476 removed outlier: 3.508A pdb=" N GLN A1458 " --> pdb=" O THR A1454 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA A1469 " --> pdb=" O ASN A1465 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1509 Processing helix chain 'A' and resid 1520 through 1529 removed outlier: 3.767A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N TYR A1529 " --> pdb=" O ALA A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.766A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.569A 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 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 3.597A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A1621 " --> pdb=" O LEU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 4.110A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.763A 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 1734 through 1738 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 4.108A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 removed outlier: 3.600A pdb=" N ILE A1756 " --> pdb=" O THR A1752 " (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 removed outlier: 3.529A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1802 removed outlier: 3.573A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A1802 " --> pdb=" O TYR A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1823 Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.766A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.519A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.684A pdb=" N THR B 204 " --> pdb=" O PRO B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.849A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP B 215 " --> pdb=" O GLU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.775A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 27 through 41 removed outlier: 3.742A pdb=" N GLN G 32 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 49 removed outlier: 4.292A pdb=" N ALA G 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 72 removed outlier: 3.546A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.690A pdb=" N LEU G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.553A pdb=" N GLU G 111 " --> pdb=" O LYS G 107 " (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 removed outlier: 3.621A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 6.486A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 removed outlier: 3.744A pdb=" N TRP G 218 " --> pdb=" O ASN G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 233 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 276 through 284 removed outlier: 3.660A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 314 removed outlier: 3.682A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 309 " --> pdb=" O PHE G 305 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU G 312 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 Processing helix chain 'G' and resid 345 through 360 removed outlier: 4.053A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU G 360 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.598A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 431 No H-bonds generated for 'chain 'G' and resid 429 through 431' Processing helix chain 'G' and resid 432 through 444 removed outlier: 3.796A pdb=" N SER G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP G 437 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS G 441 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 removed outlier: 3.507A pdb=" N ARG G 478 " --> pdb=" O SER G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.847A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.957A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.734A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 614 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: 3.718A pdb=" N GLN G 640 " --> pdb=" O SER G 636 " (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: 3.554A 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: 5.199A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 783 Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 790 removed outlier: 3.783A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP G 790 " --> pdb=" O THR G 787 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 806 Processing helix chain 'G' and resid 814 through 824 removed outlier: 3.576A pdb=" N CYS G 824 " --> pdb=" O CYS G 820 " (cutoff:3.500A) Processing helix chain 'G' and resid 831 through 837 removed outlier: 3.647A pdb=" N TYR G 836 " --> pdb=" O GLU G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 898 removed outlier: 4.440A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.405A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 917 Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 removed outlier: 3.503A pdb=" N ALA G 979 " --> pdb=" O LYS G 975 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA G 986 " --> pdb=" O LYS G 982 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1035 through 1051 removed outlier: 5.026A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N VAL G1044 " --> pdb=" O GLU G1041 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N ASP G1045 " --> pdb=" O ALA G1042 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N VAL G1048 " --> pdb=" O ASP G1045 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLN G1049 " --> pdb=" O GLN G1046 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1062 removed outlier: 3.592A pdb=" N PHE G1062 " --> pdb=" O ALA G1059 " (cutoff:3.500A) Processing helix chain 'G' and resid 1069 through 1090 Processing helix chain 'G' and resid 1093 through 1097 removed outlier: 3.559A pdb=" N ILE G1097 " --> pdb=" O GLU G1094 " (cutoff:3.500A) 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 Processing helix chain 'G' and resid 1257 through 1271 removed outlier: 3.606A 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 1325 through 1335 removed outlier: 5.034A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) Processing helix chain 'G' and resid 1336 through 1339 removed outlier: 3.500A pdb=" N PHE G1339 " --> pdb=" O LYS G1336 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1336 through 1339' Processing helix chain 'G' and resid 1346 through 1348 No H-bonds generated for 'chain 'G' and resid 1346 through 1348' Processing helix chain 'G' and resid 1438 through 1447 removed outlier: 3.648A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 removed outlier: 3.538A pdb=" N ASP G1518 " --> pdb=" O ASN G1514 " (cutoff:3.500A) Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.502A pdb=" N ALA G1554 " --> pdb=" O ASN G1550 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 removed outlier: 3.701A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) Processing helix chain 'G' and resid 1601 through 1603 No H-bonds generated for 'chain 'G' and resid 1601 through 1603' Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.609A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 removed outlier: 3.640A pdb=" N LYS G1727 " --> pdb=" O GLY G1723 " (cutoff:3.500A) Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1819 removed outlier: 3.827A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1841 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.838A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.599A 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 1905 through 1921 removed outlier: 3.863A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1926 through 1931 removed outlier: 3.579A pdb=" N LEU G1931 " --> pdb=" O LEU G1927 " (cutoff:3.500A) Processing helix chain 'G' and resid 1934 through 1952 removed outlier: 4.389A pdb=" N GLY G1938 " --> pdb=" O GLU G1934 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1978 through 1983 removed outlier: 4.115A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.909A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) Processing helix chain 'G' and resid 2022 through 2033 removed outlier: 3.692A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2035 through 2044 removed outlier: 4.084A pdb=" N ILE G2041 " --> pdb=" O PRO G2037 " (cutoff:3.500A) Processing helix chain 'G' and resid 2044 through 2050 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.601A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.230A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 7.955A 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: 6.515A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.860A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N TYR A 677 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE A 769 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE A 768 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) 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 981 through 982 Processing sheet with id=AA6, first strand: chain 'A' and resid 1019 through 1027 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1019 through 1027 current: chain 'A' and resid 1326 through 1333 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1381 through 1389 current: chain 'A' and resid 1572 through 1575 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1624 through 1625 current: chain 'A' and resid 1650 through 1656 Processing sheet with id=AA7, first strand: chain 'A' and resid 1060 through 1066 removed outlier: 4.110A pdb=" N TRP A1075 " --> pdb=" O VAL A1084 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 3.961A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB1, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB2, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB3, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB4, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB5, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB6, first strand: chain 'G' and resid 6 through 13 Processing sheet with id=AB7, first strand: chain 'G' and resid 459 through 460 removed outlier: 8.484A pdb=" N TYR G 460 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ALA G 270 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LEU G 156 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA G 270 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA G 158 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLY G 272 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE G 160 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 417 through 420 removed outlier: 7.380A pdb=" N ASN G 376 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N VAL G 371 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC1, first strand: chain 'G' and resid 592 through 594 removed outlier: 3.869A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE G 728 " --> pdb=" O MET G 764 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLY G 768 " --> pdb=" O LEU G 730 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N TRP G 732 " --> pdb=" O GLY G 768 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 739 through 740 Processing sheet with id=AC3, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC4, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC5, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 6.448A pdb=" N VAL G1195 " --> pdb=" O ILE G1210 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ILE G1210 " --> pdb=" O VAL G1195 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU G1197 " --> pdb=" O THR G1208 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU G1204 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE G1251 " --> pdb=" O PHE G1158 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 1285 through 1286 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1285 through 1286 current: chain 'G' and resid 1387 through 1393 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1387 through 1393 current: chain 'G' and resid 1401 through 1413 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 removed outlier: 6.220A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 1426 through 1427 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1426 through 1427 current: chain 'G' and resid 1485 through 1491 removed outlier: 6.197A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1473 through 1474 Processing sheet with id=AC9, first strand: chain 'G' and resid 1717 through 1720 Processing sheet with id=AD1, first strand: chain 'G' and resid 1740 through 1741 1386 hydrogen bonds defined for protein. 3867 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: 8.35 Time building geometry restraints manager: 3.47 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: 5087 1.31 - 1.45: 7675 1.45 - 1.59: 17359 1.59 - 1.73: 3 1.73 - 1.87: 190 Bond restraints: 30314 Sorted by residual: bond pdb=" C PRO A1658 " pdb=" O PRO A1658 " ideal model delta sigma weight residual 1.238 1.168 0.070 1.37e-02 5.33e+03 2.58e+01 bond pdb=" C PRO G 795 " pdb=" O PRO G 795 " ideal model delta sigma weight residual 1.234 1.177 0.056 1.14e-02 7.69e+03 2.43e+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 2.43e+01 bond pdb=" N ASN G1713 " pdb=" CA ASN G1713 " ideal model delta sigma weight residual 1.460 1.494 -0.034 7.10e-03 1.98e+04 2.32e+01 bond pdb=" N ILE B 166 " pdb=" CA ILE B 166 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.60e-03 1.73e+04 2.26e+01 ... (remaining 30309 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.97: 39602 3.97 - 7.93: 1442 7.93 - 11.90: 13 11.90 - 15.86: 1 15.86 - 19.83: 2 Bond angle restraints: 41060 Sorted by residual: angle pdb=" CB GLU A 841 " pdb=" CG GLU A 841 " pdb=" CD GLU A 841 " ideal model delta sigma weight residual 112.60 132.43 -19.83 1.70e+00 3.46e-01 1.36e+02 angle pdb=" CB GLU A 780 " pdb=" CG GLU A 780 " pdb=" CD GLU A 780 " ideal model delta sigma weight residual 112.60 128.64 -16.04 1.70e+00 3.46e-01 8.91e+01 angle pdb=" C GLU G 852 " pdb=" CA GLU G 852 " pdb=" CB GLU G 852 " ideal model delta sigma weight residual 108.76 117.68 -8.92 1.37e+00 5.33e-01 4.24e+01 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 123.21 -10.61 1.70e+00 3.46e-01 3.89e+01 angle pdb=" C GLY G 662 " pdb=" N ILE G 663 " pdb=" CA ILE G 663 " ideal model delta sigma weight residual 120.33 125.20 -4.87 8.00e-01 1.56e+00 3.70e+01 ... (remaining 41055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.65: 16788 19.65 - 39.30: 1210 39.30 - 58.95: 214 58.95 - 78.59: 62 78.59 - 98.24: 21 Dihedral angle restraints: 18295 sinusoidal: 7356 harmonic: 10939 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual 93.00 10.67 82.33 1 1.00e+01 1.00e-02 8.32e+01 dihedral pdb=" CA GLY A 892 " pdb=" C GLY A 892 " pdb=" N VAL A 893 " pdb=" CA VAL A 893 " ideal model delta harmonic sigma weight residual 180.00 152.66 27.34 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 153.66 26.34 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 18292 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 2773 0.082 - 0.165: 1581 0.165 - 0.247: 240 0.247 - 0.330: 19 0.330 - 0.412: 1 Chirality restraints: 4614 Sorted by residual: chirality pdb=" CA GLU A 841 " pdb=" N GLU A 841 " pdb=" C GLU A 841 " pdb=" CB GLU A 841 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.24e+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 2.75 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" CA GLN A1389 " pdb=" N GLN A1389 " pdb=" C GLN A1389 " pdb=" CB GLN A1389 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 4611 not shown) Planarity restraints: 5299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1901 " 0.086 2.00e-02 2.50e+03 8.79e-02 9.66e+01 pdb=" C34 PNS B1901 " -0.051 2.00e-02 2.50e+03 pdb=" C37 PNS B1901 " 0.107 2.00e-02 2.50e+03 pdb=" N36 PNS B1901 " -0.131 2.00e-02 2.50e+03 pdb=" O35 PNS B1901 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.000 2.00e-02 2.50e+03 3.19e-02 4.83e+01 pdb=" C10 FMN G2101 " 0.008 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.009 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.019 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.060 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.036 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.072 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.028 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.012 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.047 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.020 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.028 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.038 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.012 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PNS B1901 " 0.008 2.00e-02 2.50e+03 4.90e-02 3.01e+01 pdb=" C39 PNS B1901 " 0.024 2.00e-02 2.50e+03 pdb=" C42 PNS B1901 " -0.056 2.00e-02 2.50e+03 pdb=" N41 PNS B1901 " 0.075 2.00e-02 2.50e+03 pdb=" O40 PNS B1901 " -0.051 2.00e-02 2.50e+03 ... (remaining 5296 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 631 2.69 - 3.24: 28637 3.24 - 3.79: 46072 3.79 - 4.35: 65842 4.35 - 4.90: 106234 Nonbonded interactions: 247416 Sorted by model distance: nonbonded pdb=" OH TYR A 89 " pdb=" OD2 ASP G1791 " model vdw 2.135 3.040 nonbonded pdb=" O3P FMN G2101 " pdb=" O4' FMN G2101 " model vdw 2.138 3.040 nonbonded pdb=" O GLY G 161 " pdb=" NE2 GLN G 245 " model vdw 2.252 3.120 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.286 3.040 nonbonded pdb=" O PRO G1975 " pdb=" OG SER G1978 " model vdw 2.292 3.040 ... (remaining 247411 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 30.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:8.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 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 : 0.013 0.160 30316 Z= 1.003 Angle : 1.863 19.826 41062 Z= 1.361 Chirality : 0.091 0.412 4614 Planarity : 0.007 0.088 5299 Dihedral : 14.790 98.243 11250 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.32 % Allowed : 5.53 % Favored : 94.15 % Rotamer: Outliers : 0.89 % Allowed : 4.06 % Favored : 95.05 % Cbeta Deviations : 0.11 % 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: -3.17 (0.12), residues: 3776 helix: -2.60 (0.09), residues: 1667 sheet: -1.94 (0.20), residues: 538 loop : -1.31 (0.15), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1680 TYR 0.060 0.007 TYR A 722 PHE 0.061 0.006 PHE G 799 TRP 0.061 0.009 TRP A1286 HIS 0.026 0.004 HIS G1581 Details of bonding type rmsd/Z covalent geometry : bond 0.01345 / 1.00 (30314) covalent geometry : angle 1.85921 / 1.36 (41060) SS BOND : bond 0.16048 / 8.45 ( 1) SS BOND : angle 17.87381 / 9.97 ( 2) hydrogen bonds : bond 0.22468 / 14.78 ( 1386) hydrogen bonds : angle 9.20549 / 6.49 ( 3867) Misc. bond : bond 0.06359 / 3.35 ( 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 414 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 385 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8146 (mp0) REVERT: A 56 MET cc_start: 0.8995 (mtt) cc_final: 0.8769 (mtt) REVERT: A 492 ASP cc_start: 0.7994 (t0) cc_final: 0.7765 (t0) REVERT: A 505 LYS cc_start: 0.8200 (ptmm) cc_final: 0.7994 (tttm) REVERT: A 691 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8577 (mm-30) REVERT: A 780 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6493 (mm-30) REVERT: A 788 SER cc_start: 0.9182 (OUTLIER) cc_final: 0.8851 (m) REVERT: A 841 GLU cc_start: 0.7231 (tp30) cc_final: 0.5609 (tp30) REVERT: A 881 ASN cc_start: 0.7873 (m-40) cc_final: 0.7575 (m110) REVERT: A 945 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8491 (ttpt) REVERT: A 1283 MET cc_start: 0.8905 (mpp) cc_final: 0.8678 (mpt) REVERT: A 1317 GLU cc_start: 0.7291 (tm-30) cc_final: 0.6886 (tm-30) REVERT: A 1391 ASP cc_start: 0.8824 (t70) cc_final: 0.8617 (t0) REVERT: A 1437 LYS cc_start: 0.5036 (pttt) cc_final: 0.4731 (pttt) REVERT: A 1468 GLU cc_start: 0.8662 (mm-30) cc_final: 0.7894 (tp30) REVERT: A 1749 THR cc_start: 0.7420 (m) cc_final: 0.7138 (m) REVERT: A 1790 ASN cc_start: 0.7587 (m-40) cc_final: 0.7235 (t0) REVERT: B 211 GLU cc_start: 0.7869 (pt0) cc_final: 0.7663 (pt0) REVERT: B 237 MET cc_start: 0.6107 (OUTLIER) cc_final: 0.5658 (mpt) REVERT: B 243 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.7020 (pt) REVERT: B 251 GLN cc_start: 0.6821 (tp40) cc_final: 0.6567 (tp40) REVERT: B 276 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5192 (mmm160) REVERT: G 13 HIS cc_start: 0.5881 (t70) cc_final: 0.5627 (t-90) REVERT: G 38 ASN cc_start: 0.7782 (t0) cc_final: 0.7560 (t0) REVERT: G 80 PHE cc_start: 0.6657 (m-80) cc_final: 0.6245 (m-80) REVERT: G 82 GLN cc_start: 0.7842 (mp-120) cc_final: 0.7417 (mp-120) REVERT: G 85 ASN cc_start: 0.7015 (m-40) cc_final: 0.6446 (m-40) REVERT: G 116 LEU cc_start: 0.8101 (mm) cc_final: 0.7863 (mm) REVERT: G 117 VAL cc_start: 0.8560 (m) cc_final: 0.8006 (p) REVERT: G 121 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7553 (mt-10) REVERT: G 181 HIS cc_start: 0.8772 (p90) cc_final: 0.8568 (p90) REVERT: G 217 GLU cc_start: 0.7574 (tp30) cc_final: 0.7215 (tp30) REVERT: G 539 ASP cc_start: 0.8039 (t0) cc_final: 0.7805 (t0) REVERT: G 753 MET cc_start: 0.9231 (mmm) cc_final: 0.8943 (mmm) REVERT: G 1011 MET cc_start: 0.8319 (mtp) cc_final: 0.8101 (mtp) REVERT: G 1079 ASP cc_start: 0.8546 (m-30) cc_final: 0.8321 (m-30) REVERT: G 1134 ASP cc_start: 0.8216 (t70) cc_final: 0.7890 (t70) REVERT: G 1276 ASN cc_start: 0.8735 (t0) cc_final: 0.8511 (t0) REVERT: G 1364 LYS cc_start: 0.8635 (pttm) cc_final: 0.8130 (mppt) REVERT: G 1433 MET cc_start: 0.9140 (mtm) cc_final: 0.8619 (mtp) REVERT: G 1492 GLU cc_start: 0.8282 (tt0) cc_final: 0.7985 (mm-30) REVERT: G 1609 THR cc_start: 0.8935 (OUTLIER) cc_final: 0.8726 (p) REVERT: G 1673 GLU cc_start: 0.8126 (pm20) cc_final: 0.7838 (pm20) REVERT: G 1838 MET cc_start: 0.8867 (mmt) cc_final: 0.8609 (mmm) REVERT: G 1849 ARG cc_start: 0.7129 (ptt-90) cc_final: 0.6665 (ptm-80) REVERT: G 1880 LYS cc_start: 0.8443 (mptt) cc_final: 0.8001 (mppt) outliers start: 29 outliers final: 5 residues processed: 410 average time/residue: 0.8006 time to fit residues: 379.5806 Evaluate side-chains 286 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 275 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 788 SER Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 276 ARG Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1397 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1759 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 63 ASN A 422 HIS A 618 ASN A1239 HIS A1432 HIS A1748 ASN B 292 GLN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN G 440 ASN G 517 HIS G 718 ASN G 723 HIS G1202 GLN G1355 ASN G1451 GLN G1514 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1595 ASN G1619 ASN G1697 HIS G1716 ASN G1912 ASN G2020 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.106812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.076404 restraints weight = 52435.579| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 1.91 r_work: 0.2806 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 30316 Z= 0.160 Angle : 0.592 8.341 41062 Z= 0.312 Chirality : 0.043 0.176 4614 Planarity : 0.004 0.041 5299 Dihedral : 5.780 95.816 4067 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.20 % Favored : 97.72 % Rotamer: Outliers : 1.48 % Allowed : 8.86 % Favored : 89.66 % 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 (0.13), residues: 3776 helix: 0.24 (0.12), residues: 1684 sheet: -1.20 (0.21), residues: 521 loop : -0.37 (0.16), residues: 1571 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1261 TYR 0.020 0.002 TYR G 615 PHE 0.023 0.002 PHE A 35 TRP 0.015 0.002 TRP G1138 HIS 0.011 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (30314) covalent geometry : angle 0.58974 / 0.31 (41060) SS BOND : bond 0.03309 / 1.74 ( 1) SS BOND : angle 7.13942 / 3.92 ( 2) hydrogen bonds : bond 0.04742 / 3.12 ( 1386) hydrogen bonds : angle 5.31947 / 3.74 ( 3867) Misc. bond : bond 0.00080 / 0.04 ( 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 342 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7963 (mp0) REVERT: A 56 MET cc_start: 0.8965 (mtt) cc_final: 0.8749 (mtt) REVERT: A 505 LYS cc_start: 0.7988 (ptmm) cc_final: 0.7727 (tttm) REVERT: A 750 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7719 (tm-30) REVERT: A 841 GLU cc_start: 0.6104 (tp30) cc_final: 0.4494 (mp0) REVERT: A 881 ASN cc_start: 0.7115 (m-40) cc_final: 0.6834 (m110) REVERT: A 901 MET cc_start: 0.9287 (tpt) cc_final: 0.9015 (tpt) REVERT: A 945 LYS cc_start: 0.8716 (ttpp) cc_final: 0.8400 (ttpt) REVERT: A 1123 GLN cc_start: 0.9182 (OUTLIER) cc_final: 0.8876 (tt0) REVERT: A 1162 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7031 (tt0) REVERT: A 1317 GLU cc_start: 0.7256 (tm-30) cc_final: 0.7033 (tm-30) REVERT: A 1498 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: A 1681 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: A 1751 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7240 (mm-30) REVERT: B 236 LYS cc_start: 0.6561 (OUTLIER) cc_final: 0.6179 (mptp) REVERT: B 237 MET cc_start: 0.6501 (mmt) cc_final: 0.6016 (mpt) REVERT: B 243 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6478 (pt) REVERT: B 280 GLU cc_start: 0.5296 (tm-30) cc_final: 0.5008 (tm-30) REVERT: G 82 GLN cc_start: 0.7628 (mp-120) cc_final: 0.7348 (mp-120) REVERT: G 85 ASN cc_start: 0.6600 (m-40) cc_final: 0.6188 (m-40) REVERT: G 116 LEU cc_start: 0.8112 (mm) cc_final: 0.7854 (mm) REVERT: G 117 VAL cc_start: 0.8511 (m) cc_final: 0.8109 (p) REVERT: G 168 ASP cc_start: 0.7797 (p0) cc_final: 0.7560 (p0) REVERT: G 326 ASP cc_start: 0.8278 (t70) cc_final: 0.8007 (t0) REVERT: G 447 ASN cc_start: 0.7886 (m-40) cc_final: 0.7664 (m-40) REVERT: G 753 MET cc_start: 0.9444 (mmm) cc_final: 0.9108 (mmm) REVERT: G 1011 MET cc_start: 0.8325 (mtp) cc_final: 0.8112 (mtp) REVERT: G 1079 ASP cc_start: 0.8382 (m-30) cc_final: 0.8164 (m-30) REVERT: G 1134 ASP cc_start: 0.7837 (t70) cc_final: 0.7603 (t0) REVERT: G 1276 ASN cc_start: 0.8808 (t0) cc_final: 0.8523 (t0) REVERT: G 1673 GLU cc_start: 0.7562 (pm20) cc_final: 0.7278 (pm20) REVERT: G 1678 MET cc_start: 0.8517 (mmm) cc_final: 0.7835 (mmp) REVERT: G 1849 ARG cc_start: 0.7107 (ptt-90) cc_final: 0.6433 (ptm-80) REVERT: G 1936 VAL cc_start: 0.7752 (OUTLIER) cc_final: 0.7323 (p) outliers start: 48 outliers final: 12 residues processed: 323 average time/residue: 0.8005 time to fit residues: 300.6846 Evaluate side-chains 259 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 239 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1681 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 340 SER Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1397 SER Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1759 SER Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 40 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 115 optimal weight: 6.9990 chunk 58 optimal weight: 9.9990 chunk 253 optimal weight: 0.7980 chunk 228 optimal weight: 7.9990 chunk 117 optimal weight: 5.9990 chunk 70 optimal weight: 8.9990 chunk 283 optimal weight: 0.0170 chunk 153 optimal weight: 30.0000 overall best weight: 2.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1482 GLN A1873 HIS ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1186 ASN G1241 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1851 ASN G1912 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.077377 restraints weight = 52605.018| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.91 r_work: 0.2825 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30316 Z= 0.137 Angle : 0.529 7.902 41062 Z= 0.277 Chirality : 0.042 0.165 4614 Planarity : 0.004 0.046 5299 Dihedral : 5.206 93.929 4054 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.78 % Favored : 97.14 % Rotamer: Outliers : 1.81 % Allowed : 10.12 % Favored : 88.07 % 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: 0.43 (0.14), residues: 3776 helix: 1.15 (0.13), residues: 1683 sheet: -0.90 (0.21), residues: 546 loop : -0.07 (0.16), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1261 TYR 0.018 0.001 TYR B 294 PHE 0.025 0.001 PHE A 35 TRP 0.012 0.001 TRP G1138 HIS 0.010 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (30314) covalent geometry : angle 0.52744 / 0.28 (41060) SS BOND : bond 0.02185 / 1.15 ( 1) SS BOND : angle 5.98364 / 3.28 ( 2) hydrogen bonds : bond 0.04115 / 2.71 ( 1386) hydrogen bonds : angle 4.91152 / 3.47 ( 3867) Misc. bond : bond 0.00027 / 0.01 ( 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 323 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 1.270 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7987 (mp0) REVERT: A 341 GLN cc_start: 0.8504 (OUTLIER) cc_final: 0.8067 (mt0) REVERT: A 348 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8116 (ttp-110) REVERT: A 505 LYS cc_start: 0.7966 (ptmm) cc_final: 0.7683 (tttm) REVERT: A 750 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.7688 (tm-30) REVERT: A 754 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7830 (t0) REVERT: A 841 GLU cc_start: 0.6579 (tp30) cc_final: 0.4807 (mm-30) REVERT: A 881 ASN cc_start: 0.7123 (m-40) cc_final: 0.6815 (m110) REVERT: A 945 LYS cc_start: 0.8707 (ttpp) cc_final: 0.8393 (ttpt) REVERT: A 1094 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7859 (tt0) REVERT: A 1121 MET cc_start: 0.8890 (mtm) cc_final: 0.8634 (mtt) REVERT: A 1162 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7019 (mt-10) REVERT: A 1298 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8700 (tp) REVERT: A 1484 GLU cc_start: 0.6830 (tm-30) cc_final: 0.5600 (tp30) REVERT: A 1498 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7894 (tt0) REVERT: A 1751 GLU cc_start: 0.7273 (mt-10) cc_final: 0.7019 (mm-30) REVERT: B 237 MET cc_start: 0.6439 (mmt) cc_final: 0.6011 (mpt) REVERT: G 38 ASN cc_start: 0.7080 (OUTLIER) cc_final: 0.6764 (t0) REVERT: G 82 GLN cc_start: 0.7658 (mp-120) cc_final: 0.7378 (mp-120) REVERT: G 85 ASN cc_start: 0.6581 (m-40) cc_final: 0.6090 (m-40) REVERT: G 116 LEU cc_start: 0.8060 (mm) cc_final: 0.7749 (mm) REVERT: G 117 VAL cc_start: 0.8361 (m) cc_final: 0.8124 (p) REVERT: G 168 ASP cc_start: 0.7847 (p0) cc_final: 0.7546 (p0) REVERT: G 175 ASP cc_start: 0.8323 (t70) cc_final: 0.8080 (t0) REVERT: G 447 ASN cc_start: 0.7951 (m-40) cc_final: 0.7729 (m-40) REVERT: G 753 MET cc_start: 0.9454 (mmm) cc_final: 0.9180 (mmm) REVERT: G 1011 MET cc_start: 0.8322 (mtp) cc_final: 0.8116 (mtp) REVERT: G 1079 ASP cc_start: 0.8403 (m-30) cc_final: 0.8162 (m-30) REVERT: G 1276 ASN cc_start: 0.8803 (t0) cc_final: 0.8508 (t0) REVERT: G 1673 GLU cc_start: 0.7551 (pm20) cc_final: 0.7283 (pm20) REVERT: G 1678 MET cc_start: 0.8578 (mmm) cc_final: 0.7944 (mmp) REVERT: G 1838 MET cc_start: 0.8766 (mmt) cc_final: 0.8544 (mmm) REVERT: G 1847 LEU cc_start: 0.7705 (mp) cc_final: 0.7282 (mm) REVERT: G 1849 ARG cc_start: 0.7215 (ptt-90) cc_final: 0.6495 (ptm-80) REVERT: G 1962 ARG cc_start: 0.7673 (tpp-160) cc_final: 0.6928 (tmm-80) outliers start: 59 outliers final: 19 residues processed: 303 average time/residue: 0.7264 time to fit residues: 259.8494 Evaluate side-chains 266 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1759 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 135 optimal weight: 9.9990 chunk 357 optimal weight: 4.9990 chunk 153 optimal weight: 50.0000 chunk 96 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 186 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 207 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 HIS A1873 HIS ** G 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1186 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1716 ASN G1890 ASN ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.107524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.077444 restraints weight = 52447.236| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 1.90 r_work: 0.2825 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30316 Z= 0.150 Angle : 0.532 10.065 41062 Z= 0.275 Chirality : 0.042 0.157 4614 Planarity : 0.004 0.046 5299 Dihedral : 5.082 93.999 4051 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 1.94 % Allowed : 11.23 % Favored : 86.83 % 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: 0.68 (0.14), residues: 3776 helix: 1.33 (0.13), residues: 1687 sheet: -0.68 (0.21), residues: 540 loop : 0.05 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 632 TYR 0.023 0.002 TYR B 294 PHE 0.025 0.001 PHE A 35 TRP 0.012 0.001 TRP G 661 HIS 0.008 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (30314) covalent geometry : angle 0.53009 / 0.27 (41060) SS BOND : bond 0.02814 / 1.48 ( 1) SS BOND : angle 6.93305 / 3.80 ( 2) hydrogen bonds : bond 0.04022 / 2.65 ( 1386) hydrogen bonds : angle 4.79977 / 3.39 ( 3867) Misc. bond : bond 0.00034 / 0.02 ( 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 322 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 259 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7977 (mp0) REVERT: A 341 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 501 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8698 (t) REVERT: A 505 LYS cc_start: 0.7936 (ptmm) cc_final: 0.7603 (tttm) REVERT: A 750 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: A 754 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7711 (t0) REVERT: A 826 MET cc_start: 0.8783 (mtm) cc_final: 0.8577 (mtm) REVERT: A 841 GLU cc_start: 0.6492 (tp30) cc_final: 0.4815 (mp0) REVERT: A 881 ASN cc_start: 0.7319 (m-40) cc_final: 0.6992 (m110) REVERT: A 945 LYS cc_start: 0.8683 (ttpp) cc_final: 0.8407 (ttpt) REVERT: A 1070 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.6130 (ptm-80) REVERT: A 1094 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7970 (tt0) REVERT: A 1162 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7004 (mt-10) REVERT: A 1298 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8669 (tp) REVERT: A 1498 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7882 (tt0) REVERT: A 1751 GLU cc_start: 0.7345 (mt-10) cc_final: 0.7057 (mm-30) REVERT: B 236 LYS cc_start: 0.6583 (OUTLIER) cc_final: 0.6318 (mptp) REVERT: B 237 MET cc_start: 0.6444 (mmt) cc_final: 0.6095 (mpt) REVERT: B 280 GLU cc_start: 0.5608 (tm-30) cc_final: 0.5305 (tm-30) REVERT: G 37 PHE cc_start: 0.6840 (t80) cc_final: 0.6637 (t80) REVERT: G 38 ASN cc_start: 0.7418 (t0) cc_final: 0.7168 (t0) REVERT: G 80 PHE cc_start: 0.6486 (m-80) cc_final: 0.6258 (m-80) REVERT: G 82 GLN cc_start: 0.7637 (mp-120) cc_final: 0.7352 (mp-120) REVERT: G 85 ASN cc_start: 0.6637 (m-40) cc_final: 0.6137 (m-40) REVERT: G 116 LEU cc_start: 0.7956 (mm) cc_final: 0.7652 (mm) REVERT: G 168 ASP cc_start: 0.7717 (p0) cc_final: 0.7455 (p0) REVERT: G 175 ASP cc_start: 0.8365 (t70) cc_final: 0.8132 (t0) REVERT: G 447 ASN cc_start: 0.7958 (m-40) cc_final: 0.7750 (m-40) REVERT: G 753 MET cc_start: 0.9461 (mmm) cc_final: 0.9151 (mmm) REVERT: G 1011 MET cc_start: 0.8350 (mtp) cc_final: 0.8143 (mtp) REVERT: G 1079 ASP cc_start: 0.8478 (m-30) cc_final: 0.8230 (m-30) REVERT: G 1276 ASN cc_start: 0.8798 (t0) cc_final: 0.8505 (t0) REVERT: G 1673 GLU cc_start: 0.7573 (pm20) cc_final: 0.7279 (pm20) REVERT: G 1678 MET cc_start: 0.8589 (mmm) cc_final: 0.7650 (mmp) REVERT: G 1838 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8547 (mmm) REVERT: G 1962 ARG cc_start: 0.7656 (tpp-160) cc_final: 0.6984 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8224 (mp) outliers start: 63 outliers final: 29 residues processed: 299 average time/residue: 0.7535 time to fit residues: 263.4333 Evaluate side-chains 282 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 241 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1162 GLU Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 153 ASN Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1588 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1759 SER Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1969 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 37 optimal weight: 2.9990 chunk 279 optimal weight: 7.9990 chunk 233 optimal weight: 2.9990 chunk 238 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 353 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 87 optimal weight: 5.9990 chunk 329 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 280 optimal weight: 0.5980 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN A1873 HIS G 38 ASN ** G 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1186 ASN G1226 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.077226 restraints weight = 52903.833| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.91 r_work: 0.2823 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30316 Z= 0.168 Angle : 0.531 9.702 41062 Z= 0.274 Chirality : 0.043 0.153 4614 Planarity : 0.004 0.047 5299 Dihedral : 5.018 94.862 4051 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.40 % Rotamer: Outliers : 2.03 % Allowed : 12.03 % Favored : 85.94 % 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: 1.36 (0.13), residues: 1696 sheet: -0.55 (0.21), residues: 531 loop : 0.12 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1017 TYR 0.018 0.002 TYR B 294 PHE 0.025 0.002 PHE A 35 TRP 0.013 0.001 TRP G 865 HIS 0.009 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (30314) covalent geometry : angle 0.52970 / 0.27 (41060) SS BOND : bond 0.02119 / 1.12 ( 1) SS BOND : angle 5.92891 / 3.26 ( 2) hydrogen bonds : bond 0.04055 / 2.67 ( 1386) hydrogen bonds : angle 4.76470 / 3.37 ( 3867) Misc. bond : bond 0.00003 / 0.00 ( 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 320 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 1.241 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8376 (mt-10) cc_final: 0.8056 (mp0) REVERT: A 341 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8051 (mt0) REVERT: A 501 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8702 (t) REVERT: A 750 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.7645 (tm-30) REVERT: A 754 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7768 (t0) REVERT: A 826 MET cc_start: 0.8839 (mtm) cc_final: 0.8627 (mtm) REVERT: A 841 GLU cc_start: 0.6506 (tp30) cc_final: 0.4825 (mp0) REVERT: A 881 ASN cc_start: 0.7332 (m-40) cc_final: 0.6989 (m110) REVERT: A 945 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8399 (ttpt) REVERT: A 1094 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7991 (tt0) REVERT: A 1180 ARG cc_start: 0.6985 (OUTLIER) cc_final: 0.5651 (mtt90) REVERT: A 1298 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8655 (tp) REVERT: A 1498 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7903 (tt0) REVERT: A 1751 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7057 (mm-30) REVERT: B 237 MET cc_start: 0.6452 (mmt) cc_final: 0.6076 (mpt) REVERT: G 37 PHE cc_start: 0.6652 (t80) cc_final: 0.6447 (t80) REVERT: G 38 ASN cc_start: 0.7320 (OUTLIER) cc_final: 0.7036 (t0) REVERT: G 80 PHE cc_start: 0.6454 (m-80) cc_final: 0.6210 (m-80) REVERT: G 82 GLN cc_start: 0.7778 (mp-120) cc_final: 0.7368 (mp-120) REVERT: G 85 ASN cc_start: 0.6689 (m-40) cc_final: 0.6177 (m-40) REVERT: G 116 LEU cc_start: 0.8046 (mm) cc_final: 0.7724 (mm) REVERT: G 168 ASP cc_start: 0.7725 (p0) cc_final: 0.7470 (p0) REVERT: G 175 ASP cc_start: 0.8337 (t70) cc_final: 0.8119 (t0) REVERT: G 442 ASP cc_start: 0.7460 (m-30) cc_final: 0.7212 (m-30) REVERT: G 539 ASP cc_start: 0.8269 (t0) cc_final: 0.7443 (t0) REVERT: G 753 MET cc_start: 0.9468 (mmm) cc_final: 0.9179 (mmm) REVERT: G 1079 ASP cc_start: 0.8468 (m-30) cc_final: 0.8218 (m-30) REVERT: G 1276 ASN cc_start: 0.8793 (t0) cc_final: 0.8510 (t0) REVERT: G 1505 ASP cc_start: 0.8280 (t70) cc_final: 0.8053 (t0) REVERT: G 1673 GLU cc_start: 0.7587 (pm20) cc_final: 0.7325 (pm20) REVERT: G 1678 MET cc_start: 0.8589 (mmm) cc_final: 0.7683 (mmp) REVERT: G 1838 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8523 (mmm) REVERT: G 1920 GLN cc_start: 0.6443 (OUTLIER) cc_final: 0.6202 (mp10) REVERT: G 1946 GLU cc_start: 0.7840 (tp30) cc_final: 0.7568 (mm-30) REVERT: G 1962 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6921 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8208 (mp) REVERT: G 1986 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7653 (tmmt) outliers start: 66 outliers final: 33 residues processed: 295 average time/residue: 0.7616 time to fit residues: 263.0654 Evaluate side-chains 287 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1094 GLU Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1443 LEU Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 553 ASN Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 975 LYS Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1920 GLN Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1962 ARG Chi-restraints excluded: chain G residue 1969 LEU Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 342 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 137 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 278 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 291 optimal weight: 9.9990 chunk 267 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 27 optimal weight: 0.0470 chunk 205 optimal weight: 3.9990 overall best weight: 1.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN A1873 HIS G 38 ASN G 112 ASN G 273 HIS ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.078443 restraints weight = 52384.559| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.91 r_work: 0.2848 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 30316 Z= 0.119 Angle : 0.501 10.288 41062 Z= 0.257 Chirality : 0.041 0.153 4614 Planarity : 0.004 0.046 5299 Dihedral : 4.815 92.240 4050 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Rotamer: Outliers : 2.06 % Allowed : 12.12 % Favored : 85.82 % 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: 0.97 (0.14), residues: 3776 helix: 1.52 (0.13), residues: 1686 sheet: -0.45 (0.21), residues: 532 loop : 0.21 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1849 TYR 0.017 0.001 TYR B 294 PHE 0.025 0.001 PHE A 35 TRP 0.014 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (30314) covalent geometry : angle 0.49933 / 0.26 (41060) SS BOND : bond 0.02409 / 1.27 ( 1) SS BOND : angle 6.44981 / 3.52 ( 2) hydrogen bonds : bond 0.03705 / 2.45 ( 1386) hydrogen bonds : angle 4.66269 / 3.30 ( 3867) Misc. bond : bond 0.00006 / 0.00 ( 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 326 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 259 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8059 (mp0) REVERT: A 341 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.8018 (mt0) REVERT: A 750 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7556 (tm-30) REVERT: A 754 ASP cc_start: 0.8124 (OUTLIER) cc_final: 0.7759 (t0) REVERT: A 826 MET cc_start: 0.8817 (mtm) cc_final: 0.8610 (mtm) REVERT: A 841 GLU cc_start: 0.6533 (tp30) cc_final: 0.5066 (mm-30) REVERT: A 881 ASN cc_start: 0.7323 (m-40) cc_final: 0.6988 (m110) REVERT: A 945 LYS cc_start: 0.8693 (ttpp) cc_final: 0.8399 (ttpt) REVERT: A 1180 ARG cc_start: 0.6925 (OUTLIER) cc_final: 0.5609 (mtt90) REVERT: A 1298 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8629 (tp) REVERT: A 1484 GLU cc_start: 0.6816 (tm-30) cc_final: 0.5636 (tp30) REVERT: A 1498 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: A 1667 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8310 (tp30) REVERT: A 1751 GLU cc_start: 0.7302 (mt-10) cc_final: 0.7025 (mm-30) REVERT: B 236 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6187 (mptt) REVERT: B 237 MET cc_start: 0.6478 (mmt) cc_final: 0.6072 (mpt) REVERT: G 80 PHE cc_start: 0.6437 (m-80) cc_final: 0.6133 (m-80) REVERT: G 82 GLN cc_start: 0.7740 (mp-120) cc_final: 0.7301 (mp-120) REVERT: G 85 ASN cc_start: 0.6819 (m-40) cc_final: 0.6274 (m-40) REVERT: G 116 LEU cc_start: 0.8024 (mm) cc_final: 0.7699 (mm) REVERT: G 168 ASP cc_start: 0.7738 (p0) cc_final: 0.7507 (p0) REVERT: G 402 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6653 (pp) REVERT: G 442 ASP cc_start: 0.7370 (m-30) cc_final: 0.7146 (m-30) REVERT: G 539 ASP cc_start: 0.8265 (t0) cc_final: 0.7404 (t0) REVERT: G 753 MET cc_start: 0.9464 (mmm) cc_final: 0.9188 (mmm) REVERT: G 1079 ASP cc_start: 0.8438 (m-30) cc_final: 0.8170 (m-30) REVERT: G 1216 GLU cc_start: 0.7206 (tm-30) cc_final: 0.6978 (tp30) REVERT: G 1276 ASN cc_start: 0.8792 (t0) cc_final: 0.8503 (t0) REVERT: G 1673 GLU cc_start: 0.7536 (pm20) cc_final: 0.7283 (pm20) REVERT: G 1678 MET cc_start: 0.8585 (mmm) cc_final: 0.7684 (mmp) REVERT: G 1838 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8468 (mmm) REVERT: G 1946 GLU cc_start: 0.7852 (tp30) cc_final: 0.7364 (tp30) REVERT: G 1962 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6870 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8139 (mp) REVERT: G 1986 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7654 (tmmt) outliers start: 67 outliers final: 25 residues processed: 301 average time/residue: 0.7682 time to fit residues: 270.4433 Evaluate side-chains 290 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 1.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 402 LEU Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1588 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1962 ARG Chi-restraints excluded: chain G residue 1969 LEU Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR 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: 10.0000 chunk 245 optimal weight: 1.9990 chunk 174 optimal weight: 30.0000 chunk 319 optimal weight: 6.9990 chunk 228 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 200 optimal weight: 10.0000 chunk 184 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1873 HIS B 183 GLN G 38 ASN G1202 GLN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.107556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.077515 restraints weight = 52592.168| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 1.91 r_work: 0.2831 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30316 Z= 0.172 Angle : 0.536 11.506 41062 Z= 0.275 Chirality : 0.043 0.151 4614 Planarity : 0.004 0.047 5299 Dihedral : 4.894 93.468 4050 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.25 % Rotamer: Outliers : 1.94 % Allowed : 13.07 % Favored : 84.99 % 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: 0.93 (0.14), residues: 3776 helix: 1.45 (0.13), residues: 1688 sheet: -0.41 (0.21), residues: 534 loop : 0.22 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1849 TYR 0.021 0.002 TYR B 294 PHE 0.024 0.002 PHE A 35 TRP 0.012 0.001 TRP G 865 HIS 0.009 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 (30314) covalent geometry : angle 0.53436 / 0.27 (41060) SS BOND : bond 0.02494 / 1.31 ( 1) SS BOND : angle 6.78031 / 3.72 ( 2) hydrogen bonds : bond 0.03987 / 2.63 ( 1386) hydrogen bonds : angle 4.72485 / 3.35 ( 3867) Misc. bond : bond 0.00011 / 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 314 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 251 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8432 (mt-10) cc_final: 0.8051 (mp0) REVERT: A 43 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7072 (mtp85) REVERT: A 333 LYS cc_start: 0.8841 (tppp) cc_final: 0.8520 (ttpp) REVERT: A 341 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8053 (mt0) REVERT: A 501 THR cc_start: 0.8902 (OUTLIER) cc_final: 0.8671 (t) REVERT: A 750 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.7686 (tm-30) REVERT: A 754 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7771 (t0) REVERT: A 826 MET cc_start: 0.8842 (mtm) cc_final: 0.8632 (mtm) REVERT: A 841 GLU cc_start: 0.6515 (tp30) cc_final: 0.4447 (mp0) REVERT: A 945 LYS cc_start: 0.8698 (ttpp) cc_final: 0.8392 (ttpt) REVERT: A 1162 GLU cc_start: 0.7229 (tp30) cc_final: 0.6775 (tt0) REVERT: A 1180 ARG cc_start: 0.6954 (OUTLIER) cc_final: 0.5495 (mtt90) REVERT: A 1298 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8653 (tp) REVERT: A 1484 GLU cc_start: 0.6810 (tm-30) cc_final: 0.5609 (tp30) REVERT: A 1498 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: A 1667 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8385 (tp30) REVERT: A 1751 GLU cc_start: 0.7319 (mt-10) cc_final: 0.7040 (mm-30) REVERT: B 208 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7736 (mp0) REVERT: B 236 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6203 (mptt) REVERT: B 237 MET cc_start: 0.6448 (mmt) cc_final: 0.6051 (mpt) REVERT: G 80 PHE cc_start: 0.6480 (m-80) cc_final: 0.6241 (m-80) REVERT: G 82 GLN cc_start: 0.7734 (mp-120) cc_final: 0.7287 (mp-120) REVERT: G 85 ASN cc_start: 0.6835 (m-40) cc_final: 0.6296 (m-40) REVERT: G 116 LEU cc_start: 0.8016 (mm) cc_final: 0.7692 (mm) REVERT: G 168 ASP cc_start: 0.7701 (p0) cc_final: 0.7427 (p0) REVERT: G 442 ASP cc_start: 0.7425 (m-30) cc_final: 0.7129 (m-30) REVERT: G 753 MET cc_start: 0.9464 (mmm) cc_final: 0.9201 (mmm) REVERT: G 1079 ASP cc_start: 0.8438 (m-30) cc_final: 0.8171 (m-30) REVERT: G 1216 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6986 (tp30) REVERT: G 1276 ASN cc_start: 0.8760 (t0) cc_final: 0.8526 (t0) REVERT: G 1673 GLU cc_start: 0.7564 (pm20) cc_final: 0.7339 (pm20) REVERT: G 1678 MET cc_start: 0.8585 (mmm) cc_final: 0.7690 (mmp) REVERT: G 1838 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: G 1946 GLU cc_start: 0.7809 (tp30) cc_final: 0.7352 (tp30) REVERT: G 1962 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.6891 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8166 (mp) REVERT: G 1986 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7640 (tmmt) outliers start: 63 outliers final: 30 residues processed: 297 average time/residue: 0.7610 time to fit residues: 265.8134 Evaluate side-chains 285 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1380 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1588 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1962 ARG Chi-restraints excluded: chain G residue 1969 LEU Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR 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: 3.9990 chunk 221 optimal weight: 5.9990 chunk 281 optimal weight: 2.9990 chunk 226 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 48 optimal weight: 0.0170 chunk 227 optimal weight: 7.9990 chunk 321 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1873 HIS G 38 ASN G1186 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.107807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.077751 restraints weight = 52676.809| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 1.92 r_work: 0.2835 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 30316 Z= 0.157 Angle : 0.537 11.007 41062 Z= 0.275 Chirality : 0.043 0.153 4614 Planarity : 0.004 0.047 5299 Dihedral : 4.861 93.005 4050 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 1.91 % Allowed : 13.23 % 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: 0.97 (0.14), residues: 3776 helix: 1.48 (0.13), residues: 1686 sheet: -0.38 (0.21), residues: 534 loop : 0.24 (0.16), residues: 1556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1849 TYR 0.031 0.002 TYR B 294 PHE 0.025 0.001 PHE G 37 TRP 0.013 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (30314) covalent geometry : angle 0.53479 / 0.27 (41060) SS BOND : bond 0.02212 / 1.16 ( 1) SS BOND : angle 6.15536 / 3.39 ( 2) hydrogen bonds : bond 0.03892 / 2.57 ( 1386) hydrogen bonds : angle 4.70400 / 3.33 ( 3867) Misc. bond : bond 0.00005 / 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 322 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 260 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8434 (mt-10) cc_final: 0.8049 (mp0) REVERT: A 43 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7043 (mtp85) REVERT: A 341 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8041 (mt0) REVERT: A 501 THR cc_start: 0.8918 (OUTLIER) cc_final: 0.8694 (t) REVERT: A 750 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7647 (tm-30) REVERT: A 754 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7770 (t0) REVERT: A 826 MET cc_start: 0.8835 (mtm) cc_final: 0.8628 (mtm) REVERT: A 841 GLU cc_start: 0.6614 (tp30) cc_final: 0.5013 (mm-30) REVERT: A 945 LYS cc_start: 0.8691 (ttpp) cc_final: 0.8383 (ttpt) REVERT: A 1180 ARG cc_start: 0.6949 (OUTLIER) cc_final: 0.5482 (mtt90) REVERT: A 1298 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8647 (tp) REVERT: A 1484 GLU cc_start: 0.6808 (tm-30) cc_final: 0.5620 (tp30) REVERT: A 1498 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7930 (tt0) REVERT: A 1667 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8409 (tp30) REVERT: A 1751 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7035 (mm-30) REVERT: B 208 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7744 (mp0) REVERT: B 236 LYS cc_start: 0.6576 (OUTLIER) cc_final: 0.6191 (mptt) REVERT: B 237 MET cc_start: 0.6461 (mmt) cc_final: 0.6076 (mpt) REVERT: G 80 PHE cc_start: 0.6478 (m-80) cc_final: 0.6242 (m-80) REVERT: G 82 GLN cc_start: 0.7777 (mp-120) cc_final: 0.7335 (mp-120) REVERT: G 85 ASN cc_start: 0.6846 (m-40) cc_final: 0.6298 (m-40) REVERT: G 116 LEU cc_start: 0.8007 (mm) cc_final: 0.7676 (mm) REVERT: G 168 ASP cc_start: 0.7670 (p0) cc_final: 0.7448 (p0) REVERT: G 442 ASP cc_start: 0.7399 (m-30) cc_final: 0.7139 (m-30) REVERT: G 753 MET cc_start: 0.9452 (mmm) cc_final: 0.9206 (mmm) REVERT: G 1216 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6980 (tp30) REVERT: G 1276 ASN cc_start: 0.8758 (t0) cc_final: 0.8521 (t0) REVERT: G 1673 GLU cc_start: 0.7559 (pm20) cc_final: 0.7341 (pm20) REVERT: G 1678 MET cc_start: 0.8580 (mmm) cc_final: 0.7690 (mmp) REVERT: G 1838 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8508 (mmm) REVERT: G 1946 GLU cc_start: 0.7854 (tp30) cc_final: 0.7395 (tp30) REVERT: G 1962 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.6923 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8135 (mp) REVERT: G 1986 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7636 (tmmt) outliers start: 62 outliers final: 31 residues processed: 301 average time/residue: 0.7462 time to fit residues: 264.5147 Evaluate side-chains 294 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1588 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1962 ARG Chi-restraints excluded: chain G residue 1969 LEU Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 116 optimal weight: 0.9990 chunk 162 optimal weight: 6.9990 chunk 156 optimal weight: 20.0000 chunk 236 optimal weight: 6.9990 chunk 283 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 224 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1873 HIS G 38 ASN G1186 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.108442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.078555 restraints weight = 52508.397| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.91 r_work: 0.2851 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30316 Z= 0.125 Angle : 0.520 10.762 41062 Z= 0.266 Chirality : 0.042 0.296 4614 Planarity : 0.004 0.047 5299 Dihedral : 4.732 90.803 4049 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.41 % Favored : 97.54 % Rotamer: Outliers : 1.75 % Allowed : 13.53 % Favored : 84.71 % 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: 1.05 (0.14), residues: 3776 helix: 1.56 (0.13), residues: 1685 sheet: -0.36 (0.22), residues: 534 loop : 0.27 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1849 TYR 0.028 0.001 TYR B 294 PHE 0.025 0.001 PHE A 35 TRP 0.014 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (30314) covalent geometry : angle 0.51868 / 0.27 (41060) SS BOND : bond 0.01777 / 0.94 ( 1) SS BOND : angle 5.41432 / 2.98 ( 2) hydrogen bonds : bond 0.03686 / 2.44 ( 1386) hydrogen bonds : angle 4.63070 / 3.29 ( 3867) Misc. bond : bond 0.00012 / 0.01 ( 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 315 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 258 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8026 (mp0) REVERT: A 43 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7021 (mtp85) REVERT: A 333 LYS cc_start: 0.8803 (tppp) cc_final: 0.8499 (ttpp) REVERT: A 341 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8049 (mt0) REVERT: A 501 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8698 (t) REVERT: A 750 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7574 (tm-30) REVERT: A 754 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7754 (t0) REVERT: A 841 GLU cc_start: 0.6503 (tp30) cc_final: 0.5071 (mm-30) REVERT: A 881 ASN cc_start: 0.7374 (m-40) cc_final: 0.7017 (m110) REVERT: A 945 LYS cc_start: 0.8677 (ttpp) cc_final: 0.8367 (ttpt) REVERT: A 1162 GLU cc_start: 0.7110 (tp30) cc_final: 0.6673 (tt0) REVERT: A 1298 ILE cc_start: 0.8909 (OUTLIER) cc_final: 0.8626 (tp) REVERT: A 1484 GLU cc_start: 0.6764 (tm-30) cc_final: 0.5587 (tp30) REVERT: A 1498 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7880 (tt0) REVERT: A 1667 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8318 (tp30) REVERT: A 1708 ASP cc_start: 0.8749 (m-30) cc_final: 0.8545 (t0) REVERT: A 1751 GLU cc_start: 0.7314 (mt-10) cc_final: 0.7037 (mm-30) REVERT: B 208 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7755 (mp0) REVERT: B 236 LYS cc_start: 0.6627 (OUTLIER) cc_final: 0.6241 (mptt) REVERT: G 80 PHE cc_start: 0.6467 (m-80) cc_final: 0.6237 (m-80) REVERT: G 85 ASN cc_start: 0.6846 (m-40) cc_final: 0.6274 (m-40) REVERT: G 116 LEU cc_start: 0.7989 (mm) cc_final: 0.7651 (mm) REVERT: G 168 ASP cc_start: 0.7693 (p0) cc_final: 0.7480 (p0) REVERT: G 753 MET cc_start: 0.9447 (mmm) cc_final: 0.9204 (mmm) REVERT: G 1216 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6967 (tp30) REVERT: G 1276 ASN cc_start: 0.8747 (t0) cc_final: 0.8509 (t0) REVERT: G 1678 MET cc_start: 0.8587 (mmm) cc_final: 0.7694 (mmp) REVERT: G 1838 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.8489 (mmm) REVERT: G 1849 ARG cc_start: 0.7410 (ptt-90) cc_final: 0.6509 (ptm-80) REVERT: G 1946 GLU cc_start: 0.7825 (tp30) cc_final: 0.7368 (tp30) REVERT: G 1962 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.6917 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8126 (mp) REVERT: G 1986 LYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7626 (tmmt) outliers start: 57 outliers final: 32 residues processed: 299 average time/residue: 0.7487 time to fit residues: 262.8654 Evaluate side-chains 292 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 332 THR Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1667 GLU Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 224 ASN Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1588 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1731 GLU Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1962 ARG Chi-restraints excluded: chain G residue 1969 LEU Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 246 optimal weight: 0.1980 chunk 99 optimal weight: 8.9990 chunk 287 optimal weight: 6.9990 chunk 230 optimal weight: 10.0000 chunk 10 optimal weight: 8.9990 chunk 12 optimal weight: 6.9990 chunk 255 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 359 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 overall best weight: 4.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 GLN A1873 HIS G 38 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** 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 = 0.3440 r_free = 0.3440 target = 0.106933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.077590 restraints weight = 52852.570| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 1.85 r_work: 0.2823 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 30316 Z= 0.213 Angle : 0.585 11.037 41062 Z= 0.300 Chirality : 0.044 0.303 4614 Planarity : 0.004 0.046 5299 Dihedral : 4.930 93.667 4049 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.67 % Favored : 97.27 % Rotamer: Outliers : 1.57 % Allowed : 13.93 % Favored : 84.50 % 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: 0.90 (0.14), residues: 3776 helix: 1.40 (0.13), residues: 1685 sheet: -0.37 (0.22), residues: 534 loop : 0.21 (0.16), residues: 1557 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G1881 TYR 0.035 0.002 TYR B 294 PHE 0.025 0.002 PHE A 35 TRP 0.013 0.002 TRP G 661 HIS 0.009 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (30314) covalent geometry : angle 0.58286 / 0.30 (41060) SS BOND : bond 0.03045 / 1.60 ( 1) SS BOND : angle 7.67079 / 4.21 ( 2) hydrogen bonds : bond 0.04159 / 2.74 ( 1386) hydrogen bonds : angle 4.78089 / 3.38 ( 3867) Misc. bond : bond 0.00015 / 0.01 ( 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 305 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 254 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8039 (mp0) REVERT: A 43 ARG cc_start: 0.8033 (OUTLIER) cc_final: 0.7035 (mtp85) REVERT: A 333 LYS cc_start: 0.8810 (tppp) cc_final: 0.8481 (ttpp) REVERT: A 341 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8056 (mt0) REVERT: A 501 THR cc_start: 0.8929 (OUTLIER) cc_final: 0.8685 (t) REVERT: A 750 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7680 (tm-30) REVERT: A 754 ASP cc_start: 0.8181 (OUTLIER) cc_final: 0.7687 (t0) REVERT: A 841 GLU cc_start: 0.6345 (tp30) cc_final: 0.4315 (mp0) REVERT: A 945 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8386 (ttpt) REVERT: A 1162 GLU cc_start: 0.7119 (tp30) cc_final: 0.6674 (tt0) REVERT: A 1180 ARG cc_start: 0.6927 (OUTLIER) cc_final: 0.5449 (mtt90) REVERT: A 1298 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8663 (tp) REVERT: A 1484 GLU cc_start: 0.6801 (tm-30) cc_final: 0.5611 (tp30) REVERT: A 1498 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: A 1751 GLU cc_start: 0.7514 (mt-10) cc_final: 0.7232 (mm-30) REVERT: B 236 LYS cc_start: 0.6494 (OUTLIER) cc_final: 0.6148 (mptt) REVERT: B 237 MET cc_start: 0.5735 (mmp) cc_final: 0.5119 (mpt) REVERT: G 48 PHE cc_start: 0.6290 (m-80) cc_final: 0.5751 (m-80) REVERT: G 80 PHE cc_start: 0.6468 (m-80) cc_final: 0.6233 (m-80) REVERT: G 85 ASN cc_start: 0.6669 (m-40) cc_final: 0.6182 (m-40) REVERT: G 116 LEU cc_start: 0.8019 (mm) cc_final: 0.7735 (mm) REVERT: G 121 GLU cc_start: 0.7682 (tt0) cc_final: 0.7383 (mt-10) REVERT: G 753 MET cc_start: 0.9454 (mmm) cc_final: 0.9223 (mmm) REVERT: G 1216 GLU cc_start: 0.7263 (tm-30) cc_final: 0.6993 (tp30) REVERT: G 1276 ASN cc_start: 0.8773 (t0) cc_final: 0.8535 (t0) REVERT: G 1678 MET cc_start: 0.8585 (mmm) cc_final: 0.7710 (mmp) REVERT: G 1838 MET cc_start: 0.8837 (OUTLIER) cc_final: 0.8573 (mmm) REVERT: G 1849 ARG cc_start: 0.7388 (ptt-90) cc_final: 0.6520 (ptm-80) REVERT: G 1946 GLU cc_start: 0.7873 (tp30) cc_final: 0.7268 (tp30) REVERT: G 1962 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.6958 (tmm-80) REVERT: G 1969 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8116 (mp) REVERT: G 1986 LYS cc_start: 0.8024 (OUTLIER) cc_final: 0.7631 (tmmt) outliers start: 51 outliers final: 30 residues processed: 292 average time/residue: 0.7359 time to fit residues: 252.1668 Evaluate side-chains 290 residues out of total 3252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 43 ARG Chi-restraints excluded: chain A residue 341 GLN Chi-restraints excluded: chain A residue 348 ARG Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 1139 GLU Chi-restraints excluded: chain A residue 1180 ARG Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1617 ILE Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1842 VAL Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain G residue 240 LEU Chi-restraints excluded: chain G residue 243 VAL Chi-restraints excluded: chain G residue 593 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 721 LYS Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1272 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1415 ASN Chi-restraints excluded: chain G residue 1498 THR Chi-restraints excluded: chain G residue 1548 SER Chi-restraints excluded: chain G residue 1588 SER Chi-restraints excluded: chain G residue 1647 ASP Chi-restraints excluded: chain G residue 1676 MET Chi-restraints excluded: chain G residue 1740 THR Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1940 LEU Chi-restraints excluded: chain G residue 1962 ARG Chi-restraints excluded: chain G residue 1969 LEU Chi-restraints excluded: chain G residue 1986 LYS Chi-restraints excluded: chain G residue 2033 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 chunk 220 optimal weight: 20.0000 chunk 238 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 242 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 257 optimal weight: 0.0370 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 HIS A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G1186 ASN ** G1568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.109757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.080057 restraints weight = 52713.232| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.91 r_work: 0.2881 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30316 Z= 0.101 Angle : 0.520 11.304 41062 Z= 0.265 Chirality : 0.041 0.258 4614 Planarity : 0.004 0.046 5299 Dihedral : 4.605 87.733 4049 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.12 % Favored : 97.83 % Rotamer: Outliers : 1.32 % Allowed : 14.36 % Favored : 84.31 % 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: 1.15 (0.14), residues: 3776 helix: 1.65 (0.13), residues: 1686 sheet: -0.30 (0.22), residues: 539 loop : 0.32 (0.17), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1849 TYR 0.025 0.001 TYR B 294 PHE 0.027 0.001 PHE G 37 TRP 0.016 0.001 TRP G 661 HIS 0.008 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (30314) covalent geometry : angle 0.51864 / 0.26 (41060) SS BOND : bond 0.01534 / 0.81 ( 1) SS BOND : angle 5.05380 / 2.77 ( 2) hydrogen bonds : bond 0.03402 / 2.26 ( 1386) hydrogen bonds : angle 4.54201 / 3.23 ( 3867) Misc. bond : bond 0.00026 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12171.16 seconds wall clock time: 208 minutes 5.35 seconds (12485.35 seconds total)