Starting phenix.real_space_refine on Sun Jul 5 19:14:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.cif" model { file = "/net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psm_17856/07_2026/8psm_17856.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.010 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 107 5.16 5 C 18878 2.51 5 N 4956 2.21 5 O 5682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 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: 29625 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 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: 16004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16004 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.92, per 1000 atoms: 0.20 Number of scatterers: 29625 At special positions: 0 Unit cell: (184.625, 182.515, 173.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 107 16.00 P 2 15.00 O 5682 8.00 N 4956 7.00 C 18878 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=2.87 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 1.4 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 177 helices and 32 sheets defined 51.6% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.544A pdb=" N GLU A 8 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N TYR A 20 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.518A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 382 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: 4.338A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLN A 411 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 442 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 removed outlier: 3.566A pdb=" N GLN A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.561A pdb=" N TYR A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 687 through 699 Processing helix chain 'A' and resid 711 through 725 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 755 through 759 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 838 through 846 removed outlier: 3.571A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 856 removed outlier: 4.135A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.489A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 907 Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.571A pdb=" N LYS A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.729A pdb=" N VAL A 933 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 969 removed outlier: 3.502A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.522A pdb=" N VAL A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.597A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.069A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.801A 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 1199 removed outlier: 4.074A pdb=" N TYR A1198 " --> pdb=" O ASN A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1206 Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.562A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.547A 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 1271 through 1278 removed outlier: 4.466A pdb=" N LEU A1275 " --> pdb=" O ASN A1272 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1291 removed outlier: 4.658A pdb=" N SER A1284 " --> pdb=" O ILE A1280 " (cutoff:3.500A) Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1361 through 1365 Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1469 Processing helix chain 'A' and resid 1471 through 1477 removed outlier: 4.197A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1510 removed outlier: 3.587A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE A1493 " --> pdb=" O ARG A1489 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.724A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.500A pdb=" N ASP A1550 " --> pdb=" O THR A1546 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.772A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1603 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 3.669A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 3.971A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.662A 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: 3.964A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1760 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 1790 removed outlier: 3.607A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 3.598A pdb=" N GLU A1797 " --> pdb=" O PRO A1793 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 4.076A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLU A1861 " --> pdb=" O LYS A1857 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 171 through 177 removed outlier: 3.545A pdb=" N LEU B 175 " --> pdb=" O THR B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.505A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 217 removed outlier: 4.230A pdb=" N THR B 216 " --> pdb=" O THR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 237 removed outlier: 3.534A pdb=" N MET B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 253 removed outlier: 3.986A pdb=" N LEU B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 270 removed outlier: 4.036A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 267 " --> pdb=" O GLY B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 289 through 299 removed outlier: 3.568A pdb=" N LYS B 293 " --> pdb=" O SER B 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 41 removed outlier: 4.181A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 Processing helix chain 'G' and resid 80 through 96 removed outlier: 3.551A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.590A pdb=" N LEU G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASN G 112 " --> pdb=" O LEU G 108 " (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: 3.613A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.306A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 removed outlier: 3.540A pdb=" N TRP G 218 " --> pdb=" O ASN G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 225 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 275 through 286 removed outlier: 4.156A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU G 285 " --> pdb=" O VAL G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 314 removed outlier: 3.934A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N TYR G 314 " --> pdb=" O CYS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 removed outlier: 3.562A pdb=" N LEU G 324 " --> pdb=" O PRO G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 4.107A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU G 360 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 removed outlier: 3.542A pdb=" N LYS G 364 " --> pdb=" O PRO G 361 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN G 365 " --> pdb=" O ALA G 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 361 through 365' Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.544A 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 434 Proline residue: G 434 - end of helix Processing helix chain 'G' and resid 435 through 445 removed outlier: 3.628A pdb=" N LYS G 441 " --> pdb=" O ASP G 437 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL G 444 " --> pdb=" O ASN G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 removed outlier: 3.518A pdb=" N ARG G 478 " --> pdb=" O SER G 474 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 removed outlier: 3.608A pdb=" N THR G 494 " --> pdb=" O TRP G 490 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 490 through 494' Processing helix chain 'G' and resid 507 through 510 Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.560A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN G 519 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.923A 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: 3.650A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 613 Processing helix chain 'G' and resid 626 through 641 Processing helix chain 'G' and resid 655 through 671 removed outlier: 3.525A pdb=" N LEU G 659 " --> pdb=" O ASN G 655 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.517A 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: 5.172A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 777 through 783 Processing helix chain 'G' and resid 784 through 789 removed outlier: 3.504A pdb=" N THR G 787 " --> pdb=" O GLU G 784 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 808 removed outlier: 4.508A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 removed outlier: 3.788A pdb=" N CYS G 824 " --> pdb=" O CYS G 820 " (cutoff:3.500A) Processing helix chain 'G' and resid 831 through 836 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 887 removed outlier: 4.220A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 3.807A pdb=" N GLU G 885 " --> pdb=" O VAL G 881 " (cutoff:3.500A) Processing helix chain 'G' and resid 887 through 898 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 removed outlier: 3.579A pdb=" N ARG G 944 " --> pdb=" O ASP G 940 " (cutoff:3.500A) Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 removed outlier: 3.541A pdb=" N ALA G 979 " --> pdb=" O LYS G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 991 Processing helix chain 'G' and resid 996 through 1007 removed outlier: 3.541A pdb=" N ASP G1001 " --> pdb=" O ALA G 997 " (cutoff:3.500A) Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1034 through 1043 removed outlier: 3.689A pdb=" N SER G1037 " --> pdb=" O LEU G1034 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1175 Processing helix chain 'G' and resid 1257 through 1271 removed outlier: 3.524A 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 1322 through 1324 No H-bonds generated for 'chain 'G' and resid 1322 through 1324' Processing helix chain 'G' and resid 1325 through 1335 removed outlier: 5.324A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) Processing helix chain 'G' and resid 1336 through 1339 removed outlier: 3.730A 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 1340 through 1344 Processing helix chain 'G' and resid 1418 through 1422 Processing helix chain 'G' and resid 1438 through 1447 removed outlier: 3.525A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1523 Processing helix chain 'G' and resid 1550 through 1558 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 Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.705A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1685 through 1703 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 removed outlier: 3.597A pdb=" N GLY G1726 " --> pdb=" O GLY G1722 " (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: 4.037A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1839 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.859A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1883 Processing helix chain 'G' and resid 1904 through 1914 removed outlier: 3.656A pdb=" N VAL G1910 " --> pdb=" O ALA G1906 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASN G1912 " --> pdb=" O ASP G1908 " (cutoff:3.500A) Processing helix chain 'G' and resid 1916 through 1921 Processing helix chain 'G' and resid 1924 through 1929 Processing helix chain 'G' and resid 1935 through 1952 removed outlier: 3.811A pdb=" N HIS G1939 " --> pdb=" O GLU G1935 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE G1941 " --> pdb=" O GLU G1937 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS G1949 " --> pdb=" O ASP G1945 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA G1952 " --> pdb=" O SER G1948 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1984 removed outlier: 4.391A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY G1984 " --> pdb=" O LEU G1981 " (cutoff:3.500A) Processing helix chain 'G' and resid 1985 through 1993 removed outlier: 3.802A pdb=" N SER G1990 " --> pdb=" O LYS G1986 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 Processing helix chain 'G' and resid 2022 through 2033 removed outlier: 3.568A pdb=" N LEU G2032 " --> pdb=" O ASP G2028 " (cutoff:3.500A) Processing helix chain 'G' and resid 2035 through 2044 Processing helix chain 'G' and resid 2044 through 2050 removed outlier: 3.960A pdb=" N TYR G2048 " --> pdb=" O ASN G2044 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN G2050 " --> pdb=" O GLU G2046 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 3.504A pdb=" N GLU G1887 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 78 through 80 removed outlier: 6.677A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE G1804 " --> pdb=" O ILE G2011 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.777A pdb=" N VAL A 703 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 735 " --> pdb=" O VAL A 703 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 705 " --> pdb=" O VAL A 735 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR A 677 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N ILE A 769 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE A 768 " --> pdb=" O ILE A 823 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU A 926 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA7, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA8, first strand: chain 'A' and resid 1243 through 1245 Processing sheet with id=AA9, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 7.085A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AB2, first strand: chain 'A' and resid 1102 through 1105 removed outlier: 4.165A pdb=" N GLY A1102 " --> pdb=" O GLN A1188 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A1188 " --> pdb=" O GLY A1102 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1121 through 1126 Processing sheet with id=AB4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB5, first strand: chain 'A' and resid 1538 through 1540 removed outlier: 6.546A pdb=" N ALA A1539 " --> pdb=" O VAL A1575 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB7, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB8, first strand: chain 'A' and resid 1769 through 1775 removed outlier: 3.629A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AC1, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.818A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 267 through 269 removed outlier: 7.726A pdb=" N LEU G 156 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL G 157 " --> pdb=" O LEU G 502 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 419 through 420 removed outlier: 7.192A pdb=" N ASN G 376 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL G 371 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC5, first strand: chain 'G' and resid 592 through 594 removed outlier: 4.021A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.136A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.587A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC8, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC9, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 3.511A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE G1158 " --> pdb=" O ILE G1251 " (cutoff:3.500A) removed outlier: 8.517A pdb=" N GLU G1253 " --> pdb=" O PHE G1158 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR G1160 " --> pdb=" O GLU G1253 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 5.142A pdb=" N LYS G1286 " --> pdb=" O ALA G1376 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA G1376 " --> pdb=" O LYS G1286 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS G1288 " --> pdb=" O THR G1374 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR G1374 " --> pdb=" O LYS G1288 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL G1393 " --> pdb=" O ILE G1378 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N ILE G1378 " --> pdb=" O VAL G1393 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 5.142A pdb=" N LYS G1286 " --> pdb=" O ALA G1376 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N ALA G1376 " --> pdb=" O LYS G1286 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS G1288 " --> pdb=" O THR G1374 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N THR G1374 " --> pdb=" O LYS G1288 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G1354 " --> pdb=" O SER G1409 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G1605 " --> pdb=" O GLU G1658 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLU G1658 " --> pdb=" O VAL G1605 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU G1654 " --> pdb=" O THR G1609 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU G1651 " --> pdb=" O THR G1642 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY G1653 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS G1639 " --> pdb=" O HIS G1628 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N HIS G1628 " --> pdb=" O LYS G1639 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLU G1641 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N ILE G1626 " --> pdb=" O GLU G1641 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ARG G1643 " --> pdb=" O THR G1624 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N THR G1624 " --> pdb=" O ARG G1643 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) removed outlier: 14.573A pdb=" N ILE G1632 " --> pdb=" O GLU G1534 " (cutoff:3.500A) removed outlier: 14.698A pdb=" N GLU G1534 " --> pdb=" O ILE G1632 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 1451 through 1452 removed outlier: 6.923A pdb=" N ILE G1489 " --> pdb=" O ILE G1501 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N ILE G1503 " --> pdb=" O GLY G1487 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY G1487 " --> pdb=" O ILE G1503 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N TYR G1431 " --> pdb=" O PHE G1466 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD5, first strand: chain 'G' and resid 1741 through 1742 1427 hydrogen bonds defined for protein. 3963 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: 8.84 Time building geometry restraints manager: 3.55 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: 5071 1.31 - 1.45: 7647 1.45 - 1.59: 17333 1.59 - 1.72: 3 1.72 - 1.86: 188 Bond restraints: 30242 Sorted by residual: bond pdb=" CD GLU A1317 " pdb=" OE2 GLU A1317 " ideal model delta sigma weight residual 1.249 1.380 -0.131 1.90e-02 2.77e+03 4.72e+01 bond pdb=" NE ARG A1515 " pdb=" CZ ARG A1515 " ideal model delta sigma weight residual 1.326 1.398 -0.072 1.10e-02 8.26e+03 4.30e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.299 -0.063 1.14e-02 7.69e+03 3.06e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.458 1.498 -0.040 7.70e-03 1.69e+04 2.76e+01 bond pdb=" N VAL G 334 " pdb=" CA VAL G 334 " ideal model delta sigma weight residual 1.460 1.498 -0.039 7.50e-03 1.78e+04 2.68e+01 ... (remaining 30237 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 33912 2.59 - 5.19: 6768 5.19 - 7.78: 270 7.78 - 10.38: 10 10.38 - 12.97: 2 Bond angle restraints: 40962 Sorted by residual: angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 125.57 -12.97 1.70e+00 3.46e-01 5.82e+01 angle pdb=" C SER G 233 " pdb=" N ILE G 234 " pdb=" CA ILE G 234 " ideal model delta sigma weight residual 120.24 124.94 -4.70 6.30e-01 2.52e+00 5.57e+01 angle pdb=" N SER B 180 " pdb=" CA SER B 180 " pdb=" C SER B 180 " ideal model delta sigma weight residual 111.07 118.52 -7.45 1.07e+00 8.73e-01 4.84e+01 angle pdb=" CA GLY G1577 " pdb=" C GLY G1577 " pdb=" O GLY G1577 " ideal model delta sigma weight residual 122.33 116.81 5.52 8.10e-01 1.52e+00 4.65e+01 angle pdb=" CA ASP A1612 " pdb=" CB ASP A1612 " pdb=" CG ASP A1612 " ideal model delta sigma weight residual 112.60 119.30 -6.70 1.00e+00 1.00e+00 4.50e+01 ... (remaining 40957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.89: 16535 18.89 - 37.79: 1383 37.79 - 56.68: 236 56.68 - 75.57: 69 75.57 - 94.46: 30 Dihedral angle restraints: 18253 sinusoidal: 7344 harmonic: 10909 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 37.41 55.59 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" C5' FMN G2101 " pdb=" O5' FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 169.72 -94.46 1 2.00e+01 2.50e-03 2.59e+01 dihedral pdb=" CA SER G 769 " pdb=" C SER G 769 " pdb=" N GLY G 770 " pdb=" CA GLY G 770 " ideal model delta harmonic sigma weight residual 180.00 154.78 25.22 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 18250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2136 0.062 - 0.124: 1718 0.124 - 0.185: 608 0.185 - 0.247: 127 0.247 - 0.309: 14 Chirality restraints: 4603 Sorted by residual: 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 2.74 -0.31 2.00e-01 2.50e+01 2.38e+00 chirality pdb=" CA VAL G1616 " pdb=" N VAL G1616 " pdb=" C VAL G1616 " pdb=" CB VAL G1616 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA VAL A 893 " pdb=" N VAL A 893 " pdb=" C VAL A 893 " pdb=" CB VAL A 893 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 4600 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1901 " -0.064 2.00e-02 2.50e+03 6.56e-02 5.37e+01 pdb=" C34 PNS B1901 " 0.036 2.00e-02 2.50e+03 pdb=" C37 PNS B1901 " -0.079 2.00e-02 2.50e+03 pdb=" N36 PNS B1901 " 0.099 2.00e-02 2.50e+03 pdb=" O35 PNS B1901 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.008 2.00e-02 2.50e+03 2.72e-02 3.51e+01 pdb=" C10 FMN G2101 " 0.010 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.028 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.008 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.054 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.063 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.019 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.001 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.022 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.014 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.029 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.045 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.018 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=" CB TYR A 722 " 0.066 2.00e-02 2.50e+03 3.54e-02 2.50e+01 pdb=" CG TYR A 722 " -0.061 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.020 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.034 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 464 2.66 - 3.22: 27502 3.22 - 3.78: 45528 3.78 - 4.34: 65681 4.34 - 4.90: 106734 Nonbonded interactions: 245909 Sorted by model distance: nonbonded pdb=" O PHE A 35 " pdb=" OG1 THR A 41 " model vdw 2.097 3.040 nonbonded pdb=" O TRP A1030 " pdb=" OG1 THR A1035 " model vdw 2.209 3.040 nonbonded pdb=" O3P FMN G2101 " pdb=" O4' FMN G2101 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR G 778 " pdb=" OE1 GLN G1088 " model vdw 2.244 3.040 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.259 3.040 ... (remaining 245904 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: 1.060 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 30.480 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.842 30244 Z= 1.045 Angle : 1.896 48.031 40964 Z= 1.379 Chirality : 0.089 0.309 4603 Planarity : 0.007 0.066 5286 Dihedral : 15.079 94.463 11224 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.38 % Favored : 93.14 % Rotamer: Outliers : 0.55 % Allowed : 4.07 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.52 (0.11), residues: 3760 helix: -2.83 (0.09), residues: 1627 sheet: -2.17 (0.20), residues: 502 loop : -1.61 (0.14), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1104 TYR 0.066 0.007 TYR A 722 PHE 0.043 0.007 PHE G 799 TRP 0.038 0.007 TRP G 943 HIS 0.017 0.004 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.01362 / 1.02 (30242) covalent geometry : angle 1.88074 / 1.37 (40962) SS BOND : bond 0.84228 / 44.33 ( 1) SS BOND : angle 34.87615 / 20.41 ( 2) hydrogen bonds : bond 0.21634 / 14.58 ( 1419) hydrogen bonds : angle 9.28381 / 6.63 ( 3963) Misc. bond : bond 0.05872 / 3.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 232 time to evaluate : 1.209 Fit side-chains REVERT: A 56 MET cc_start: 0.9267 (mtt) cc_final: 0.9060 (mtt) REVERT: A 431 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8888 (mp0) REVERT: A 917 CYS cc_start: 0.9446 (OUTLIER) cc_final: 0.9219 (m) REVERT: A 1112 ASN cc_start: 0.8961 (t0) cc_final: 0.8485 (t0) REVERT: A 1317 GLU cc_start: 0.7055 (tt0) cc_final: 0.5657 (mm-30) REVERT: A 1741 LYS cc_start: 0.4000 (mmmt) cc_final: 0.3573 (mmmt) REVERT: A 1755 MET cc_start: 0.8796 (mmp) cc_final: 0.8338 (mtp) REVERT: A 1790 ASN cc_start: 0.8494 (m110) cc_final: 0.8289 (m110) REVERT: B 168 MET cc_start: 0.8707 (tpp) cc_final: 0.8118 (tpp) REVERT: B 200 LYS cc_start: 0.7663 (ptmm) cc_final: 0.7277 (ttmt) REVERT: B 237 MET cc_start: 0.6924 (mmp) cc_final: 0.6425 (mmt) REVERT: B 290 MET cc_start: 0.3282 (mmm) cc_final: 0.3049 (mmm) REVERT: G 132 MET cc_start: 0.9398 (mmm) cc_final: 0.9154 (mmm) REVERT: G 553 ASN cc_start: 0.9113 (m-40) cc_final: 0.8047 (t0) REVERT: G 1216 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8440 (pm20) outliers start: 18 outliers final: 10 residues processed: 249 average time/residue: 0.1991 time to fit residues: 80.4490 Evaluate side-chains 198 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain A residue 434 SER Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 917 CYS Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1255 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1366 SER Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain G residue 1216 GLU Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1761 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 ASN A 457 ASN A 713 GLN A 969 ASN A1123 GLN A1549 ASN A1601 ASN B 183 GLN B 224 GLN B 271 ASN G 110 GLN G 718 ASN G1055 HIS G1186 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.078192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.056932 restraints weight = 80387.782| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.48 r_work: 0.2683 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8905 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30244 Z= 0.128 Angle : 0.529 11.920 40964 Z= 0.281 Chirality : 0.042 0.161 4603 Planarity : 0.004 0.049 5286 Dihedral : 5.406 89.263 4051 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.50 % Favored : 97.45 % Rotamer: Outliers : 0.49 % Allowed : 6.84 % Favored : 92.66 % 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: -0.59 (0.13), residues: 3760 helix: 0.29 (0.12), residues: 1684 sheet: -1.60 (0.20), residues: 551 loop : -0.51 (0.16), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1765 TYR 0.018 0.001 TYR A 68 PHE 0.021 0.001 PHE A 35 TRP 0.014 0.001 TRP G 661 HIS 0.004 0.001 HIS G 741 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (30242) covalent geometry : angle 0.52764 / 0.28 (40962) SS BOND : bond 0.00791 / 0.42 ( 1) SS BOND : angle 4.97828 / 2.92 ( 2) hydrogen bonds : bond 0.04086 / 2.70 ( 1419) hydrogen bonds : angle 4.99642 / 3.53 ( 3963) Misc. bond : bond 0.00041 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 216 time to evaluate : 1.178 Fit side-chains REVERT: A 56 MET cc_start: 0.9280 (mtt) cc_final: 0.8833 (mtt) REVERT: A 75 HIS cc_start: 0.7763 (m90) cc_final: 0.7355 (m-70) REVERT: A 431 GLU cc_start: 0.9099 (mm-30) cc_final: 0.8793 (mp0) REVERT: A 1121 MET cc_start: 0.8503 (mtp) cc_final: 0.8199 (mtm) REVERT: A 1741 LYS cc_start: 0.4284 (mmmt) cc_final: 0.3073 (mmtp) REVERT: A 1790 ASN cc_start: 0.7002 (m110) cc_final: 0.6748 (m110) REVERT: B 168 MET cc_start: 0.8602 (tpp) cc_final: 0.8267 (tpp) REVERT: B 193 GLU cc_start: 0.7585 (OUTLIER) cc_final: 0.7138 (mm-30) REVERT: G 11 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7463 (pp) REVERT: G 338 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: G 553 ASN cc_start: 0.8955 (m-40) cc_final: 0.8053 (t0) REVERT: G 1981 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9095 (pp) outliers start: 16 outliers final: 7 residues processed: 228 average time/residue: 0.2061 time to fit residues: 75.3639 Evaluate side-chains 193 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 182 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1759 MET Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1761 SER Chi-restraints excluded: chain G residue 1981 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 358 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 319 optimal weight: 7.9990 chunk 320 optimal weight: 8.9990 chunk 255 optimal weight: 0.8980 chunk 316 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 336 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 HIS A 713 GLN A 971 ASN A1194 ASN A1689 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1868 GLN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G2013 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.076702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.055401 restraints weight = 81114.870| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.51 r_work: 0.2648 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30244 Z= 0.205 Angle : 0.532 11.445 40964 Z= 0.279 Chirality : 0.043 0.154 4603 Planarity : 0.004 0.054 5286 Dihedral : 4.987 80.232 4037 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 0.96 % Allowed : 7.74 % Favored : 91.31 % 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: 0.26 (0.14), residues: 3760 helix: 1.10 (0.13), residues: 1676 sheet: -1.23 (0.21), residues: 536 loop : -0.19 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1765 TYR 0.021 0.001 TYR A 722 PHE 0.028 0.002 PHE A 22 TRP 0.012 0.001 TRP G1138 HIS 0.005 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (30242) covalent geometry : angle 0.52994 / 0.28 (40962) SS BOND : bond 0.01722 / 0.91 ( 1) SS BOND : angle 7.29903 / 4.02 ( 2) hydrogen bonds : bond 0.04095 / 2.70 ( 1419) hydrogen bonds : angle 4.73045 / 3.34 ( 3963) Misc. bond : bond 0.00035 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 1.154 Fit side-chains REVERT: A 56 MET cc_start: 0.9300 (mtt) cc_final: 0.8989 (mtt) REVERT: A 431 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8797 (mp0) REVERT: A 949 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: A 1121 MET cc_start: 0.8670 (mtp) cc_final: 0.8362 (mtm) REVERT: A 1741 LYS cc_start: 0.4080 (mmmt) cc_final: 0.3713 (mmtt) REVERT: A 1790 ASN cc_start: 0.6859 (m110) cc_final: 0.6549 (m110) REVERT: B 193 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: G 175 ASP cc_start: 0.8997 (OUTLIER) cc_final: 0.8772 (t70) REVERT: G 338 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9073 (mtt) REVERT: G 553 ASN cc_start: 0.8967 (m-40) cc_final: 0.8121 (t0) REVERT: G 1656 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8754 (mt-10) REVERT: G 1868 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8267 (pp30) outliers start: 31 outliers final: 12 residues processed: 212 average time/residue: 0.1931 time to fit residues: 66.6117 Evaluate side-chains 194 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 177 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1868 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 146 optimal weight: 30.0000 chunk 276 optimal weight: 0.9990 chunk 316 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 293 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 294 optimal weight: 0.8980 chunk 335 optimal weight: 5.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A 971 ASN ** B 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1055 HIS G1633 ASN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.056100 restraints weight = 80473.057| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.50 r_work: 0.2664 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2547 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30244 Z= 0.165 Angle : 0.502 11.125 40964 Z= 0.261 Chirality : 0.042 0.153 4603 Planarity : 0.004 0.056 5286 Dihedral : 4.858 77.402 4036 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.99 % Allowed : 9.09 % Favored : 89.92 % 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: 0.58 (0.14), residues: 3760 helix: 1.36 (0.13), residues: 1684 sheet: -1.09 (0.21), residues: 553 loop : -0.00 (0.16), residues: 1523 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1023 TYR 0.017 0.001 TYR A 722 PHE 0.020 0.001 PHE A 35 TRP 0.011 0.001 TRP G1138 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (30242) covalent geometry : angle 0.49959 / 0.26 (40962) SS BOND : bond 0.01602 / 0.84 ( 1) SS BOND : angle 6.42411 / 3.55 ( 2) hydrogen bonds : bond 0.03737 / 2.46 ( 1419) hydrogen bonds : angle 4.57950 / 3.23 ( 3963) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 194 time to evaluate : 1.266 Fit side-chains REVERT: A 56 MET cc_start: 0.9274 (mtt) cc_final: 0.8927 (mtt) REVERT: A 328 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6534 (tt) REVERT: A 431 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8770 (mp0) REVERT: A 838 MET cc_start: 0.9316 (mtp) cc_final: 0.9094 (mtm) REVERT: A 949 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: A 1121 MET cc_start: 0.8678 (mtp) cc_final: 0.8377 (mtm) REVERT: A 1741 LYS cc_start: 0.4006 (mmmt) cc_final: 0.2757 (mmtp) REVERT: B 168 MET cc_start: 0.8562 (tpp) cc_final: 0.8095 (tpp) REVERT: B 193 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7133 (mm-30) REVERT: G 175 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8790 (t70) REVERT: G 338 MET cc_start: 0.9250 (OUTLIER) cc_final: 0.9013 (mtt) REVERT: G 553 ASN cc_start: 0.9000 (m-40) cc_final: 0.8164 (t0) REVERT: G 1379 GLU cc_start: 0.8431 (tt0) cc_final: 0.8153 (tm-30) REVERT: G 1656 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8721 (mt-10) outliers start: 32 outliers final: 13 residues processed: 217 average time/residue: 0.2009 time to fit residues: 70.2944 Evaluate side-chains 194 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 176 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 70 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 269 optimal weight: 8.9990 chunk 128 optimal weight: 0.8980 chunk 150 optimal weight: 9.9990 chunk 332 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 158 optimal weight: 30.0000 chunk 194 optimal weight: 7.9990 chunk 355 optimal weight: 7.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A1689 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 261 GLN G1633 ASN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.077936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.056865 restraints weight = 80947.918| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.51 r_work: 0.2678 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30244 Z= 0.136 Angle : 0.481 11.004 40964 Z= 0.249 Chirality : 0.041 0.150 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.735 74.505 4036 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.83 % Allowed : 9.90 % Favored : 89.27 % 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: 0.80 (0.14), residues: 3760 helix: 1.52 (0.13), residues: 1680 sheet: -0.91 (0.21), residues: 544 loop : 0.10 (0.17), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1023 TYR 0.015 0.001 TYR A 722 PHE 0.021 0.001 PHE A 22 TRP 0.011 0.001 TRP G1138 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (30242) covalent geometry : angle 0.47904 / 0.25 (40962) SS BOND : bond 0.01427 / 0.75 ( 1) SS BOND : angle 5.58405 / 3.09 ( 2) hydrogen bonds : bond 0.03509 / 2.31 ( 1419) hydrogen bonds : angle 4.46679 / 3.16 ( 3963) Misc. bond : bond 0.00024 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 196 time to evaluate : 1.194 Fit side-chains REVERT: A 56 MET cc_start: 0.9266 (mtt) cc_final: 0.8881 (mtt) REVERT: A 328 LEU cc_start: 0.6857 (OUTLIER) cc_final: 0.6593 (tt) REVERT: A 431 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8802 (mp0) REVERT: A 838 MET cc_start: 0.9305 (mtp) cc_final: 0.9082 (mtm) REVERT: A 1044 GLU cc_start: 0.9072 (OUTLIER) cc_final: 0.8735 (pp20) REVERT: A 1121 MET cc_start: 0.8680 (mtp) cc_final: 0.8375 (mtm) REVERT: A 1332 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.7541 (p90) REVERT: A 1790 ASN cc_start: 0.6912 (m110) cc_final: 0.6369 (m110) REVERT: B 193 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: G 175 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8807 (t70) REVERT: G 326 ASP cc_start: 0.9256 (t0) cc_final: 0.8801 (t0) REVERT: G 338 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8976 (mtt) REVERT: G 553 ASN cc_start: 0.9035 (m-40) cc_final: 0.8199 (t0) REVERT: G 1180 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.8174 (mtp) REVERT: G 1379 GLU cc_start: 0.8404 (tt0) cc_final: 0.8123 (tm-30) REVERT: G 1656 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8711 (mt-10) outliers start: 27 outliers final: 14 residues processed: 214 average time/residue: 0.1973 time to fit residues: 67.7576 Evaluate side-chains 205 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1180 MET Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 28 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 246 optimal weight: 20.0000 chunk 286 optimal weight: 0.9990 chunk 256 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 307 optimal weight: 0.0770 chunk 35 optimal weight: 9.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A 987 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1341 ASN G1868 GLN ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.078394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.057282 restraints weight = 80470.472| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.48 r_work: 0.2695 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2577 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30244 Z= 0.122 Angle : 0.471 10.743 40964 Z= 0.243 Chirality : 0.041 0.147 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.646 71.485 4036 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.23 % Allowed : 10.08 % Favored : 88.69 % 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: 0.95 (0.14), residues: 3760 helix: 1.63 (0.13), residues: 1681 sheet: -0.74 (0.22), residues: 541 loop : 0.16 (0.17), residues: 1538 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1023 TYR 0.014 0.001 TYR A 722 PHE 0.022 0.001 PHE A 35 TRP 0.010 0.001 TRP G1138 HIS 0.003 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (30242) covalent geometry : angle 0.47006 / 0.24 (40962) SS BOND : bond 0.01371 / 0.72 ( 1) SS BOND : angle 5.17549 / 2.87 ( 2) hydrogen bonds : bond 0.03379 / 2.22 ( 1419) hydrogen bonds : angle 4.39261 / 3.11 ( 3963) Misc. bond : bond 0.00023 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 1.223 Fit side-chains revert: symmetry clash REVERT: A 328 LEU cc_start: 0.6904 (OUTLIER) cc_final: 0.6659 (tt) REVERT: A 431 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8788 (mp0) REVERT: A 838 MET cc_start: 0.9315 (mtp) cc_final: 0.9086 (mtm) REVERT: A 856 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.6055 (mt-10) REVERT: A 1121 MET cc_start: 0.8670 (mtp) cc_final: 0.8367 (mtm) REVERT: A 1332 TYR cc_start: 0.9267 (OUTLIER) cc_final: 0.8158 (p90) REVERT: A 1741 LYS cc_start: 0.4051 (mmtt) cc_final: 0.3096 (mmtt) REVERT: A 1790 ASN cc_start: 0.6876 (m110) cc_final: 0.6340 (m110) REVERT: B 193 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7156 (mm-30) REVERT: G 175 ASP cc_start: 0.9046 (OUTLIER) cc_final: 0.8830 (t70) REVERT: G 326 ASP cc_start: 0.9256 (t0) cc_final: 0.8804 (t0) REVERT: G 338 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8956 (mtt) REVERT: G 553 ASN cc_start: 0.9009 (m-40) cc_final: 0.8224 (t0) REVERT: G 1180 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8082 (mtp) REVERT: G 1379 GLU cc_start: 0.8428 (tt0) cc_final: 0.8144 (tm-30) REVERT: G 1868 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7992 (pp30) outliers start: 40 outliers final: 26 residues processed: 223 average time/residue: 0.2028 time to fit residues: 73.6423 Evaluate side-chains 217 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 328 LEU Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1557 ILE Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1180 MET Chi-restraints excluded: chain G residue 1189 THR Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1811 GLU Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1868 GLN Chi-restraints excluded: chain G residue 1958 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 200 optimal weight: 6.9990 chunk 339 optimal weight: 5.9990 chunk 359 optimal weight: 0.8980 chunk 257 optimal weight: 0.6980 chunk 148 optimal weight: 30.0000 chunk 240 optimal weight: 10.0000 chunk 178 optimal weight: 0.9980 chunk 351 optimal weight: 0.3980 chunk 346 optimal weight: 0.0170 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 112 ASN G 723 HIS G1633 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.080191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.059403 restraints weight = 80534.808| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.46 r_work: 0.2748 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8861 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 30244 Z= 0.084 Angle : 0.455 10.774 40964 Z= 0.233 Chirality : 0.040 0.164 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.447 70.365 4036 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.02 % Allowed : 10.60 % Favored : 88.38 % 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: 1.11 (0.14), residues: 3760 helix: 1.75 (0.13), residues: 1688 sheet: -0.55 (0.22), residues: 548 loop : 0.21 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1023 TYR 0.013 0.001 TYR A 68 PHE 0.024 0.001 PHE B 286 TRP 0.011 0.001 TRP G 661 HIS 0.003 0.001 HIS G1002 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (30242) covalent geometry : angle 0.45421 / 0.23 (40962) SS BOND : bond 0.00949 / 0.50 ( 1) SS BOND : angle 4.35422 / 2.40 ( 2) hydrogen bonds : bond 0.02947 / 1.93 ( 1419) hydrogen bonds : angle 4.22575 / 2.99 ( 3963) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 202 time to evaluate : 1.169 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9237 (mtt) cc_final: 0.9010 (mtm) REVERT: A 431 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8796 (mp0) REVERT: A 838 MET cc_start: 0.9268 (mtp) cc_final: 0.9046 (mtm) REVERT: A 1121 MET cc_start: 0.8691 (mtp) cc_final: 0.8364 (mtm) REVERT: A 1332 TYR cc_start: 0.9179 (OUTLIER) cc_final: 0.8879 (p90) REVERT: A 1741 LYS cc_start: 0.4025 (mmtt) cc_final: 0.3060 (mmtp) REVERT: A 1790 ASN cc_start: 0.6824 (m110) cc_final: 0.6274 (m110) REVERT: B 193 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7103 (mm-30) REVERT: G 326 ASP cc_start: 0.9213 (t0) cc_final: 0.8819 (t0) REVERT: G 338 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8847 (mtt) REVERT: G 553 ASN cc_start: 0.8978 (m-40) cc_final: 0.8233 (t0) REVERT: G 1379 GLU cc_start: 0.8426 (tt0) cc_final: 0.8155 (tm-30) outliers start: 33 outliers final: 21 residues processed: 226 average time/residue: 0.2012 time to fit residues: 73.3516 Evaluate side-chains 215 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 338 MET Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 917 MET Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1189 THR Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1868 GLN Chi-restraints excluded: chain G residue 1916 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 120 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 79 optimal weight: 3.9990 chunk 148 optimal weight: 10.0000 chunk 308 optimal weight: 10.0000 chunk 333 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 chunk 197 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A1689 HIS A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1055 HIS G1868 GLN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.077773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.056639 restraints weight = 80991.902| |-----------------------------------------------------------------------------| r_work (start): 0.2797 rms_B_bonded: 2.47 r_work: 0.2677 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2559 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30244 Z= 0.182 Angle : 0.513 11.928 40964 Z= 0.264 Chirality : 0.042 0.169 4603 Planarity : 0.004 0.057 5286 Dihedral : 4.658 71.549 4036 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.36 % Allowed : 10.45 % Favored : 88.19 % 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: 1.12 (0.14), residues: 3760 helix: 1.72 (0.13), residues: 1682 sheet: -0.41 (0.22), residues: 528 loop : 0.21 (0.17), residues: 1550 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G1765 TYR 0.017 0.001 TYR A 722 PHE 0.019 0.001 PHE A 35 TRP 0.010 0.001 TRP G1596 HIS 0.005 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (30242) covalent geometry : angle 0.51143 / 0.26 (40962) SS BOND : bond 0.01644 / 0.87 ( 1) SS BOND : angle 5.46743 / 3.06 ( 2) hydrogen bonds : bond 0.03652 / 2.38 ( 1419) hydrogen bonds : angle 4.39336 / 3.11 ( 3963) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.9152 (mm-30) cc_final: 0.8752 (mp0) REVERT: A 838 MET cc_start: 0.9334 (mtp) cc_final: 0.9096 (mtm) REVERT: A 847 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: A 856 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6062 (mt-10) REVERT: A 1044 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8810 (pp20) REVERT: A 1121 MET cc_start: 0.8691 (mtp) cc_final: 0.8375 (mtm) REVERT: A 1332 TYR cc_start: 0.9254 (OUTLIER) cc_final: 0.8188 (p90) REVERT: A 1741 LYS cc_start: 0.4073 (mmtt) cc_final: 0.3250 (mmtt) REVERT: A 1790 ASN cc_start: 0.6898 (m110) cc_final: 0.6377 (m110) REVERT: B 193 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7173 (mm-30) REVERT: G 175 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8831 (t70) REVERT: G 553 ASN cc_start: 0.8961 (m-40) cc_final: 0.8217 (t0) REVERT: G 1868 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7986 (pp30) outliers start: 44 outliers final: 29 residues processed: 221 average time/residue: 0.1967 time to fit residues: 70.8479 Evaluate side-chains 221 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 1.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 805 VAL Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1180 MET Chi-restraints excluded: chain G residue 1189 THR Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1625 SER Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1868 GLN Chi-restraints excluded: chain G residue 1916 PHE Chi-restraints excluded: chain G residue 1958 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 106 optimal weight: 0.0470 chunk 344 optimal weight: 9.9990 chunk 134 optimal weight: 4.9990 chunk 68 optimal weight: 0.0170 chunk 275 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 162 optimal weight: 7.9990 chunk 368 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 256 optimal weight: 0.0980 overall best weight: 2.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A1689 HIS A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1868 GLN ** G1892 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.078314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.057242 restraints weight = 80392.842| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.47 r_work: 0.2693 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2575 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8897 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30244 Z= 0.138 Angle : 0.495 11.405 40964 Z= 0.254 Chirality : 0.041 0.161 4603 Planarity : 0.003 0.057 5286 Dihedral : 4.616 69.198 4036 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.11 % Allowed : 10.73 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.14), residues: 3760 helix: 1.75 (0.13), residues: 1681 sheet: -0.39 (0.22), residues: 531 loop : 0.23 (0.17), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G1765 TYR 0.015 0.001 TYR A 722 PHE 0.021 0.001 PHE A 35 TRP 0.010 0.001 TRP G1138 HIS 0.005 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (30242) covalent geometry : angle 0.49421 / 0.25 (40962) SS BOND : bond 0.01458 / 0.77 ( 1) SS BOND : angle 5.07599 / 2.83 ( 2) hydrogen bonds : bond 0.03419 / 2.23 ( 1419) hydrogen bonds : angle 4.34761 / 3.08 ( 3963) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 1.171 Fit side-chains revert: symmetry clash REVERT: A 431 GLU cc_start: 0.9127 (mm-30) cc_final: 0.8799 (mp0) REVERT: A 838 MET cc_start: 0.9329 (mtp) cc_final: 0.9094 (mtm) REVERT: A 847 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8115 (mp0) REVERT: A 856 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.6066 (mt-10) REVERT: A 1044 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8803 (pp20) REVERT: A 1121 MET cc_start: 0.8685 (mtp) cc_final: 0.8378 (mtm) REVERT: A 1332 TYR cc_start: 0.9237 (OUTLIER) cc_final: 0.8365 (p90) REVERT: A 1741 LYS cc_start: 0.4064 (mmtt) cc_final: 0.2621 (mmtt) REVERT: A 1775 LEU cc_start: 0.8754 (mt) cc_final: 0.8433 (mp) REVERT: A 1790 ASN cc_start: 0.6865 (m110) cc_final: 0.6346 (m110) REVERT: B 193 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: G 175 ASP cc_start: 0.9055 (OUTLIER) cc_final: 0.8825 (t70) REVERT: G 326 ASP cc_start: 0.9220 (t0) cc_final: 0.8793 (t0) REVERT: G 553 ASN cc_start: 0.8949 (m-40) cc_final: 0.8239 (t0) outliers start: 36 outliers final: 28 residues processed: 216 average time/residue: 0.1980 time to fit residues: 69.8022 Evaluate side-chains 219 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 811 SER Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 175 ASP Chi-restraints excluded: chain G residue 322 SER Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1180 MET Chi-restraints excluded: chain G residue 1189 THR Chi-restraints excluded: chain G residue 1323 MET Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1842 VAL Chi-restraints excluded: chain G residue 1868 GLN Chi-restraints excluded: chain G residue 1916 PHE Chi-restraints excluded: chain G residue 1958 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 169 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 170 optimal weight: 0.2980 chunk 25 optimal weight: 0.7980 chunk 231 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 97 optimal weight: 0.0670 chunk 61 optimal weight: 0.9980 chunk 236 optimal weight: 0.0980 chunk 294 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1868 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.080338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.059970 restraints weight = 80008.762| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.41 r_work: 0.2763 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30244 Z= 0.084 Angle : 0.469 11.137 40964 Z= 0.239 Chirality : 0.040 0.161 4603 Planarity : 0.003 0.056 5286 Dihedral : 4.368 67.417 4036 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.89 % Allowed : 10.97 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.30 (0.14), residues: 3760 helix: 1.86 (0.13), residues: 1692 sheet: -0.27 (0.22), residues: 544 loop : 0.28 (0.17), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G1023 TYR 0.015 0.001 TYR G 67 PHE 0.030 0.001 PHE B 286 TRP 0.012 0.001 TRP G 661 HIS 0.004 0.001 HIS A1873 Details of bonding type rmsd/Z covalent geometry : bond 0.00183 / 0.08 (30242) covalent geometry : angle 0.46841 / 0.24 (40962) SS BOND : bond 0.00896 / 0.47 ( 1) SS BOND : angle 4.18365 / 2.30 ( 2) hydrogen bonds : bond 0.02876 / 1.87 ( 1419) hydrogen bonds : angle 4.17049 / 2.96 ( 3963) Misc. bond : bond 0.00010 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 196 time to evaluate : 1.150 Fit side-chains revert: symmetry clash REVERT: A 56 MET cc_start: 0.9235 (mtt) cc_final: 0.9005 (mtm) REVERT: A 333 LYS cc_start: 0.8194 (mptt) cc_final: 0.7974 (mppt) REVERT: A 431 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8754 (mp0) REVERT: A 838 MET cc_start: 0.9268 (mtp) cc_final: 0.9043 (mtm) REVERT: A 847 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: A 856 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.6069 (mt-10) REVERT: A 1121 MET cc_start: 0.8681 (mtp) cc_final: 0.8357 (mtm) REVERT: A 1741 LYS cc_start: 0.4048 (mmtt) cc_final: 0.2903 (mmtt) REVERT: A 1775 LEU cc_start: 0.8772 (mt) cc_final: 0.8466 (mp) REVERT: A 1790 ASN cc_start: 0.6811 (m110) cc_final: 0.6258 (m110) REVERT: B 193 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7159 (mm-30) REVERT: G 326 ASP cc_start: 0.9220 (t0) cc_final: 0.8825 (t0) REVERT: G 553 ASN cc_start: 0.8944 (m-40) cc_final: 0.8291 (t0) outliers start: 29 outliers final: 23 residues processed: 219 average time/residue: 0.1833 time to fit residues: 65.6384 Evaluate side-chains 215 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 189 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 847 GLU Chi-restraints excluded: chain A residue 856 GLU Chi-restraints excluded: chain A residue 949 GLU Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1745 ILE Chi-restraints excluded: chain B residue 157 HIS Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 193 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 215 ILE Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 616 THR Chi-restraints excluded: chain G residue 805 VAL Chi-restraints excluded: chain G residue 1131 SER Chi-restraints excluded: chain G residue 1189 THR Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1632 ILE Chi-restraints excluded: chain G residue 1822 MET Chi-restraints excluded: chain G residue 1916 PHE Chi-restraints excluded: chain G residue 1958 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 126 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 8.9990 chunk 346 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 129 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 chunk 337 optimal weight: 9.9990 chunk 218 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 713 GLN A 854 HIS A1689 HIS A1873 HIS ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G1868 GLN ** G1897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1928 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.077500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.056325 restraints weight = 81314.038| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.48 r_work: 0.2672 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8914 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 30244 Z= 0.211 Angle : 0.542 12.162 40964 Z= 0.277 Chirality : 0.043 0.217 4603 Planarity : 0.004 0.057 5286 Dihedral : 4.653 69.582 4036 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.11 % Allowed : 10.97 % Favored : 87.92 % 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: 1.20 (0.14), residues: 3760 helix: 1.76 (0.13), residues: 1680 sheet: -0.31 (0.22), residues: 531 loop : 0.26 (0.17), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G1023 TYR 0.018 0.001 TYR A1332 PHE 0.022 0.001 PHE G 28 TRP 0.011 0.001 TRP G1596 HIS 0.005 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (30242) covalent geometry : angle 0.54012 / 0.28 (40962) SS BOND : bond 0.01898 / 1.00 ( 1) SS BOND : angle 5.62756 / 3.16 ( 2) hydrogen bonds : bond 0.03752 / 2.45 ( 1419) hydrogen bonds : angle 4.40505 / 3.13 ( 3963) Misc. bond : bond 0.00013 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8990.13 seconds wall clock time: 154 minutes 25.31 seconds (9265.31 seconds total)