Starting phenix.real_space_refine on Sun Aug 24 09:40:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ps8_17846/08_2025/8ps8_17846.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ps8_17846/08_2025/8ps8_17846.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ps8_17846/08_2025/8ps8_17846.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ps8_17846/08_2025/8ps8_17846.map" model { file = "/net/cci-nas-00/data/ceres_data/8ps8_17846/08_2025/8ps8_17846.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ps8_17846/08_2025/8ps8_17846.cif" } resolution = 4.0 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= -0.000 sd= 0.006 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: 3 Type Number sf(0) Gaussians C 11098 2.51 5 N 3788 2.21 5 O 3788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18674 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1589, 7827 Classifications: {'peptide': 1589} Incomplete info: {'truncation_to_alanine': 1343} Link IDs: {'PTRANS': 61, 'TRANS': 1527} Chain breaks: 3 Unresolved chain link angles: 61 Unresolved non-hydrogen bonds: 4822 Unresolved non-hydrogen angles: 6154 Unresolved non-hydrogen dihedrals: 4011 Unresolved non-hydrogen chiralities: 434 Planarities with less than four sites: {'GLU:plan': 140, 'GLN:plan1': 62, 'HIS:plan': 28, 'TYR:plan': 52, 'PHE:plan': 61, 'ARG:plan': 59, 'TRP:plan': 18, 'ASP:plan': 80, 'ASN:plan1': 72} Unresolved non-hydrogen planarities: 2591 Chain: "B" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 801 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 8, 'TRANS': 154} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 441 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 360 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'HIS:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 2, 'PHE:plan': 5, 'ARG:plan': 5, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "G" Number of atoms: 10046 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2036, 10046 Classifications: {'peptide': 2036} Incomplete info: {'truncation_to_alanine': 1775} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1926} Chain breaks: 1 Unresolved chain link angles: 109 Unresolved non-hydrogen bonds: 6339 Unresolved non-hydrogen angles: 8142 Unresolved non-hydrogen dihedrals: 5291 Unresolved non-hydrogen chiralities: 605 Planarities with less than four sites: {'ARG:plan': 73, 'HIS:plan': 39, 'GLU:plan': 136, 'PHE:plan': 112, 'GLN:plan1': 70, 'ASN:plan1': 98, 'ASP:plan': 112, 'TYR:plan': 61, 'TRP:plan': 23} Unresolved non-hydrogen planarities: 3320 Time building chain proxies: 4.34, per 1000 atoms: 0.23 Number of scatterers: 18674 At special positions: 0 Unit cell: (182.515, 178.295, 174.075, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3788 8.00 N 3788 7.00 C 11098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 1.38 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 715.3 nanoseconds 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7044 Finding SS restraints... Secondary structure from input PDB file: 167 helices and 31 sheets defined 51.0% alpha, 14.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 Processing helix chain 'A' and resid 27 through 32 removed outlier: 3.732A pdb=" N THR A 31 " --> pdb=" O ARG A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 65 Processing helix chain 'A' and resid 66 through 72 removed outlier: 3.911A pdb=" N ALA A 70 " --> pdb=" O GLU A 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ALA A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 72 " --> pdb=" O TYR A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 66 through 72' Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 329 through 350 removed outlier: 3.993A pdb=" N LYS A 333 " --> pdb=" O GLU A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 383 removed outlier: 4.675A pdb=" N PHE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 404 through 422 removed outlier: 3.639A pdb=" N TRP A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 441 removed outlier: 4.102A pdb=" N VAL A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 458 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.601A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 670 Processing helix chain 'A' and resid 687 through 700 removed outlier: 3.966A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 removed outlier: 3.729A pdb=" N VAL A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 836 through 838 No H-bonds generated for 'chain 'A' and resid 836 through 838' Processing helix chain 'A' and resid 839 through 846 removed outlier: 3.738A pdb=" N LEU A 846 " --> pdb=" O SER A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 847 through 856 removed outlier: 4.061A pdb=" N ASN A 851 " --> pdb=" O GLU A 847 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 855 " --> pdb=" O ASN A 851 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLU A 856 " --> pdb=" O ARG A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.275A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 881 through 883 No H-bonds generated for 'chain 'A' and resid 881 through 883' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.584A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 935 through 974 removed outlier: 4.157A pdb=" N PHE A 939 " --> pdb=" O GLU A 935 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA A 962 " --> pdb=" O SER A 958 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N GLU A 964 " --> pdb=" O GLU A 960 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASN A 971 " --> pdb=" O VAL A 967 " (cutoff:3.500A) removed outlier: 8.840A pdb=" N SER A 972 " --> pdb=" O VAL A 968 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA A 973 " --> pdb=" O ASN A 969 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASP A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1003 removed outlier: 3.627A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.562A pdb=" N LEU A1009 " --> pdb=" O PRO A1006 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1006 through 1010' Processing helix chain 'A' and resid 1014 through 1017 Processing helix chain 'A' and resid 1033 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1099 removed outlier: 4.298A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.667A 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: 3.981A pdb=" N TYR A1198 " --> pdb=" O ASN A1194 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1209 through 1226 Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1253 through 1262 Processing helix chain 'A' and resid 1275 through 1278 Processing helix chain 'A' and resid 1279 through 1291 removed outlier: 4.268A pdb=" N MET A1283 " --> pdb=" O PHE A1279 " (cutoff:3.500A) removed outlier: 4.557A 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 1362 through 1366 removed outlier: 4.420A pdb=" N SER A1366 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1477 removed outlier: 4.051A pdb=" N ARG A1448 " --> pdb=" O ASN A1444 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1510 removed outlier: 4.064A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.549A 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: 3.643A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A1554 " --> pdb=" O ASP A1550 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A1564 " --> pdb=" O MET A1560 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.610A 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 removed outlier: 3.566A pdb=" N MET A1592 " --> pdb=" O ALA A1588 " (cutoff:3.500A) Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 3.677A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 3.824A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.611A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1758 Processing helix chain 'A' and resid 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 3.964A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 removed outlier: 3.761A pdb=" N GLY A1824 " --> pdb=" O PHE A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.663A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.603A pdb=" N LEU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 159 " --> pdb=" O VAL B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.637A pdb=" N VAL B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.631A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.792A pdb=" N LEU B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 236 Processing helix chain 'B' and resid 242 through 254 removed outlier: 3.569A pdb=" N LYS B 248 " --> pdb=" O THR B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.603A pdb=" N SER B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 removed outlier: 3.584A pdb=" N ALA B 285 " --> pdb=" O ALA B 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.618A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 Processing helix chain 'G' and resid 79 through 93 removed outlier: 4.532A pdb=" N VAL G 83 " --> pdb=" O GLN G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 removed outlier: 3.781A pdb=" N LEU G 104 " --> pdb=" O ASP G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.525A pdb=" N GLU G 172 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.691A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 3.562A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 227 through 233 removed outlier: 3.598A pdb=" N LEU G 231 " --> pdb=" O ASP G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 257 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 273 through 275 No H-bonds generated for 'chain 'G' and resid 273 through 275' Processing helix chain 'G' and resid 276 through 286 removed outlier: 3.523A pdb=" N VAL G 281 " --> pdb=" O LEU G 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 292 through 314 removed outlier: 3.721A pdb=" N CYS G 310 " --> pdb=" O ILE G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 removed outlier: 3.593A pdb=" N LEU G 324 " --> pdb=" O PRO G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 4.036A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 397 removed outlier: 3.616A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 446 removed outlier: 4.338A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ASN G 446 " --> pdb=" O ASP G 442 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 471 removed outlier: 3.735A pdb=" N VAL G 470 " --> pdb=" O ASP G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 removed outlier: 3.684A 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 520 removed outlier: 3.572A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.900A 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 Processing helix chain 'G' and resid 603 through 613 Processing helix chain 'G' and resid 626 through 641 removed outlier: 3.812A pdb=" N ALA G 633 " --> pdb=" O GLY G 629 " (cutoff:3.500A) Processing helix chain 'G' and resid 655 through 672 removed outlier: 4.679A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.972A pdb=" N GLY G 699 " --> pdb=" O ILE G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 759 removed outlier: 4.947A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ARG G 759 " --> pdb=" O SER G 755 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 783 removed outlier: 4.012A pdb=" N THR G 777 " --> pdb=" O SER G 773 " (cutoff:3.500A) Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 788 removed outlier: 3.506A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 803 through 808 removed outlier: 4.057A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 Processing helix chain 'G' and resid 828 through 835 removed outlier: 3.566A pdb=" N LYS G 831 " --> pdb=" O PRO G 828 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 899 removed outlier: 4.374A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.443A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 917 Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 976 through 987 removed outlier: 4.035A pdb=" N LYS G 982 " --> pdb=" O GLU G 978 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1008 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1034 through 1039 removed outlier: 3.520A pdb=" N SER G1037 " --> pdb=" O LEU G1034 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1063 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 1174 removed outlier: 3.507A pdb=" N LYS G1172 " --> pdb=" O ASN G1168 " (cutoff:3.500A) Processing helix chain 'G' and resid 1189 through 1193 Processing helix chain 'G' and resid 1257 through 1271 Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1325 through 1337 removed outlier: 3.590A pdb=" N VAL G1329 " --> pdb=" O PHE G1325 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS G1336 " --> pdb=" O ARG G1332 " (cutoff:3.500A) Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 4.190A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ALA G1442 " --> pdb=" O SER G1438 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 removed outlier: 3.613A pdb=" N ASP G1518 " --> pdb=" O ASN G1514 " (cutoff:3.500A) Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 4.053A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 Processing helix chain 'G' and resid 1677 through 1684 Processing helix chain 'G' and resid 1684 through 1702 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1724 through 1733 removed outlier: 3.806A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ASN G1732 " --> pdb=" O ARG G1728 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR G1733 " --> pdb=" O ILE G1729 " (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 1820 removed outlier: 3.871A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1840 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 3.886A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.709A 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 removed outlier: 3.733A pdb=" N LEU G1871 " --> pdb=" O SER G1867 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G1880 " --> pdb=" O GLU G1876 " (cutoff:3.500A) Processing helix chain 'G' and resid 1904 through 1921 Processing helix chain 'G' and resid 1923 through 1930 removed outlier: 3.786A pdb=" N LEU G1927 " --> pdb=" O ASP G1923 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1940 through 1954 removed outlier: 3.754A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL G1953 " --> pdb=" O LYS G1949 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS G1954 " --> pdb=" O LYS G1950 " (cutoff:3.500A) Processing helix chain 'G' and resid 1978 through 1983 removed outlier: 3.809A pdb=" N LEU G1981 " --> pdb=" O SER G1978 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.762A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS G1994 " --> pdb=" O SER G1990 " (cutoff:3.500A) Processing helix chain 'G' and resid 2002 through 2007 Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2035 through 2044 Processing helix chain 'G' and resid 2044 through 2049 removed outlier: 3.778A pdb=" N TYR G2048 " --> pdb=" O ASN G2044 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU G2049 " --> pdb=" O TRP G2045 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2044 through 2049' Processing sheet with id=AA1, first strand: chain 'A' and resid 78 through 80 removed outlier: 5.801A pdb=" N VAL A 44 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.339A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 9.492A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N LEU A 926 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU A 640 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.339A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N MET A 826 " --> pdb=" O ILE A 869 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA6, first strand: chain 'A' and resid 981 through 982 removed outlier: 3.807A pdb=" N THR G 963 " --> pdb=" O ILE A 982 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 5.597A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.912A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE A1654 " --> pdb=" O ALA A1405 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA A1407 " --> pdb=" O GLN A1652 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLN A1652 " --> pdb=" O ALA A1407 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N THR A1409 " --> pdb=" O GLY A1650 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N GLY A1650 " --> pdb=" O THR A1409 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A1642 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL A1575 " --> pdb=" O ALA A1539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1060 through 1067 Processing sheet with id=AB1, first strand: chain 'A' and resid 1104 through 1105 Processing sheet with id=AB2, first strand: chain 'A' and resid 1122 through 1126 Processing sheet with id=AB3, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB4, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB5, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB6, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB7, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.844A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 269 through 270 removed outlier: 3.933A pdb=" N GLY G 269 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 158 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL G 527 " --> pdb=" O GLY G 542 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 417 through 420 removed outlier: 3.811A pdb=" N SER G 417 " --> pdb=" O SER G 342 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN G 376 " --> pdb=" O ASN G 372 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC3, first strand: chain 'G' and resid 592 through 594 removed outlier: 4.205A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU G 618 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ILE G 728 " --> pdb=" O MET G 764 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE G 766 " --> pdb=" O ILE G 728 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU G 730 " --> pdb=" O ILE G 766 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 739 through 740 removed outlier: 4.196A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC6, first strand: chain 'G' and resid 931 through 932 removed outlier: 3.549A pdb=" N ILE G 932 " --> pdb=" O SER G 937 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.698A pdb=" N VAL G1195 " --> pdb=" O ILE G1210 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE G1210 " --> pdb=" O VAL G1195 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU G1197 " --> pdb=" O THR G1208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G1204 " --> pdb=" O VAL G1201 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1285 through 1291 removed outlier: 3.969A pdb=" N THR G1374 " --> pdb=" O GLY G1287 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASP G1289 " --> pdb=" O VAL G1372 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N VAL G1372 " --> pdb=" O ASP G1289 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N MET G1404 " --> pdb=" O LEU G1396 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE G1411 " --> pdb=" O HIS G1352 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N HIS G1352 " --> pdb=" O PHE G1411 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ARG G1413 " --> pdb=" O LEU G1350 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU G1350 " --> pdb=" O ARG G1413 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU G1656 " --> pdb=" O GLY G1607 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N THR G1642 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR G1652 " --> pdb=" O PHE G1640 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N PHE G1640 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU G1654 " --> pdb=" O ILE G1638 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ILE G1638 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLU G1656 " --> pdb=" O LYS G1636 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LYS G1636 " --> pdb=" O GLU G1656 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) removed outlier: 15.226A pdb=" N ILE G1632 " --> pdb=" O GLU G1534 " (cutoff:3.500A) removed outlier: 15.492A pdb=" N GLU G1534 " --> pdb=" O ILE G1632 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1423 through 1424 removed outlier: 6.843A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1423 through 1424 removed outlier: 5.048A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE G1466 " --> pdb=" O TYR G1431 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N TYR G1431 " --> pdb=" O PHE G1466 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN G1432 " --> pdb=" O SER G1525 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER G1525 " --> pdb=" O GLN G1432 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 1716 through 1720 Processing sheet with id=AD3, first strand: chain 'G' and resid 1737 through 1742 removed outlier: 3.729A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS G1745 " --> pdb=" O VAL G1742 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 1886 through 1893 removed outlier: 6.831A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) 1450 hydrogen bonds defined for protein. 4089 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.26 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.27: 3787 1.27 - 1.34: 3413 1.34 - 1.42: 369 1.42 - 1.49: 2238 1.49 - 1.56: 8860 Bond restraints: 18667 Sorted by residual: bond pdb=" N ILE B 166 " pdb=" CA ILE B 166 " ideal model delta sigma weight residual 1.460 1.497 -0.037 7.60e-03 1.73e+04 2.35e+01 bond pdb=" N GLY G 78 " pdb=" CA GLY G 78 " ideal model delta sigma weight residual 1.442 1.479 -0.037 7.70e-03 1.69e+04 2.35e+01 bond pdb=" N ILE G 484 " pdb=" CA ILE G 484 " ideal model delta sigma weight residual 1.456 1.501 -0.045 9.50e-03 1.11e+04 2.20e+01 bond pdb=" N ILE A1157 " pdb=" CA ILE A1157 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.60e-03 1.73e+04 2.20e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.12e+01 ... (remaining 18662 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 12991 1.66 - 3.32: 10475 3.32 - 4.98: 2213 4.98 - 6.64: 268 6.64 - 8.30: 16 Bond angle restraints: 25963 Sorted by residual: angle pdb=" C PHE G 160 " pdb=" N GLY G 161 " pdb=" CA GLY G 161 " ideal model delta sigma weight residual 120.10 126.73 -6.63 9.50e-01 1.11e+00 4.87e+01 angle pdb=" C GLU A 886 " pdb=" N GLY A 887 " pdb=" CA GLY A 887 " ideal model delta sigma weight residual 119.98 126.30 -6.32 1.11e+00 8.12e-01 3.24e+01 angle pdb=" C PRO G 707 " pdb=" N GLY G 708 " pdb=" CA GLY G 708 " ideal model delta sigma weight residual 119.94 126.13 -6.19 1.09e+00 8.42e-01 3.23e+01 angle pdb=" C ASN G1186 " pdb=" N GLY G1187 " pdb=" CA GLY G1187 " ideal model delta sigma weight residual 120.03 125.98 -5.95 1.12e+00 7.97e-01 2.82e+01 angle pdb=" C ASP B 262 " pdb=" N GLY B 263 " pdb=" CA GLY B 263 " ideal model delta sigma weight residual 119.98 125.82 -5.84 1.11e+00 8.12e-01 2.76e+01 ... (remaining 25958 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 4.80: 9241 4.80 - 9.60: 1160 9.60 - 14.39: 320 14.39 - 19.19: 88 19.19 - 23.99: 16 Dihedral angle restraints: 10825 sinusoidal: 0 harmonic: 10825 Sorted by residual: dihedral pdb=" CA LEU G1213 " pdb=" C LEU G1213 " pdb=" N LEU G1214 " pdb=" CA LEU G1214 " ideal model delta harmonic sigma weight residual 180.00 156.01 23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA GLU A 960 " pdb=" C GLU A 960 " pdb=" N THR A 961 " pdb=" CA THR A 961 " ideal model delta harmonic sigma weight residual 180.00 156.33 23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA ALA G 897 " pdb=" C ALA G 897 " pdb=" N ASP G 898 " pdb=" CA ASP G 898 " ideal model delta harmonic sigma weight residual -180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 10822 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1533 0.051 - 0.102: 1158 0.102 - 0.153: 594 0.153 - 0.204: 218 0.204 - 0.255: 19 Chirality restraints: 3522 Sorted by residual: chirality pdb=" CA VAL A1084 " pdb=" N VAL A1084 " pdb=" C VAL A1084 " pdb=" CB VAL A1084 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA LEU G1238 " pdb=" N LEU G1238 " pdb=" C LEU G1238 " pdb=" CB LEU G1238 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE A1228 " pdb=" N ILE A1228 " pdb=" C ILE A1228 " pdb=" CB ILE A1228 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 3519 not shown) Planarity restraints: 3781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A1404 " -0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C VAL A1404 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL A1404 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA A1405 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1249 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C SER A1249 " 0.042 2.00e-02 2.50e+03 pdb=" O SER A1249 " -0.016 2.00e-02 2.50e+03 pdb=" N GLY A1250 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1731 " -0.011 2.00e-02 2.50e+03 2.30e-02 5.29e+00 pdb=" C LEU A1731 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU A1731 " -0.015 2.00e-02 2.50e+03 pdb=" N THR A1732 " -0.014 2.00e-02 2.50e+03 ... (remaining 3778 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 7968 2.93 - 3.42: 18629 3.42 - 3.91: 26089 3.91 - 4.41: 24932 4.41 - 4.90: 43514 Nonbonded interactions: 121132 Sorted by model distance: nonbonded pdb=" O PRO G1562 " pdb=" N SER G1566 " model vdw 2.435 3.120 nonbonded pdb=" O LEU A 905 " pdb=" N LEU A 908 " model vdw 2.453 3.120 nonbonded pdb=" O ARG G1604 " pdb=" N GLU G1658 " model vdw 2.461 3.120 nonbonded pdb=" O VAL A 44 " pdb=" N LEU A 79 " model vdw 2.466 3.120 nonbonded pdb=" O TYR A1093 " pdb=" N SER A1096 " model vdw 2.477 3.120 ... (remaining 121127 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 20.150 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 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 : 0.016 0.052 18667 Z= 1.283 Angle : 2.112 8.297 25963 Z= 1.628 Chirality : 0.084 0.255 3522 Planarity : 0.006 0.025 3781 Dihedral : 6.124 23.988 3781 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.68 % Favored : 93.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -2.93 (0.12), residues: 3774 helix: -2.11 (0.10), residues: 1611 sheet: -1.64 (0.22), residues: 472 loop : -1.68 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.01630 (18667) covalent geometry : angle 2.11207 (25963) hydrogen bonds : bond 0.19456 ( 1420) hydrogen bonds : angle 9.02984 ( 4089) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.607 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0733 time to fit residues: 12.1724 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0010 chunk 298 optimal weight: 7.9990 overall best weight: 4.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.069875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.059082 restraints weight = 140755.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.059096 restraints weight = 103158.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059109 restraints weight = 84011.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059123 restraints weight = 72710.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.059161 restraints weight = 73916.950| |-----------------------------------------------------------------------------| r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 18667 Z= 0.139 Angle : 0.437 11.517 25963 Z= 0.274 Chirality : 0.043 0.138 3522 Planarity : 0.003 0.017 3781 Dihedral : 4.181 23.537 3781 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.54 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.27 (0.13), residues: 3774 helix: 0.77 (0.12), residues: 1660 sheet: -1.24 (0.21), residues: 517 loop : -0.71 (0.16), residues: 1597 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00190 (18667) covalent geometry : angle 0.43743 (25963) hydrogen bonds : bond 0.03489 ( 1420) hydrogen bonds : angle 4.97479 ( 4089) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.700 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0680 time to fit residues: 11.2878 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 20 optimal weight: 9.9990 chunk 343 optimal weight: 0.0040 chunk 44 optimal weight: 30.0000 chunk 268 optimal weight: 20.0000 chunk 334 optimal weight: 30.0000 chunk 249 optimal weight: 20.0000 chunk 15 optimal weight: 0.3980 chunk 184 optimal weight: 10.0000 chunk 289 optimal weight: 0.0070 chunk 297 optimal weight: 30.0000 chunk 51 optimal weight: 6.9990 overall best weight: 3.4814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.069321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3228 r_free = 0.3228 target = 0.058130 restraints weight = 140633.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.058191 restraints weight = 99799.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.058264 restraints weight = 79538.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.058399 restraints weight = 69463.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.058451 restraints weight = 64229.782| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.015 18667 Z= 0.092 Angle : 0.367 10.634 25963 Z= 0.225 Chirality : 0.043 0.135 3522 Planarity : 0.002 0.013 3781 Dihedral : 3.525 22.821 3781 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.50 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 1.03 (0.14), residues: 3774 helix: 2.20 (0.13), residues: 1663 sheet: -1.02 (0.22), residues: 529 loop : -0.29 (0.16), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00125 (18667) covalent geometry : angle 0.36701 (25963) hydrogen bonds : bond 0.02737 ( 1420) hydrogen bonds : angle 4.15441 ( 4089) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.590 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0661 time to fit residues: 10.8423 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 30 optimal weight: 50.0000 chunk 48 optimal weight: 30.0000 chunk 121 optimal weight: 2.9990 chunk 373 optimal weight: 50.0000 chunk 150 optimal weight: 0.7980 chunk 9 optimal weight: 50.0000 chunk 98 optimal weight: 0.9980 chunk 38 optimal weight: 20.0000 chunk 272 optimal weight: 40.0000 chunk 355 optimal weight: 40.0000 chunk 173 optimal weight: 50.0000 overall best weight: 10.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.066281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.055285 restraints weight = 141632.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055450 restraints weight = 109011.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.055445 restraints weight = 79062.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055446 restraints weight = 73054.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.055467 restraints weight = 69574.298| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18667 Z= 0.235 Angle : 0.527 12.418 25963 Z= 0.331 Chirality : 0.046 0.151 3522 Planarity : 0.003 0.017 3781 Dihedral : 5.035 25.273 3781 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.38 % Favored : 94.59 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.04 (0.14), residues: 3774 helix: 1.23 (0.12), residues: 1638 sheet: -1.35 (0.24), residues: 454 loop : -0.85 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00324 (18667) covalent geometry : angle 0.52694 (25963) hydrogen bonds : bond 0.04189 ( 1420) hydrogen bonds : angle 5.37955 ( 4089) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.683 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0702 time to fit residues: 11.5708 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 120 optimal weight: 30.0000 chunk 356 optimal weight: 0.1980 chunk 2 optimal weight: 9.9990 chunk 338 optimal weight: 50.0000 chunk 153 optimal weight: 20.0000 chunk 361 optimal weight: 3.9990 chunk 214 optimal weight: 40.0000 chunk 200 optimal weight: 40.0000 chunk 174 optimal weight: 50.0000 chunk 191 optimal weight: 50.0000 chunk 289 optimal weight: 0.0770 overall best weight: 6.8546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.066586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.055618 restraints weight = 139734.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.055732 restraints weight = 101748.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.055776 restraints weight = 79734.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055860 restraints weight = 65314.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.055906 restraints weight = 67095.776| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 18667 Z= 0.148 Angle : 0.421 9.915 25963 Z= 0.260 Chirality : 0.044 0.135 3522 Planarity : 0.002 0.013 3781 Dihedral : 4.324 23.514 3781 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.58 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: 0.40 (0.14), residues: 3774 helix: 1.67 (0.13), residues: 1656 sheet: -1.27 (0.24), residues: 467 loop : -0.68 (0.16), residues: 1651 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00204 (18667) covalent geometry : angle 0.42095 (25963) hydrogen bonds : bond 0.03164 ( 1420) hydrogen bonds : angle 4.72389 ( 4089) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.556 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0727 time to fit residues: 12.0448 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 26 optimal weight: 40.0000 chunk 339 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 244 optimal weight: 0.8980 chunk 273 optimal weight: 30.0000 chunk 92 optimal weight: 30.0000 chunk 54 optimal weight: 6.9990 chunk 103 optimal weight: 30.0000 chunk 5 optimal weight: 10.0000 chunk 3 optimal weight: 50.0000 chunk 298 optimal weight: 40.0000 overall best weight: 9.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.065292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054426 restraints weight = 140825.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.054460 restraints weight = 118930.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054487 restraints weight = 87667.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054558 restraints weight = 78108.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054631 restraints weight = 72317.504| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18667 Z= 0.204 Angle : 0.498 11.858 25963 Z= 0.310 Chirality : 0.045 0.138 3522 Planarity : 0.003 0.017 3781 Dihedral : 5.020 24.905 3781 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.18 (0.14), residues: 3774 helix: 1.21 (0.13), residues: 1651 sheet: -1.43 (0.24), residues: 454 loop : -1.06 (0.16), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00281 (18667) covalent geometry : angle 0.49820 (25963) hydrogen bonds : bond 0.03954 ( 1420) hydrogen bonds : angle 5.32295 ( 4089) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.677 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0712 time to fit residues: 11.7756 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 26 optimal weight: 40.0000 chunk 207 optimal weight: 0.9990 chunk 234 optimal weight: 50.0000 chunk 314 optimal weight: 40.0000 chunk 163 optimal weight: 0.0970 chunk 123 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 19 optimal weight: 50.0000 chunk 196 optimal weight: 10.0000 chunk 153 optimal weight: 50.0000 chunk 49 optimal weight: 40.0000 overall best weight: 9.4190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.065290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054462 restraints weight = 141823.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054693 restraints weight = 103943.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.054701 restraints weight = 74930.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054740 restraints weight = 67293.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.054773 restraints weight = 65338.371| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18667 Z= 0.192 Angle : 0.461 10.358 25963 Z= 0.287 Chirality : 0.045 0.136 3522 Planarity : 0.002 0.014 3781 Dihedral : 4.732 25.291 3781 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.09 (0.14), residues: 3774 helix: 1.32 (0.13), residues: 1652 sheet: -1.44 (0.24), residues: 441 loop : -1.05 (0.16), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00265 (18667) covalent geometry : angle 0.46138 (25963) hydrogen bonds : bond 0.03416 ( 1420) hydrogen bonds : angle 5.04405 ( 4089) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.527 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0717 time to fit residues: 11.7798 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 359 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 118 optimal weight: 50.0000 chunk 369 optimal weight: 50.0000 chunk 196 optimal weight: 3.9990 chunk 30 optimal weight: 50.0000 chunk 358 optimal weight: 50.0000 chunk 302 optimal weight: 50.0000 chunk 179 optimal weight: 9.9990 chunk 301 optimal weight: 50.0000 chunk 33 optimal weight: 0.3980 overall best weight: 18.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.063688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.053337 restraints weight = 142643.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053326 restraints weight = 123448.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.053316 restraints weight = 94559.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053411 restraints weight = 80076.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.053426 restraints weight = 78578.527| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.5701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 18667 Z= 0.376 Angle : 0.689 13.759 25963 Z= 0.439 Chirality : 0.049 0.179 3522 Planarity : 0.004 0.020 3781 Dihedral : 6.341 28.769 3781 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.88 % Favored : 90.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -1.59 (0.13), residues: 3774 helix: 0.01 (0.12), residues: 1618 sheet: -2.01 (0.24), residues: 432 loop : -1.80 (0.15), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00520 (18667) covalent geometry : angle 0.68891 (25963) hydrogen bonds : bond 0.05385 ( 1420) hydrogen bonds : angle 6.53315 ( 4089) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.689 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0820 time to fit residues: 13.6521 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 12 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 242 optimal weight: 30.0000 chunk 201 optimal weight: 30.0000 chunk 129 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 340 optimal weight: 40.0000 chunk 342 optimal weight: 8.9990 chunk 298 optimal weight: 50.0000 chunk 275 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.065136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.054425 restraints weight = 141389.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054563 restraints weight = 113486.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054545 restraints weight = 76444.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.054625 restraints weight = 68672.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054653 restraints weight = 64588.899| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 18667 Z= 0.138 Angle : 0.428 9.431 25963 Z= 0.264 Chirality : 0.044 0.134 3522 Planarity : 0.002 0.011 3781 Dihedral : 4.729 25.804 3781 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.43 (0.14), residues: 3774 helix: 1.13 (0.13), residues: 1643 sheet: -1.82 (0.24), residues: 436 loop : -1.26 (0.16), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00190 (18667) covalent geometry : angle 0.42814 (25963) hydrogen bonds : bond 0.03155 ( 1420) hydrogen bonds : angle 5.07153 ( 4089) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.568 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0742 time to fit residues: 12.2309 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 48 optimal weight: 30.0000 chunk 108 optimal weight: 20.0000 chunk 120 optimal weight: 30.0000 chunk 137 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 315 optimal weight: 7.9990 chunk 211 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 20.0000 chunk 11 optimal weight: 40.0000 chunk 259 optimal weight: 10.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.065006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.054334 restraints weight = 142131.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.054448 restraints weight = 111994.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.054468 restraints weight = 86432.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.054610 restraints weight = 75194.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.054667 restraints weight = 67541.131| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 18667 Z= 0.183 Angle : 0.463 11.127 25963 Z= 0.287 Chirality : 0.045 0.135 3522 Planarity : 0.002 0.012 3781 Dihedral : 4.831 24.663 3781 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.42 (0.14), residues: 3774 helix: 1.16 (0.13), residues: 1651 sheet: -1.84 (0.24), residues: 462 loop : -1.27 (0.16), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00252 (18667) covalent geometry : angle 0.46300 (25963) hydrogen bonds : bond 0.03543 ( 1420) hydrogen bonds : angle 5.18823 ( 4089) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7548 Ramachandran restraints generated. 3774 Oldfield, 0 Emsley, 3774 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.602 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0828 time to fit residues: 13.6573 Evaluate side-chains 82 residues out of total 3253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 172 optimal weight: 50.0000 chunk 234 optimal weight: 50.0000 chunk 40 optimal weight: 30.0000 chunk 180 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 57 optimal weight: 0.5980 chunk 284 optimal weight: 50.0000 chunk 202 optimal weight: 60.0000 chunk 258 optimal weight: 20.0000 overall best weight: 8.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.064674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.054516 restraints weight = 142756.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.054152 restraints weight = 125643.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.054439 restraints weight = 99605.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.054502 restraints weight = 71111.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.054609 restraints weight = 66281.199| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 18667 Z= 0.178 Angle : 0.452 10.934 25963 Z= 0.281 Chirality : 0.045 0.136 3522 Planarity : 0.002 0.012 3781 Dihedral : 4.731 26.151 3781 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % 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 aren not related in a simple way. whole: -0.36 (0.14), residues: 3774 helix: 1.22 (0.13), residues: 1652 sheet: -1.71 (0.24), residues: 454 loop : -1.29 (0.16), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 20 PHE 0.000 0.000 PHE A 22 TRP 0.000 0.000 TRP A 28 Details of bonding type rmsd covalent geometry : bond 0.00244 (18667) covalent geometry : angle 0.45223 (25963) hydrogen bonds : bond 0.03387 ( 1420) hydrogen bonds : angle 5.08383 ( 4089) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2594.40 seconds wall clock time: 44 minutes 51.11 seconds (2691.11 seconds total)