Starting phenix.real_space_refine on Mon Aug 25 18:32:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psg_17852/08_2025/8psg_17852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psg_17852/08_2025/8psg_17852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psg_17852/08_2025/8psg_17852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psg_17852/08_2025/8psg_17852.map" model { file = "/net/cci-nas-00/data/ceres_data/8psg_17852/08_2025/8psg_17852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psg_17852/08_2025/8psg_17852.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 106 5.16 5 C 18870 2.51 5 N 4955 2.21 5 O 5678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.03s 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: 29610 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1223 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 8, 'TRANS': 154} Chain: "G" Number of atoms: 16010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2035, 16010 Classifications: {'peptide': 2035} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1925} Chain breaks: 1 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.29, per 1000 atoms: 0.21 Number of scatterers: 29610 At special positions: 0 Unit cell: (179.35, 181.46, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 106 16.00 P 1 15.00 O 5678 8.00 N 4955 7.00 C 18870 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A1246 " - pdb=" SG CYS A1327 " distance=2.12 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7028 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 30 sheets defined 51.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 2 through 20 Processing helix chain 'A' and resid 31 through 36 removed outlier: 3.711A pdb=" N PHE A 35 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 36 " --> pdb=" O GLN A 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 31 through 36' Processing helix chain 'A' and resid 54 through 65 removed outlier: 3.735A pdb=" N ARG A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.916A pdb=" N ILE A 88 " --> pdb=" O ASP A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 removed outlier: 4.239A pdb=" N ARG A 340 " --> pdb=" O LYS A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 360 Processing helix chain 'A' and resid 360 through 383 removed outlier: 3.756A pdb=" N LYS A 365 " --> pdb=" O PHE A 361 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ASP A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA A 369 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.172A pdb=" N LYS A 410 " --> pdb=" O TRP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 441 Processing helix chain 'A' and resid 444 through 456 removed outlier: 3.779A pdb=" N ILE A 448 " --> pdb=" O ASN A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 463 through 484 removed outlier: 3.860A pdb=" N GLU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 533 through 537 removed outlier: 3.711A pdb=" N LYS A 537 " --> pdb=" O PRO A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.520A pdb=" N GLU A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA A 614 " --> pdb=" O THR A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 669 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.658A 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: 3.600A pdb=" N VAL A 745 " --> pdb=" O SER A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 784 removed outlier: 3.753A pdb=" N ILE A 784 " --> pdb=" O LEU A 781 " (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 838 through 847 removed outlier: 3.967A pdb=" N GLU A 847 " --> pdb=" O LYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.220A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 860 removed outlier: 4.498A pdb=" N ASN A 860 " --> pdb=" O SER A 857 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 857 through 860' Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 906 Processing helix chain 'A' and resid 907 through 909 No H-bonds generated for 'chain 'A' and resid 907 through 909' Processing helix chain 'A' and resid 910 through 920 removed outlier: 3.695A pdb=" N LYS A 919 " --> pdb=" O GLU A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.558A pdb=" N PHE A 932 " --> pdb=" O GLY A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 970 removed outlier: 3.625A pdb=" N LEU A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 removed outlier: 3.802A pdb=" N ALA A 975 " --> pdb=" O SER A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.589A pdb=" N VAL A1001 " --> pdb=" O PRO A 997 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.704A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1017 Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1100 removed outlier: 4.274A pdb=" N LYS A1090 " --> pdb=" O ASP A1086 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1115 through 1118 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1199 removed outlier: 4.208A 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 removed outlier: 3.618A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1243 removed outlier: 4.140A pdb=" N VAL A1243 " --> pdb=" O VAL A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1253 through 1266 removed outlier: 3.942A pdb=" N GLY A1259 " --> pdb=" O SER A1255 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A1263 " --> pdb=" O GLY A1259 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ARG A1264 " --> pdb=" O MET A1260 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A1265 " --> pdb=" O PHE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1279 removed outlier: 3.975A pdb=" N GLU A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1306 through 1321 removed outlier: 3.709A pdb=" N VAL A1312 " --> pdb=" O SER A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1336 through 1346 removed outlier: 3.835A pdb=" N GLU A1342 " --> pdb=" O GLU A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1362 through 1366 removed outlier: 4.386A pdb=" N SER A1366 " --> pdb=" O ALA A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1424 through 1430 removed outlier: 3.502A pdb=" N THR A1427 " --> pdb=" O GLY A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1443 Processing helix chain 'A' and resid 1444 through 1475 Processing helix chain 'A' and resid 1481 through 1510 removed outlier: 3.545A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.559A pdb=" N SER A1554 " --> pdb=" O ASP A1550 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.513A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1601 Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1658 through 1661 Processing helix chain 'A' and resid 1666 through 1695 removed outlier: 3.902A pdb=" N LYS A1682 " --> pdb=" O SER A1678 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER A1683 " --> pdb=" O ALA A1679 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1693 " --> pdb=" O HIS A1689 " (cutoff:3.500A) Processing helix chain 'A' and resid 1710 through 1716 Processing helix chain 'A' and resid 1734 through 1738 removed outlier: 3.714A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.813A 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 removed outlier: 3.509A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1794 through 1801 removed outlier: 3.511A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 removed outlier: 3.629A pdb=" N GLU A1817 " --> pdb=" O TRP A1813 " (cutoff:3.500A) Processing helix chain 'A' and resid 1853 through 1863 removed outlier: 3.596A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 removed outlier: 3.721A pdb=" N LEU B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.915A pdb=" N VAL B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.979A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.738A pdb=" N THR B 212 " --> pdb=" O GLU B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 236 removed outlier: 4.335A pdb=" N SER B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.776A pdb=" N ASP B 262 " --> pdb=" O SER B 258 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.649A pdb=" N ALA G 30 " --> pdb=" O SER G 26 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN G 36 " --> pdb=" O GLN G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 72 Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.536A pdb=" N THR G 89 " --> pdb=" O ASN G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 116 through 133 Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.636A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.867A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG G 200 " --> pdb=" O SER G 196 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 233 through 257 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 267 Processing helix chain 'G' and resid 275 through 286 removed outlier: 4.188A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 314 removed outlier: 3.664A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR G 311 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 331 removed outlier: 3.603A pdb=" N LEU G 324 " --> pdb=" O PRO G 320 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 360 removed outlier: 3.590A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU G 360 " --> pdb=" O THR G 356 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 395 removed outlier: 3.758A pdb=" N LYS G 395 " --> pdb=" O LEU G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 434 Proline residue: G 434 - end of helix Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 451 through 455 Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 491 through 495 removed outlier: 3.953A pdb=" N GLN G 495 " --> pdb=" O THR G 492 " (cutoff:3.500A) Processing helix chain 'G' and resid 507 through 510 Processing helix chain 'G' and resid 511 through 520 removed outlier: 3.819A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.589A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.763A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 613 removed outlier: 3.675A pdb=" N ALA G 609 " --> pdb=" O ASP G 605 " (cutoff:3.500A) Processing helix chain 'G' and resid 626 through 639 Processing helix chain 'G' and resid 655 through 672 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 699 removed outlier: 3.646A pdb=" N LEU G 698 " --> pdb=" O TYR G 694 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY G 699 " --> pdb=" O ILE G 695 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 752 Processing helix chain 'G' and resid 753 through 758 Processing helix chain 'G' and resid 773 through 783 removed outlier: 3.999A 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 790 removed outlier: 3.704A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 806 removed outlier: 3.769A pdb=" N VAL G 805 " --> pdb=" O GLY G 802 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 824 Processing helix chain 'G' and resid 830 through 835 removed outlier: 4.186A pdb=" N GLU G 833 " --> pdb=" O ASP G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 887 removed outlier: 4.389A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix Processing helix chain 'G' and resid 887 through 898 Processing helix chain 'G' and resid 913 through 917 removed outlier: 3.969A pdb=" N MET G 917 " --> pdb=" O LEU G 914 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 930 removed outlier: 3.549A pdb=" N ARG G 925 " --> pdb=" O GLU G 921 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 957 removed outlier: 3.515A pdb=" N ARG G 944 " --> pdb=" O ASP G 940 " (cutoff:3.500A) Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 removed outlier: 3.679A pdb=" N ASP G1001 " --> pdb=" O ALA G 997 " (cutoff:3.500A) Processing helix chain 'G' and resid 1024 through 1031 removed outlier: 3.589A pdb=" N PHE G1028 " --> pdb=" O ARG G1024 " (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 removed outlier: 3.515A pdb=" N HIS G1087 " --> pdb=" O LYS G1083 " (cutoff:3.500A) Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 removed outlier: 3.653A pdb=" N ALA G1152 " --> pdb=" O ASN G1148 " (cutoff:3.500A) Processing helix chain 'G' and resid 1168 through 1174 removed outlier: 3.712A pdb=" N LYS G1172 " --> pdb=" O ASN G1168 " (cutoff:3.500A) Processing helix chain 'G' and resid 1189 through 1192 Processing helix chain 'G' and resid 1258 through 1271 removed outlier: 3.844A pdb=" N LEU G1269 " --> pdb=" O MET G1265 " (cutoff:3.500A) Processing helix chain 'G' and resid 1294 through 1305 removed outlier: 4.096A pdb=" N PHE G1300 " --> pdb=" O GLU G1296 " (cutoff:3.500A) Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1325 through 1330 Processing helix chain 'G' and resid 1330 through 1335 Processing helix chain 'G' and resid 1336 through 1339 Processing helix chain 'G' and resid 1439 through 1447 Processing helix chain 'G' and resid 1514 through 1524 removed outlier: 3.864A pdb=" N ARG G1522 " --> pdb=" O ASP G1518 " (cutoff:3.500A) Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.636A 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 removed outlier: 4.600A pdb=" N LEU G1592 " --> pdb=" O SER G1588 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TRP G1596 " --> pdb=" O LEU G1592 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA G1597 " --> pdb=" O ILE G1593 " (cutoff:3.500A) Processing helix chain 'G' and resid 1677 through 1684 Processing helix chain 'G' and resid 1684 through 1702 removed outlier: 3.523A pdb=" N GLN G1688 " --> pdb=" O SER G1684 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 removed outlier: 3.519A pdb=" N ILE G1709 " --> pdb=" O SER G1705 " (cutoff:3.500A) Processing helix chain 'G' and resid 1723 through 1734 removed outlier: 3.650A pdb=" N LYS G1727 " --> pdb=" O GLY G1723 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG G1728 " --> pdb=" O GLU G1724 " (cutoff:3.500A) Processing helix chain 'G' and resid 1769 through 1772 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1819 removed outlier: 3.838A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1841 removed outlier: 3.822A pdb=" N GLU G1829 " --> pdb=" O GLU G1825 " (cutoff:3.500A) Processing helix chain 'G' and resid 1858 through 1862 removed outlier: 3.660A pdb=" N VAL G1862 " --> pdb=" O PRO G1859 " (cutoff:3.500A) Processing helix chain 'G' and resid 1867 through 1882 removed outlier: 3.514A pdb=" N LEU G1871 " --> pdb=" O SER G1867 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLN G1872 " --> pdb=" O GLN G1868 " (cutoff:3.500A) Processing helix chain 'G' and resid 1909 through 1921 removed outlier: 3.652A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU G1919 " --> pdb=" O ASN G1915 " (cutoff:3.500A) Processing helix chain 'G' and resid 1926 through 1931 Processing helix chain 'G' and resid 1935 through 1950 removed outlier: 3.625A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1985 through 1996 removed outlier: 3.510A pdb=" N LYS G1989 " --> pdb=" O VAL G1985 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER G1990 " --> pdb=" O LYS G1986 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N LYS G1994 " --> pdb=" O SER G1990 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN G1995 " --> pdb=" O PHE G1991 " (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 removed outlier: 3.725A pdb=" N LYS G2039 " --> pdb=" O SER G2035 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE G2041 " --> pdb=" O PRO G2037 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN G2044 " --> pdb=" O GLU G2040 " (cutoff:3.500A) Processing helix chain 'G' and resid 2044 through 2050 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.429A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLY G1902 " --> pdb=" O GLY G1853 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 79 removed outlier: 6.015A pdb=" N VAL A 44 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N PHE G1804 " --> pdb=" O ILE G2011 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 401 through 402 removed outlier: 6.937A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA5, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA6, first strand: chain 'A' and resid 649 through 651 removed outlier: 6.957A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA8, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA9, first strand: chain 'A' and resid 1019 through 1027 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1019 through 1027 current: chain 'A' and resid 1381 through 1389 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1381 through 1389 current: chain 'A' and resid 1572 through 1575 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1624 through 1625 current: chain 'A' and resid 1650 through 1656 Processing sheet with id=AB1, first strand: chain 'A' and resid 1060 through 1066 Processing sheet with id=AB2, first strand: chain 'A' and resid 1103 through 1105 removed outlier: 3.855A pdb=" N ARG A1104 " --> pdb=" O ALA A1186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB4, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB5, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB6, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB7, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB8, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB9, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.835A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 269 through 272 removed outlier: 7.059A pdb=" N LEU G 156 " --> pdb=" O GLY G 269 " (cutoff:3.500A) removed outlier: 8.947A pdb=" N THR G 271 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ALA G 158 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL G 157 " --> pdb=" O LEU G 502 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 338 through 342 removed outlier: 6.477A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 568 through 571 removed outlier: 3.816A pdb=" N LYS G 568 " --> pdb=" O GLU G 580 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE G 570 " --> pdb=" O PHE G 578 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 592 through 593 removed outlier: 3.588A pdb=" N LEU G 800 " --> pdb=" O PHE G 767 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.689A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC7, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC8, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.592A pdb=" N VAL G1195 " --> pdb=" O ILE G1210 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE G1210 " --> pdb=" O VAL G1195 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU G1197 " --> pdb=" O THR G1208 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N PHE G1158 " --> pdb=" O ILE G1251 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLU G1253 " --> pdb=" O PHE G1158 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR G1160 " --> pdb=" O GLU G1253 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1285 through 1291 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1285 through 1291 current: chain 'G' and resid 1387 through 1393 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1387 through 1393 current: chain 'G' and resid 1401 through 1413 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1401 through 1413 current: chain 'G' and resid 1635 through 1643 removed outlier: 3.570A pdb=" N PHE G1640 " --> pdb=" O GLY G1653 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY G1653 " --> pdb=" O PHE G1640 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1431 through 1434 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 1431 through 1434 current: chain 'G' and resid 1482 through 1492 removed outlier: 6.662A pdb=" N CYS G1485 " --> pdb=" O ASP G1505 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP G1505 " --> pdb=" O CYS G1485 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY G1487 " --> pdb=" O ILE G1503 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE G1503 " --> pdb=" O GLY G1487 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE G1489 " --> pdb=" O ILE G1501 " (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 1741 removed outlier: 3.697A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LYS G1747 " --> pdb=" O THR G1740 " (cutoff:3.500A) 1288 hydrogen bonds defined for protein. 3597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.24 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 8217 1.34 - 1.49: 6518 1.49 - 1.63: 15306 1.63 - 1.78: 0 1.78 - 1.93: 187 Bond restraints: 30228 Sorted by residual: bond pdb=" CD GLU A1026 " pdb=" OE1 GLU A1026 " ideal model delta sigma weight residual 1.249 1.378 -0.129 1.90e-02 2.77e+03 4.62e+01 bond pdb=" C TYR A1174 " pdb=" O TYR A1174 " ideal model delta sigma weight residual 1.236 1.293 -0.057 1.14e-02 7.69e+03 2.53e+01 bond pdb=" CG MET A1121 " pdb=" SD MET A1121 " ideal model delta sigma weight residual 1.803 1.926 -0.123 2.50e-02 1.60e+03 2.41e+01 bond pdb=" N ILE G1798 " pdb=" CA ILE G1798 " ideal model delta sigma weight residual 1.460 1.496 -0.036 7.60e-03 1.73e+04 2.25e+01 bond pdb=" N ILE G2011 " pdb=" CA ILE G2011 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.70e-03 1.69e+04 2.24e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.04: 36575 3.04 - 6.08: 4281 6.08 - 9.12: 82 9.12 - 12.16: 5 12.16 - 15.20: 1 Bond angle restraints: 40944 Sorted by residual: angle pdb=" CB GLU A 364 " pdb=" CG GLU A 364 " pdb=" CD GLU A 364 " ideal model delta sigma weight residual 112.60 127.80 -15.20 1.70e+00 3.46e-01 8.00e+01 angle pdb=" CB GLU A1317 " pdb=" CG GLU A1317 " pdb=" CD GLU A1317 " ideal model delta sigma weight residual 112.60 124.76 -12.16 1.70e+00 3.46e-01 5.12e+01 angle pdb=" CB GLU A1338 " pdb=" CG GLU A1338 " pdb=" CD GLU A1338 " ideal model delta sigma weight residual 112.60 124.40 -11.80 1.70e+00 3.46e-01 4.81e+01 angle pdb=" CA THR A1282 " pdb=" CB THR A1282 " pdb=" OG1 THR A1282 " ideal model delta sigma weight residual 109.60 99.51 10.09 1.50e+00 4.44e-01 4.53e+01 angle pdb=" CA ASP G1820 " pdb=" CB ASP G1820 " pdb=" CG ASP G1820 " ideal model delta sigma weight residual 112.60 118.55 -5.95 1.00e+00 1.00e+00 3.54e+01 ... (remaining 40939 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 16401 17.80 - 35.60: 1464 35.60 - 53.40: 279 53.40 - 71.21: 70 71.21 - 89.01: 38 Dihedral angle restraints: 18252 sinusoidal: 7340 harmonic: 10912 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual -86.00 -18.51 -67.49 1 1.00e+01 1.00e-02 5.92e+01 dihedral pdb=" CA CYS A1327 " pdb=" C CYS A1327 " pdb=" N ILE A1328 " pdb=" CA ILE A1328 " ideal model delta harmonic sigma weight residual 180.00 151.77 28.23 0 5.00e+00 4.00e-02 3.19e+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 -152.27 -27.73 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 18249 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1848 0.053 - 0.106: 1651 0.106 - 0.160: 869 0.160 - 0.213: 209 0.213 - 0.266: 26 Chirality restraints: 4603 Sorted by residual: chirality pdb=" CA VAL A1302 " pdb=" N VAL A1302 " pdb=" C VAL A1302 " pdb=" CB VAL A1302 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A1403 " pdb=" N ILE A1403 " pdb=" C ILE A1403 " pdb=" CB ILE A1403 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 4600 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " -0.029 2.00e-02 2.50e+03 2.00e-02 1.80e+01 pdb=" C10 FMN G2101 " 0.014 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.018 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.007 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.023 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " -0.006 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.014 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.034 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.002 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.011 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.017 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.028 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.005 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.031 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.023 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.029 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 753 " 0.049 2.00e-02 2.50e+03 2.71e-02 1.47e+01 pdb=" CG TYR A 753 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 753 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A 753 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR A 753 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 753 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 753 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 753 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1286 " 0.049 2.00e-02 2.50e+03 2.32e-02 1.34e+01 pdb=" CG TRP A1286 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A1286 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A1286 " -0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A1286 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1286 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A1286 " -0.022 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1286 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1286 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A1286 " 0.012 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1088 2.71 - 3.26: 30248 3.26 - 3.81: 46852 3.81 - 4.35: 64396 4.35 - 4.90: 103940 Nonbonded interactions: 246524 Sorted by model distance: nonbonded pdb=" OH TYR G 754 " pdb=" O PRO G 795 " model vdw 2.169 3.040 nonbonded pdb=" NH2 ARG G 888 " pdb=" OD1 ASP G 913 " model vdw 2.196 3.120 nonbonded pdb=" OD2 ASP A1534 " pdb=" OG SER A1567 " model vdw 2.223 3.040 nonbonded pdb=" NE2 HIS B 152 " pdb=" O LEU B 163 " model vdw 2.230 3.120 nonbonded pdb=" O GLY G 768 " pdb=" OG SER G 769 " model vdw 2.263 3.040 ... (remaining 246519 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 28.070 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.080 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: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.129 30229 Z= 1.046 Angle : 1.887 15.203 40946 Z= 1.375 Chirality : 0.087 0.266 4603 Planarity : 0.006 0.028 5286 Dihedral : 14.820 89.007 11221 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.31 % Favored : 92.37 % Rotamer: Outliers : 0.65 % Allowed : 4.62 % Favored : 94.73 % 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: -3.71 (0.11), residues: 3761 helix: -2.77 (0.09), residues: 1599 sheet: -2.57 (0.22), residues: 448 loop : -1.93 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G1834 TYR 0.054 0.006 TYR A 753 PHE 0.048 0.005 PHE A1376 TRP 0.049 0.006 TRP A1286 HIS 0.018 0.003 HIS A1689 Details of bonding type rmsd covalent geometry : bond 0.01389 (30228) covalent geometry : angle 1.88516 (40944) SS BOND : bond 0.08652 ( 1) SS BOND : angle 10.60502 ( 2) hydrogen bonds : bond 0.21933 ( 1288) hydrogen bonds : angle 9.45996 ( 3597) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 267 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8436 (ttp) cc_final: 0.8196 (ttt) REVERT: A 529 MET cc_start: 0.9514 (mmp) cc_final: 0.9281 (mmm) REVERT: A 746 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9324 (mt-10) REVERT: A 1121 MET cc_start: 0.3628 (tpt) cc_final: 0.1496 (tpt) REVERT: A 1268 GLU cc_start: 0.8188 (mp0) cc_final: 0.7968 (mp0) REVERT: A 1313 ASP cc_start: 0.9157 (t0) cc_final: 0.8782 (t0) REVERT: A 1317 GLU cc_start: 0.7258 (tt0) cc_final: 0.6520 (tt0) REVERT: A 1561 MET cc_start: 0.9365 (mmm) cc_final: 0.8925 (mmm) REVERT: A 1711 GLU cc_start: 0.7093 (tm-30) cc_final: 0.6777 (tp30) REVERT: A 1742 ASP cc_start: 0.9104 (m-30) cc_final: 0.8848 (m-30) REVERT: A 1817 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7421 (mt-10) REVERT: B 174 ASP cc_start: 0.7865 (t0) cc_final: 0.6811 (t70) REVERT: B 208 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.8463 (pp20) REVERT: B 243 ILE cc_start: 0.7553 (OUTLIER) cc_final: 0.7344 (mm) REVERT: B 251 GLN cc_start: 0.8515 (mm-40) cc_final: 0.8271 (mm-40) REVERT: B 292 GLN cc_start: 0.8558 (pp30) cc_final: 0.7590 (mm-40) REVERT: G 752 GLN cc_start: 0.9474 (mt0) cc_final: 0.8989 (tm-30) REVERT: G 764 MET cc_start: 0.9241 (mtm) cc_final: 0.8931 (mtm) REVERT: G 784 GLU cc_start: 0.9485 (pt0) cc_final: 0.9118 (tm-30) REVERT: G 917 MET cc_start: 0.9455 (mtt) cc_final: 0.9218 (mtt) REVERT: G 1136 GLU cc_start: 0.9306 (mp0) cc_final: 0.9021 (mp0) REVERT: G 1180 MET cc_start: 0.6939 (mtp) cc_final: 0.6550 (mtp) REVERT: G 1221 MET cc_start: 0.9004 (tmm) cc_final: 0.8656 (tmm) REVERT: G 1323 MET cc_start: 0.2488 (mmt) cc_final: 0.1518 (mmt) REVERT: G 1467 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8770 (mp0) REVERT: G 1676 MET cc_start: 0.7362 (mtt) cc_final: 0.6219 (mtt) REVERT: G 1678 MET cc_start: 0.8416 (mmp) cc_final: 0.8103 (mmm) REVERT: G 2036 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8423 (tm-30) outliers start: 21 outliers final: 9 residues processed: 279 average time/residue: 0.1765 time to fit residues: 80.7230 Evaluate side-chains 206 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1355 GLU Chi-restraints excluded: chain B residue 208 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 410 SER Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 0.0670 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.0970 chunk 298 optimal weight: 6.9990 overall best weight: 1.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 506 ASN A 527 GLN A1123 GLN A1385 GLN A1433 HIS A1482 GLN A1577 GLN A1780 ASN A1783 ASN A1790 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN G 79 GLN G 102 HIS G 245 GLN G 248 HIS G 275 GLN G 718 ASN G 747 HIS G 752 GLN G 900 GLN G 908 ASN G1008 GLN G1055 HIS G1078 HIS G1226 ASN G1307 ASN G1451 GLN G1674 GLN G1697 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1912 ASN G1915 ASN G2020 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.083796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.062086 restraints weight = 127205.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063294 restraints weight = 63256.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.063541 restraints weight = 36727.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063709 restraints weight = 35836.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063773 restraints weight = 30888.290| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 30229 Z= 0.128 Angle : 0.566 8.897 40946 Z= 0.301 Chirality : 0.042 0.262 4603 Planarity : 0.004 0.036 5286 Dihedral : 5.445 71.096 4050 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.21 % Favored : 97.69 % Rotamer: Outliers : 0.74 % Allowed : 7.30 % Favored : 91.96 % 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: -1.08 (0.13), residues: 3761 helix: -0.08 (0.12), residues: 1678 sheet: -1.97 (0.21), residues: 489 loop : -0.83 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1023 TYR 0.018 0.001 TYR A 417 PHE 0.019 0.001 PHE G 64 TRP 0.023 0.002 TRP G 661 HIS 0.004 0.001 HIS G1697 Details of bonding type rmsd covalent geometry : bond 0.00259 (30228) covalent geometry : angle 0.56559 (40944) SS BOND : bond 0.00784 ( 1) SS BOND : angle 3.85602 ( 2) hydrogen bonds : bond 0.04230 ( 1288) hydrogen bonds : angle 5.15391 ( 3597) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8535 (ttp) cc_final: 0.8334 (ttt) REVERT: A 451 MET cc_start: 0.8249 (mtp) cc_final: 0.8044 (mtp) REVERT: A 1317 GLU cc_start: 0.6111 (tt0) cc_final: 0.5492 (tm-30) REVERT: A 1742 ASP cc_start: 0.8377 (m-30) cc_final: 0.8019 (m-30) REVERT: B 174 ASP cc_start: 0.7458 (t0) cc_final: 0.6266 (t70) REVERT: B 203 GLU cc_start: 0.8258 (tp30) cc_final: 0.7722 (tp30) REVERT: B 229 LEU cc_start: 0.8504 (mt) cc_final: 0.8117 (pp) REVERT: B 237 MET cc_start: 0.8519 (mmt) cc_final: 0.8304 (mmp) REVERT: B 243 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7315 (mm) REVERT: B 292 GLN cc_start: 0.8391 (pp30) cc_final: 0.7700 (mm-40) REVERT: G 714 SER cc_start: 0.9000 (OUTLIER) cc_final: 0.8768 (p) REVERT: G 764 MET cc_start: 0.8622 (mtm) cc_final: 0.8362 (mtm) REVERT: G 870 GLU cc_start: 0.8921 (pm20) cc_final: 0.8685 (pm20) REVERT: G 1136 GLU cc_start: 0.8931 (mp0) cc_final: 0.8683 (mp0) REVERT: G 1221 MET cc_start: 0.8472 (tmm) cc_final: 0.8071 (tmm) REVERT: G 1265 MET cc_start: 0.8649 (tmm) cc_final: 0.7717 (ptp) REVERT: G 1323 MET cc_start: 0.1951 (mmt) cc_final: 0.1678 (mmt) REVERT: G 1676 MET cc_start: 0.7303 (mtt) cc_final: 0.6283 (mtt) outliers start: 24 outliers final: 11 residues processed: 249 average time/residue: 0.1751 time to fit residues: 71.6146 Evaluate side-chains 226 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 213 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1609 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 93 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 333 optimal weight: 40.0000 chunk 361 optimal weight: 30.0000 chunk 305 optimal weight: 0.9990 chunk 197 optimal weight: 9.9990 chunk 160 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 338 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 350 GLN G 896 ASN ** G1778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.083129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061939 restraints weight = 127985.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062386 restraints weight = 61003.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.063028 restraints weight = 38968.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063143 restraints weight = 33171.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.063173 restraints weight = 30672.026| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30229 Z= 0.153 Angle : 0.538 8.226 40946 Z= 0.280 Chirality : 0.042 0.309 4603 Planarity : 0.004 0.046 5286 Dihedral : 4.813 59.651 4036 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.19 % Favored : 96.73 % Rotamer: Outliers : 1.08 % Allowed : 8.72 % Favored : 90.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.30 (0.14), residues: 3761 helix: 0.76 (0.13), residues: 1689 sheet: -1.62 (0.22), residues: 488 loop : -0.66 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1566 TYR 0.019 0.001 TYR G2030 PHE 0.013 0.001 PHE A 386 TRP 0.021 0.001 TRP G 661 HIS 0.005 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00342 (30228) covalent geometry : angle 0.53744 (40944) SS BOND : bond 0.01027 ( 1) SS BOND : angle 3.76680 ( 2) hydrogen bonds : bond 0.03777 ( 1288) hydrogen bonds : angle 4.79812 ( 3597) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 222 time to evaluate : 0.925 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8564 (ttp) cc_final: 0.8332 (ttt) REVERT: A 960 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7889 (tp30) REVERT: A 1121 MET cc_start: 0.2306 (tpt) cc_final: 0.2082 (tpt) REVERT: A 1317 GLU cc_start: 0.5883 (tt0) cc_final: 0.5383 (tm-30) REVERT: A 1817 GLU cc_start: 0.6872 (mt-10) cc_final: 0.6630 (mt-10) REVERT: B 174 ASP cc_start: 0.7328 (t0) cc_final: 0.6435 (t0) REVERT: B 175 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8123 (mm) REVERT: B 203 GLU cc_start: 0.8319 (tp30) cc_final: 0.7882 (tp30) REVERT: B 229 LEU cc_start: 0.8570 (mt) cc_final: 0.8220 (pp) REVERT: B 237 MET cc_start: 0.8525 (mmt) cc_final: 0.8029 (mmm) REVERT: B 243 ILE cc_start: 0.7529 (OUTLIER) cc_final: 0.7228 (mm) REVERT: B 251 GLN cc_start: 0.8567 (mm-40) cc_final: 0.8325 (mm-40) REVERT: B 292 GLN cc_start: 0.8418 (pp30) cc_final: 0.7708 (mm-40) REVERT: G 285 GLU cc_start: 0.7636 (mm-30) cc_final: 0.6812 (mm-30) REVERT: G 714 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8519 (p) REVERT: G 1136 GLU cc_start: 0.9034 (mp0) cc_final: 0.8779 (mp0) REVERT: G 1221 MET cc_start: 0.8477 (tmm) cc_final: 0.8031 (tmm) REVERT: G 1676 MET cc_start: 0.7039 (mtt) cc_final: 0.6752 (mtt) REVERT: G 1838 MET cc_start: 0.8400 (mtp) cc_final: 0.8126 (tmm) outliers start: 35 outliers final: 17 residues processed: 248 average time/residue: 0.1580 time to fit residues: 65.4833 Evaluate side-chains 214 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 250 optimal weight: 6.9990 chunk 322 optimal weight: 30.0000 chunk 69 optimal weight: 3.9990 chunk 239 optimal weight: 10.0000 chunk 299 optimal weight: 20.0000 chunk 58 optimal weight: 8.9990 chunk 364 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 136 optimal weight: 3.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 798 ASN A1652 GLN A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1220 GLN ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1896 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.082292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.061346 restraints weight = 127835.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061759 restraints weight = 59532.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.062178 restraints weight = 39947.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.062324 restraints weight = 34447.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.062433 restraints weight = 32607.404| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30229 Z= 0.200 Angle : 0.561 8.714 40946 Z= 0.292 Chirality : 0.042 0.301 4603 Planarity : 0.004 0.043 5286 Dihedral : 4.833 58.063 4035 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.92 % Favored : 97.00 % Rotamer: Outliers : 1.17 % Allowed : 10.63 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.08 (0.14), residues: 3761 helix: 0.93 (0.13), residues: 1698 sheet: -1.51 (0.22), residues: 482 loop : -0.55 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1834 TYR 0.026 0.002 TYR B 249 PHE 0.015 0.001 PHE A1376 TRP 0.021 0.001 TRP G 661 HIS 0.005 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00447 (30228) covalent geometry : angle 0.56049 (40944) SS BOND : bond 0.01273 ( 1) SS BOND : angle 4.14172 ( 2) hydrogen bonds : bond 0.03741 ( 1288) hydrogen bonds : angle 4.77241 ( 3597) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 214 time to evaluate : 1.170 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8529 (ttp) cc_final: 0.8285 (ttt) REVERT: A 960 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: A 1120 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5880 (mt-10) REVERT: A 1121 MET cc_start: 0.2621 (tpt) cc_final: 0.2367 (tpt) REVERT: A 1817 GLU cc_start: 0.6888 (mt-10) cc_final: 0.6589 (mt-10) REVERT: B 174 ASP cc_start: 0.7480 (t0) cc_final: 0.6532 (t0) REVERT: B 203 GLU cc_start: 0.8308 (tp30) cc_final: 0.7835 (tp30) REVERT: B 229 LEU cc_start: 0.8526 (mt) cc_final: 0.8203 (pp) REVERT: B 237 MET cc_start: 0.8528 (mmt) cc_final: 0.8041 (mmm) REVERT: B 243 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7213 (mm) REVERT: B 292 GLN cc_start: 0.8485 (pp30) cc_final: 0.7708 (mm110) REVERT: G 285 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7196 (mm-30) REVERT: G 714 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8632 (p) REVERT: G 1136 GLU cc_start: 0.8989 (mp0) cc_final: 0.8737 (mp0) REVERT: G 1221 MET cc_start: 0.8299 (tmm) cc_final: 0.7237 (tmm) REVERT: G 1676 MET cc_start: 0.7355 (mtt) cc_final: 0.7099 (mtt) REVERT: G 1838 MET cc_start: 0.8312 (mtp) cc_final: 0.8091 (tmm) outliers start: 38 outliers final: 23 residues processed: 241 average time/residue: 0.1671 time to fit residues: 67.2759 Evaluate side-chains 221 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 50.0000 chunk 46 optimal weight: 8.9990 chunk 240 optimal weight: 7.9990 chunk 351 optimal weight: 10.0000 chunk 66 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1039 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2027 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061465 restraints weight = 127964.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061803 restraints weight = 61180.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062263 restraints weight = 40969.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.062414 restraints weight = 34215.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062486 restraints weight = 32874.943| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30229 Z= 0.188 Angle : 0.555 8.766 40946 Z= 0.287 Chirality : 0.042 0.199 4603 Planarity : 0.004 0.051 5286 Dihedral : 4.778 58.934 4035 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.48 % Allowed : 11.68 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.03 (0.14), residues: 3761 helix: 1.01 (0.13), residues: 1689 sheet: -1.36 (0.22), residues: 480 loop : -0.50 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1834 TYR 0.014 0.001 TYR G1833 PHE 0.014 0.001 PHE A1376 TRP 0.020 0.001 TRP G 661 HIS 0.005 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00419 (30228) covalent geometry : angle 0.55419 (40944) SS BOND : bond 0.01248 ( 1) SS BOND : angle 4.04534 ( 2) hydrogen bonds : bond 0.03627 ( 1288) hydrogen bonds : angle 4.71524 ( 3597) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 210 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8541 (ttp) cc_final: 0.8291 (ttt) REVERT: A 960 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 1120 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5898 (mt-10) REVERT: A 1561 MET cc_start: 0.8567 (mmm) cc_final: 0.8192 (mmm) REVERT: B 174 ASP cc_start: 0.7509 (t0) cc_final: 0.6569 (t0) REVERT: B 203 GLU cc_start: 0.8426 (tp30) cc_final: 0.7906 (tp30) REVERT: B 229 LEU cc_start: 0.8566 (mt) cc_final: 0.8231 (pp) REVERT: B 237 MET cc_start: 0.8466 (mmt) cc_final: 0.7979 (mmm) REVERT: B 243 ILE cc_start: 0.7550 (OUTLIER) cc_final: 0.7272 (mm) REVERT: B 292 GLN cc_start: 0.8583 (pp30) cc_final: 0.7774 (mm110) REVERT: G 454 ASP cc_start: 0.8368 (t0) cc_final: 0.8138 (t0) REVERT: G 714 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8546 (m) REVERT: G 764 MET cc_start: 0.8633 (mtm) cc_final: 0.8331 (mtm) REVERT: G 1001 ASP cc_start: 0.8288 (m-30) cc_final: 0.8050 (t0) REVERT: G 1136 GLU cc_start: 0.9100 (mp0) cc_final: 0.8784 (mp0) REVERT: G 1221 MET cc_start: 0.8233 (tmm) cc_final: 0.7127 (tmm) outliers start: 48 outliers final: 30 residues processed: 244 average time/residue: 0.1640 time to fit residues: 66.8672 Evaluate side-chains 227 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1678 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1257 ASP Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 0 optimal weight: 40.0000 chunk 116 optimal weight: 2.9990 chunk 274 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 157 optimal weight: 0.7980 chunk 326 optimal weight: 40.0000 chunk 204 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 321 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.082677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061321 restraints weight = 127238.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.062305 restraints weight = 62045.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062642 restraints weight = 36967.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.062770 restraints weight = 33866.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062868 restraints weight = 31711.509| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30229 Z= 0.163 Angle : 0.550 11.606 40946 Z= 0.281 Chirality : 0.042 0.210 4603 Planarity : 0.004 0.053 5286 Dihedral : 4.700 58.782 4035 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 1.33 % Allowed : 12.73 % Favored : 85.95 % 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: 0.15 (0.14), residues: 3761 helix: 1.09 (0.13), residues: 1699 sheet: -1.29 (0.22), residues: 481 loop : -0.43 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G1834 TYR 0.026 0.001 TYR G1762 PHE 0.013 0.001 PHE A1376 TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00366 (30228) covalent geometry : angle 0.54902 (40944) SS BOND : bond 0.01169 ( 1) SS BOND : angle 3.85480 ( 2) hydrogen bonds : bond 0.03498 ( 1288) hydrogen bonds : angle 4.63352 ( 3597) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8494 (ttp) cc_final: 0.8231 (ttt) REVERT: A 960 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7885 (tp30) REVERT: A 1120 GLU cc_start: 0.6585 (OUTLIER) cc_final: 0.5894 (mt-10) REVERT: A 1561 MET cc_start: 0.8538 (mmm) cc_final: 0.8325 (mmm) REVERT: B 203 GLU cc_start: 0.8404 (tp30) cc_final: 0.8120 (tp30) REVERT: B 229 LEU cc_start: 0.8567 (mt) cc_final: 0.8249 (pp) REVERT: B 237 MET cc_start: 0.8381 (mmt) cc_final: 0.7880 (mmm) REVERT: B 292 GLN cc_start: 0.8587 (pp30) cc_final: 0.7776 (mm110) REVERT: G 285 GLU cc_start: 0.7492 (mm-30) cc_final: 0.7259 (mm-30) REVERT: G 714 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8659 (p) REVERT: G 1001 ASP cc_start: 0.8278 (m-30) cc_final: 0.8051 (t0) REVERT: G 1136 GLU cc_start: 0.9102 (mp0) cc_final: 0.8770 (mp0) REVERT: G 1198 SER cc_start: 0.8978 (OUTLIER) cc_final: 0.8645 (p) REVERT: G 1221 MET cc_start: 0.8202 (tmm) cc_final: 0.7925 (tmm) REVERT: G 1265 MET cc_start: 0.8634 (tmm) cc_final: 0.8248 (ppp) outliers start: 43 outliers final: 26 residues processed: 237 average time/residue: 0.1746 time to fit residues: 69.0116 Evaluate side-chains 224 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 194 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 960 GLU Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain A residue 1678 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1602 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 267 optimal weight: 2.9990 chunk 176 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 247 optimal weight: 0.4980 chunk 367 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 204 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 271 optimal weight: 8.9990 chunk 363 optimal weight: 0.8980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1434 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1890 ASN G2027 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.083279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.061946 restraints weight = 126151.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.062990 restraints weight = 61575.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.063203 restraints weight = 36306.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.063398 restraints weight = 36316.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.063430 restraints weight = 31434.658| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 30229 Z= 0.128 Angle : 0.541 11.672 40946 Z= 0.275 Chirality : 0.041 0.267 4603 Planarity : 0.004 0.056 5286 Dihedral : 4.539 57.978 4033 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.14 % Allowed : 13.41 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.14), residues: 3761 helix: 1.21 (0.13), residues: 1697 sheet: -1.15 (0.23), residues: 479 loop : -0.39 (0.16), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G1834 TYR 0.023 0.001 TYR G1833 PHE 0.013 0.001 PHE G 946 TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00288 (30228) covalent geometry : angle 0.54047 (40944) SS BOND : bond 0.00999 ( 1) SS BOND : angle 3.46621 ( 2) hydrogen bonds : bond 0.03341 ( 1288) hydrogen bonds : angle 4.54757 ( 3597) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 214 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8417 (ttp) cc_final: 0.8143 (ttt) REVERT: A 1120 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.6372 (tp30) REVERT: A 1262 LYS cc_start: 0.5622 (mptt) cc_final: 0.5271 (mptt) REVERT: B 203 GLU cc_start: 0.8402 (tp30) cc_final: 0.8096 (tp30) REVERT: B 229 LEU cc_start: 0.8535 (mt) cc_final: 0.8205 (pp) REVERT: B 237 MET cc_start: 0.8318 (mmt) cc_final: 0.7824 (mmm) REVERT: B 292 GLN cc_start: 0.8619 (pp30) cc_final: 0.7779 (mm110) REVERT: G 285 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7239 (mm-30) REVERT: G 714 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8578 (m) REVERT: G 764 MET cc_start: 0.8534 (mtm) cc_final: 0.8254 (mtm) REVERT: G 1001 ASP cc_start: 0.8255 (m-30) cc_final: 0.8043 (t0) REVERT: G 1136 GLU cc_start: 0.9088 (mp0) cc_final: 0.8755 (mp0) REVERT: G 1198 SER cc_start: 0.8924 (OUTLIER) cc_final: 0.8591 (p) REVERT: G 1221 MET cc_start: 0.8115 (tmm) cc_final: 0.7778 (tmm) REVERT: G 1265 MET cc_start: 0.8637 (tmm) cc_final: 0.7713 (ptp) outliers start: 37 outliers final: 24 residues processed: 242 average time/residue: 0.1774 time to fit residues: 72.5843 Evaluate side-chains 228 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1481 SER Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 0 optimal weight: 30.0000 chunk 225 optimal weight: 0.1980 chunk 112 optimal weight: 3.9990 chunk 78 optimal weight: 6.9990 chunk 177 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 243 optimal weight: 10.0000 chunk 182 optimal weight: 20.0000 chunk 74 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 overall best weight: 5.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1939 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.082345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.061443 restraints weight = 128399.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.061730 restraints weight = 62961.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.062272 restraints weight = 41223.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062535 restraints weight = 34291.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062526 restraints weight = 32513.702| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30229 Z= 0.199 Angle : 0.588 11.143 40946 Z= 0.299 Chirality : 0.043 0.300 4603 Planarity : 0.004 0.054 5286 Dihedral : 4.634 59.099 4033 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.14 % Favored : 96.81 % Rotamer: Outliers : 1.36 % Allowed : 13.53 % Favored : 85.12 % 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: 0.24 (0.14), residues: 3761 helix: 1.16 (0.13), residues: 1696 sheet: -1.21 (0.23), residues: 474 loop : -0.39 (0.16), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1566 TYR 0.027 0.002 TYR G1762 PHE 0.015 0.001 PHE A1376 TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00447 (30228) covalent geometry : angle 0.58704 (40944) SS BOND : bond 0.01260 ( 1) SS BOND : angle 4.05658 ( 2) hydrogen bonds : bond 0.03535 ( 1288) hydrogen bonds : angle 4.65195 ( 3597) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 206 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8440 (ttp) cc_final: 0.8151 (ttt) REVERT: A 440 MET cc_start: 0.8837 (mmt) cc_final: 0.8519 (mmt) REVERT: A 1120 GLU cc_start: 0.6377 (OUTLIER) cc_final: 0.6156 (tp30) REVERT: A 1121 MET cc_start: 0.2069 (tpt) cc_final: 0.1444 (tpt) REVERT: A 1561 MET cc_start: 0.8508 (mmm) cc_final: 0.8148 (mmm) REVERT: B 229 LEU cc_start: 0.8544 (mt) cc_final: 0.8213 (pp) REVERT: B 237 MET cc_start: 0.8315 (mmt) cc_final: 0.7874 (mmm) REVERT: B 292 GLN cc_start: 0.8627 (pp30) cc_final: 0.7786 (mm110) REVERT: G 714 SER cc_start: 0.8945 (OUTLIER) cc_final: 0.8586 (p) REVERT: G 764 MET cc_start: 0.8655 (mtm) cc_final: 0.8347 (mtm) REVERT: G 1001 ASP cc_start: 0.8321 (m-30) cc_final: 0.8096 (t0) REVERT: G 1136 GLU cc_start: 0.9110 (mp0) cc_final: 0.8760 (mp0) REVERT: G 1198 SER cc_start: 0.9018 (OUTLIER) cc_final: 0.8662 (p) outliers start: 44 outliers final: 31 residues processed: 237 average time/residue: 0.1700 time to fit residues: 67.6873 Evaluate side-chains 233 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1120 GLU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1593 MET Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1481 SER Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 102 optimal weight: 6.9990 chunk 111 optimal weight: 0.5980 chunk 288 optimal weight: 4.9990 chunk 374 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 330 optimal weight: 20.0000 chunk 45 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 chunk 127 optimal weight: 1.9990 chunk 168 optimal weight: 30.0000 chunk 273 optimal weight: 0.5980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1892 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.083410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.061945 restraints weight = 126812.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.062977 restraints weight = 62155.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063303 restraints weight = 36936.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063553 restraints weight = 34192.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.063559 restraints weight = 31340.109| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30229 Z= 0.118 Angle : 0.554 11.615 40946 Z= 0.279 Chirality : 0.042 0.260 4603 Planarity : 0.004 0.057 5286 Dihedral : 4.449 58.311 4033 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 1.05 % Allowed : 14.18 % Favored : 84.78 % 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: 0.39 (0.14), residues: 3761 helix: 1.24 (0.13), residues: 1700 sheet: -1.09 (0.23), residues: 492 loop : -0.26 (0.16), residues: 1569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G1834 TYR 0.019 0.001 TYR G1833 PHE 0.013 0.001 PHE G 946 TRP 0.021 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00267 (30228) covalent geometry : angle 0.55335 (40944) SS BOND : bond 0.00853 ( 1) SS BOND : angle 3.26520 ( 2) hydrogen bonds : bond 0.03242 ( 1288) hydrogen bonds : angle 4.50368 ( 3597) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8367 (ttp) cc_final: 0.8093 (ttt) REVERT: A 1121 MET cc_start: 0.2165 (tpt) cc_final: 0.1474 (tpt) REVERT: A 1123 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8252 (tp-100) REVERT: A 1561 MET cc_start: 0.8429 (mmm) cc_final: 0.8172 (mmm) REVERT: B 229 LEU cc_start: 0.8533 (mt) cc_final: 0.8201 (pp) REVERT: B 237 MET cc_start: 0.8319 (mmt) cc_final: 0.7850 (mmm) REVERT: B 292 GLN cc_start: 0.8642 (pp30) cc_final: 0.7865 (mm110) REVERT: G 714 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8577 (p) REVERT: G 764 MET cc_start: 0.8581 (mtm) cc_final: 0.8317 (mtm) REVERT: G 1136 GLU cc_start: 0.9042 (mp0) cc_final: 0.8683 (mp0) REVERT: G 1198 SER cc_start: 0.9038 (OUTLIER) cc_final: 0.8720 (p) REVERT: G 1221 MET cc_start: 0.7965 (tmm) cc_final: 0.6923 (tmm) REVERT: G 1822 MET cc_start: 0.6484 (pmm) cc_final: 0.6073 (pmm) REVERT: G 1836 MET cc_start: 0.8783 (mmm) cc_final: 0.8568 (mmm) outliers start: 34 outliers final: 26 residues processed: 237 average time/residue: 0.1785 time to fit residues: 70.9223 Evaluate side-chains 230 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 201 time to evaluate : 1.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 244 THR Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1481 SER Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 1862 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 198 optimal weight: 8.9990 chunk 197 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 302 optimal weight: 20.0000 chunk 3 optimal weight: 40.0000 chunk 88 optimal weight: 0.0970 chunk 105 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 142 optimal weight: 4.9990 chunk 266 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.083245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.061880 restraints weight = 126735.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.062974 restraints weight = 61776.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.063106 restraints weight = 36511.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.063256 restraints weight = 37403.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.063373 restraints weight = 32340.779| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30229 Z= 0.133 Angle : 0.562 11.610 40946 Z= 0.283 Chirality : 0.042 0.243 4603 Planarity : 0.004 0.057 5286 Dihedral : 4.419 58.864 4033 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.84 % Favored : 97.10 % Rotamer: Outliers : 0.92 % Allowed : 14.33 % Favored : 84.75 % 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: 3761 helix: 1.25 (0.13), residues: 1701 sheet: -0.99 (0.24), residues: 464 loop : -0.26 (0.16), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 394 TYR 0.013 0.001 TYR A 417 PHE 0.013 0.001 PHE G 946 TRP 0.019 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00302 (30228) covalent geometry : angle 0.56170 (40944) SS BOND : bond 0.00981 ( 1) SS BOND : angle 3.43758 ( 2) hydrogen bonds : bond 0.03261 ( 1288) hydrogen bonds : angle 4.51092 ( 3597) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8392 (ttp) cc_final: 0.8126 (ttt) REVERT: A 1121 MET cc_start: 0.2057 (tpt) cc_final: 0.1477 (tpt) REVERT: A 1123 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8253 (tp-100) REVERT: A 1561 MET cc_start: 0.8446 (mmm) cc_final: 0.8228 (mmm) REVERT: B 229 LEU cc_start: 0.8535 (mt) cc_final: 0.8203 (pp) REVERT: B 237 MET cc_start: 0.8310 (mmt) cc_final: 0.7849 (mmm) REVERT: B 292 GLN cc_start: 0.8612 (pp30) cc_final: 0.7844 (mm110) REVERT: G 714 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8506 (p) REVERT: G 764 MET cc_start: 0.8603 (mtm) cc_final: 0.8316 (mtm) REVERT: G 1136 GLU cc_start: 0.9059 (mp0) cc_final: 0.8699 (mp0) REVERT: G 1198 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8625 (p) REVERT: G 1437 THR cc_start: 0.7297 (OUTLIER) cc_final: 0.7065 (t) REVERT: G 1822 MET cc_start: 0.6491 (pmm) cc_final: 0.6072 (pmm) outliers start: 30 outliers final: 24 residues processed: 228 average time/residue: 0.1863 time to fit residues: 71.2076 Evaluate side-chains 225 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 LEU Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 967 VAL Chi-restraints excluded: chain A residue 1123 GLN Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1630 THR Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain G residue 80 PHE Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1198 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1481 SER Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1830 VAL Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 319 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 162 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 275 optimal weight: 10.0000 chunk 2 optimal weight: 0.9980 chunk 357 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 363 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 304 optimal weight: 0.5980 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN ** G 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1568 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061502 restraints weight = 128271.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.062490 restraints weight = 62410.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.062923 restraints weight = 37592.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.063063 restraints weight = 35177.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.063100 restraints weight = 31898.172| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30229 Z= 0.157 Angle : 0.578 12.515 40946 Z= 0.291 Chirality : 0.042 0.241 4603 Planarity : 0.004 0.057 5286 Dihedral : 4.459 59.308 4032 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.98 % Favored : 96.97 % Rotamer: Outliers : 1.02 % Allowed : 14.39 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.14), residues: 3761 helix: 1.20 (0.13), residues: 1699 sheet: -0.98 (0.24), residues: 458 loop : -0.24 (0.16), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G1834 TYR 0.018 0.001 TYR G2030 PHE 0.014 0.001 PHE G 946 TRP 0.019 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00354 (30228) covalent geometry : angle 0.57733 (40944) SS BOND : bond 0.01112 ( 1) SS BOND : angle 3.67289 ( 2) hydrogen bonds : bond 0.03347 ( 1288) hydrogen bonds : angle 4.56518 ( 3597) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4276.84 seconds wall clock time: 75 minutes 20.50 seconds (4520.50 seconds total)