Starting phenix.real_space_refine on Tue May 27 22:01:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psg_17852/05_2025/8psg_17852.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psg_17852/05_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_17852/05_2025/8psg_17852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psg_17852/05_2025/8psg_17852.map" model { file = "/net/cci-nas-00/data/ceres_data/8psg_17852/05_2025/8psg_17852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psg_17852/05_2025/8psg_17852.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.30s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.36, per 1000 atoms: 0.52 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: 7.18 Conformation dependent library (CDL) restraints added in 3.8 seconds 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: 4.42 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: 13.83 Time building geometry restraints manager: 8.39 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.150 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 65.620 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.160 ------------------------------------------------------------------------------- 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 : 5.38 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.049 0.006 TRP A1286 HIS 0.018 0.003 HIS A1689 PHE 0.048 0.005 PHE A1376 TYR 0.054 0.006 TYR A 753 ARG 0.010 0.001 ARG G1834 Details of bonding type rmsd hydrogen bonds : bond 0.21933 ( 1288) hydrogen bonds : angle 9.45996 ( 3597) SS BOND : bond 0.08652 ( 1) SS BOND : angle 10.60502 ( 2) covalent geometry : bond 0.01389 (30228) covalent geometry : angle 1.88516 (40944) *********************** 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 : 3.440 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 1317 GLU cc_start: 0.7258 (tt0) cc_final: 0.6516 (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: 0.6778 (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: 0.4066 time to fit residues: 185.4445 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 : 3.400 ------------------------------------------------------------------------------- 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 317 optimal weight: 9.9990 chunk 284 optimal weight: 8.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 152 optimal weight: 30.0000 chunk 294 optimal weight: 40.0000 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 341 optimal weight: 0.9980 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 457 ASN A 506 ASN A 527 GLN A1123 GLN A1385 GLN 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 350 GLN G 718 ASN G 747 HIS G 752 GLN G 900 GLN G 908 ASN G1008 GLN G1055 HIS G1078 HIS G1178 GLN G1226 ASN G1307 ASN G1451 GLN G1659 GLN G1674 GLN G1697 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G1896 GLN G1912 ASN G1915 ASN G2020 GLN G2027 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.082023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.060459 restraints weight = 128602.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.061443 restraints weight = 63238.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061862 restraints weight = 38369.113| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 30229 Z= 0.211 Angle : 0.611 8.775 40946 Z= 0.325 Chirality : 0.043 0.235 4603 Planarity : 0.004 0.035 5286 Dihedral : 5.675 71.133 4050 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.10 % Rotamer: Outliers : 0.89 % Allowed : 7.83 % Favored : 91.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.13), residues: 3761 helix: -0.36 (0.12), residues: 1686 sheet: -2.09 (0.22), residues: 477 loop : -0.97 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 661 HIS 0.005 0.001 HIS G1697 PHE 0.016 0.002 PHE A 386 TYR 0.020 0.002 TYR G2030 ARG 0.005 0.001 ARG G 894 Details of bonding type rmsd hydrogen bonds : bond 0.04600 ( 1288) hydrogen bonds : angle 5.39416 ( 3597) SS BOND : bond 0.00690 ( 1) SS BOND : angle 5.04571 ( 2) covalent geometry : bond 0.00475 (30228) covalent geometry : angle 0.60972 (40944) *********************** 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 250 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 221 time to evaluate : 3.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7980 (mt-10) REVERT: A 352 MET cc_start: 0.8525 (ttp) cc_final: 0.8110 (ttt) REVERT: A 960 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.7820 (tp30) REVERT: A 1128 GLU cc_start: 0.7597 (pp20) cc_final: 0.7287 (pp20) REVERT: A 1742 ASP cc_start: 0.8359 (m-30) cc_final: 0.8055 (m-30) REVERT: B 174 ASP cc_start: 0.7494 (t0) cc_final: 0.6553 (t70) REVERT: B 203 GLU cc_start: 0.8327 (tp30) cc_final: 0.7811 (tp30) REVERT: B 229 LEU cc_start: 0.8556 (mt) cc_final: 0.8186 (pp) REVERT: B 237 MET cc_start: 0.8571 (mmt) cc_final: 0.8367 (mmp) REVERT: B 243 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.7163 (mm) REVERT: B 292 GLN cc_start: 0.8465 (pp30) cc_final: 0.7710 (mm-40) REVERT: G 71 LEU cc_start: 0.9127 (mp) cc_final: 0.8905 (pp) REVERT: G 714 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8726 (p) REVERT: G 1136 GLU cc_start: 0.8989 (mp0) cc_final: 0.8730 (mp0) REVERT: G 1221 MET cc_start: 0.8395 (tmm) cc_final: 0.8006 (tmm) REVERT: G 1265 MET cc_start: 0.8729 (tmm) cc_final: 0.7749 (ptp) REVERT: G 1323 MET cc_start: 0.2236 (mmt) cc_final: 0.1773 (mmt) REVERT: G 1676 MET cc_start: 0.7271 (mtt) cc_final: 0.6219 (mtt) outliers start: 29 outliers final: 18 residues processed: 240 average time/residue: 0.4031 time to fit residues: 160.0801 Evaluate side-chains 219 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 674 TYR Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 1257 ASP 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 1609 THR Chi-restraints excluded: chain G residue 1812 TYR Chi-restraints excluded: chain G residue 2035 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 97 optimal weight: 6.9990 chunk 322 optimal weight: 20.0000 chunk 4 optimal weight: 40.0000 chunk 318 optimal weight: 10.0000 chunk 175 optimal weight: 50.0000 chunk 331 optimal weight: 7.9990 chunk 301 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 241 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1652 GLN A1780 ASN ** B 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 896 ASN G1220 GLN ** G1716 ASN ** 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 = 0.3630 r_free = 0.3630 target = 0.082132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.061016 restraints weight = 128561.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.061382 restraints weight = 61056.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.062048 restraints weight = 40222.199| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30229 Z= 0.192 Angle : 0.562 7.085 40946 Z= 0.295 Chirality : 0.042 0.180 4603 Planarity : 0.004 0.040 5286 Dihedral : 5.101 58.928 4040 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 1.20 % Allowed : 9.52 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.13), residues: 3761 helix: 0.55 (0.13), residues: 1703 sheet: -1.74 (0.22), residues: 482 loop : -0.77 (0.15), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 661 HIS 0.005 0.001 HIS G1568 PHE 0.015 0.001 PHE A1376 TYR 0.021 0.002 TYR G2030 ARG 0.006 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1288) hydrogen bonds : angle 4.94693 ( 3597) SS BOND : bond 0.01232 ( 1) SS BOND : angle 4.31115 ( 2) covalent geometry : bond 0.00430 (30228) covalent geometry : angle 0.56118 (40944) *********************** 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 260 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 221 time to evaluate : 3.260 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8560 (ttp) cc_final: 0.8127 (ttt) REVERT: A 923 MET cc_start: 0.8410 (tpp) cc_final: 0.8192 (ttp) REVERT: A 960 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.7957 (tp30) REVERT: A 1120 GLU cc_start: 0.6323 (OUTLIER) cc_final: 0.5725 (mt-10) REVERT: B 168 MET cc_start: 0.7748 (tpp) cc_final: 0.7398 (tpp) REVERT: B 174 ASP cc_start: 0.7410 (t0) cc_final: 0.6513 (t0) REVERT: B 203 GLU cc_start: 0.8376 (tp30) cc_final: 0.7870 (tp30) REVERT: B 229 LEU cc_start: 0.8574 (mt) cc_final: 0.8223 (pp) REVERT: B 243 ILE cc_start: 0.7560 (OUTLIER) cc_final: 0.7219 (mm) REVERT: B 251 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8394 (mm-40) REVERT: B 292 GLN cc_start: 0.8459 (pp30) cc_final: 0.7704 (mm-40) REVERT: G 714 SER cc_start: 0.8943 (OUTLIER) cc_final: 0.8552 (p) REVERT: G 1136 GLU cc_start: 0.9027 (mp0) cc_final: 0.8768 (mp0) REVERT: G 1221 MET cc_start: 0.8384 (tmm) cc_final: 0.7935 (tmm) REVERT: G 1676 MET cc_start: 0.7103 (mtt) cc_final: 0.6728 (mtt) REVERT: G 1778 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8440 (pt0) outliers start: 39 outliers final: 21 residues processed: 251 average time/residue: 0.3850 time to fit residues: 159.6354 Evaluate side-chains 227 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 201 time to evaluate : 3.328 ------------------------------------------------------------------------------- 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 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 1381 VAL Chi-restraints excluded: chain G residue 1437 THR Chi-restraints excluded: chain G residue 1546 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 1778 GLN Chi-restraints excluded: chain G residue 1830 VAL 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 176 optimal weight: 20.0000 chunk 303 optimal weight: 4.9990 chunk 336 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 371 optimal weight: 0.5980 chunk 96 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 238 optimal weight: 2.9990 chunk 288 optimal weight: 10.0000 chunk 370 optimal weight: 9.9990 chunk 169 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 798 ASN 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.082747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.061582 restraints weight = 128824.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.062325 restraints weight = 62561.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062734 restraints weight = 39301.218| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30229 Z= 0.143 Angle : 0.530 8.794 40946 Z= 0.275 Chirality : 0.041 0.157 4603 Planarity : 0.004 0.047 5286 Dihedral : 4.775 57.943 4035 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.82 % Favored : 97.13 % Rotamer: Outliers : 1.36 % Allowed : 10.94 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.14), residues: 3761 helix: 0.93 (0.13), residues: 1702 sheet: -1.50 (0.22), residues: 487 loop : -0.59 (0.16), residues: 1572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 PHE 0.014 0.001 PHE G 64 TYR 0.023 0.001 TYR B 249 ARG 0.006 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1288) hydrogen bonds : angle 4.68652 ( 3597) SS BOND : bond 0.01078 ( 1) SS BOND : angle 3.71602 ( 2) covalent geometry : bond 0.00320 (30228) covalent geometry : angle 0.52955 (40944) *********************** 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 266 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 222 time to evaluate : 3.496 Fit side-chains revert: symmetry clash REVERT: A 352 MET cc_start: 0.8485 (ttp) cc_final: 0.8239 (ttt) REVERT: A 960 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: A 1120 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5862 (mt-10) REVERT: B 174 ASP cc_start: 0.7493 (t0) cc_final: 0.6599 (t0) REVERT: B 203 GLU cc_start: 0.8314 (tp30) cc_final: 0.7825 (tp30) REVERT: B 229 LEU cc_start: 0.8553 (mt) cc_final: 0.8223 (pp) REVERT: B 237 MET cc_start: 0.8355 (OUTLIER) cc_final: 0.7875 (mmm) REVERT: B 243 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7239 (mm) REVERT: B 292 GLN cc_start: 0.8474 (pp30) cc_final: 0.7746 (mm110) REVERT: G 714 SER cc_start: 0.8951 (OUTLIER) cc_final: 0.8624 (p) REVERT: G 1136 GLU cc_start: 0.9037 (mp0) cc_final: 0.8753 (mp0) REVERT: G 1198 SER cc_start: 0.8971 (OUTLIER) cc_final: 0.8105 (t) REVERT: G 1221 MET cc_start: 0.8282 (tmm) cc_final: 0.7145 (tmm) REVERT: G 1676 MET cc_start: 0.7293 (mtt) cc_final: 0.7063 (mtt) REVERT: G 1736 MET cc_start: 0.8092 (mtp) cc_final: 0.7834 (mtp) outliers start: 44 outliers final: 24 residues processed: 253 average time/residue: 0.3871 time to fit residues: 163.1734 Evaluate side-chains 232 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 3.367 ------------------------------------------------------------------------------- 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 1278 SER 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 B residue 185 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 237 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 157 optimal weight: 20.0000 chunk 297 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 175 optimal weight: 50.0000 chunk 209 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 165 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A1358 HIS A1780 ASN G 181 HIS G1039 HIS G1434 HIS ** G1716 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060567 restraints weight = 128486.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060905 restraints weight = 60829.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.061442 restraints weight = 41003.645| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 30229 Z= 0.219 Angle : 0.576 7.960 40946 Z= 0.298 Chirality : 0.042 0.154 4603 Planarity : 0.004 0.045 5286 Dihedral : 4.873 59.020 4035 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.67 % Favored : 96.28 % Rotamer: Outliers : 1.76 % Allowed : 12.33 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3761 helix: 0.92 (0.13), residues: 1708 sheet: -1.51 (0.22), residues: 483 loop : -0.50 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.005 0.001 HIS A 639 PHE 0.016 0.002 PHE A1376 TYR 0.025 0.002 TYR G1762 ARG 0.006 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 1288) hydrogen bonds : angle 4.76278 ( 3597) SS BOND : bond 0.01311 ( 1) SS BOND : angle 4.30076 ( 2) covalent geometry : bond 0.00489 (30228) covalent geometry : angle 0.57484 (40944) *********************** 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 269 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 212 time to evaluate : 3.597 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8463 (ttp) cc_final: 0.8192 (ttt) REVERT: A 440 MET cc_start: 0.8771 (mmt) cc_final: 0.8519 (mmt) REVERT: A 960 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: B 174 ASP cc_start: 0.7532 (t0) cc_final: 0.6573 (t0) REVERT: B 203 GLU cc_start: 0.8414 (tp30) cc_final: 0.7940 (tp30) REVERT: B 229 LEU cc_start: 0.8489 (mt) cc_final: 0.8168 (pp) REVERT: B 237 MET cc_start: 0.8369 (OUTLIER) cc_final: 0.7879 (mmm) REVERT: B 243 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7229 (mm) REVERT: B 276 ARG cc_start: 0.5347 (mmm160) cc_final: 0.5144 (mmp-170) REVERT: B 292 GLN cc_start: 0.8582 (pp30) cc_final: 0.7737 (mm110) REVERT: G 714 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8736 (p) REVERT: G 1136 GLU cc_start: 0.9020 (mp0) cc_final: 0.8691 (mp0) REVERT: G 1198 SER cc_start: 0.9011 (OUTLIER) cc_final: 0.8665 (p) REVERT: G 1221 MET cc_start: 0.8177 (tmm) cc_final: 0.7112 (tmm) outliers start: 57 outliers final: 33 residues processed: 251 average time/residue: 0.3950 time to fit residues: 164.3115 Evaluate side-chains 230 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 192 time to evaluate : 3.439 ------------------------------------------------------------------------------- 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 1096 SER Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1278 SER Chi-restraints excluded: chain A residue 1310 GLU Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain A residue 1666 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 237 MET 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 454 ASP 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 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 1847 LEU 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 235 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 352 optimal weight: 30.0000 chunk 126 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 271 optimal weight: 2.9990 chunk 49 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 43 optimal weight: 0.5980 chunk 278 optimal weight: 0.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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** ** G1778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1890 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.083230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.061194 restraints weight = 127827.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.062831 restraints weight = 68457.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.063006 restraints weight = 39287.751| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2470 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= 0.119 Angle : 0.530 8.931 40946 Z= 0.271 Chirality : 0.041 0.174 4603 Planarity : 0.004 0.048 5286 Dihedral : 4.627 58.110 4035 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.71 % Favored : 97.23 % Rotamer: Outliers : 1.33 % Allowed : 12.94 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.14), residues: 3761 helix: 1.17 (0.13), residues: 1696 sheet: -1.28 (0.23), residues: 475 loop : -0.45 (0.16), residues: 1590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 28 HIS 0.004 0.001 HIS A 639 PHE 0.013 0.001 PHE G1519 TYR 0.017 0.001 TYR B 249 ARG 0.007 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03362 ( 1288) hydrogen bonds : angle 4.52937 ( 3597) SS BOND : bond 0.00934 ( 1) SS BOND : angle 3.38600 ( 2) covalent geometry : bond 0.00265 (30228) covalent geometry : angle 0.52899 (40944) *********************** 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 268 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 3.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8432 (ttp) cc_final: 0.8143 (ttt) REVERT: A 1121 MET cc_start: 0.2715 (tpt) cc_final: 0.1572 (tpt) REVERT: A 1313 ASP cc_start: 0.8197 (t70) cc_final: 0.7986 (t70) REVERT: B 168 MET cc_start: 0.7854 (tpp) cc_final: 0.7585 (tpp) REVERT: B 203 GLU cc_start: 0.8391 (tp30) cc_final: 0.8136 (tp30) REVERT: B 229 LEU cc_start: 0.8584 (mt) cc_final: 0.8260 (pp) REVERT: B 237 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7743 (mmm) REVERT: B 292 GLN cc_start: 0.8630 (pp30) cc_final: 0.7820 (mm110) REVERT: G 67 TYR cc_start: 0.8427 (t80) cc_final: 0.8127 (t80) REVERT: G 714 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8627 (p) REVERT: G 870 GLU cc_start: 0.9116 (OUTLIER) cc_final: 0.8793 (pm20) REVERT: G 1136 GLU cc_start: 0.9066 (mp0) cc_final: 0.8740 (mp0) REVERT: G 1221 MET cc_start: 0.8131 (tmm) cc_final: 0.7809 (tmm) REVERT: G 1265 MET cc_start: 0.8660 (tmm) cc_final: 0.8214 (ppp) outliers start: 43 outliers final: 25 residues processed: 258 average time/residue: 0.3967 time to fit residues: 169.2989 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 : 3.354 ------------------------------------------------------------------------------- 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 16 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1275 LEU Chi-restraints excluded: chain A residue 1278 SER 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 237 MET 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 870 GLU Chi-restraints excluded: chain G residue 1355 ASN Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1481 SER Chi-restraints excluded: chain G residue 1499 VAL Chi-restraints excluded: chain G residue 1609 THR Chi-restraints excluded: chain G residue 1626 ILE Chi-restraints excluded: chain G residue 1862 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 306 optimal weight: 0.0870 chunk 326 optimal weight: 40.0000 chunk 51 optimal weight: 5.9990 chunk 225 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 148 optimal weight: 0.0670 chunk 236 optimal weight: 0.9980 chunk 185 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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** ** G1628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1778 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.084105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.062135 restraints weight = 127160.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.063935 restraints weight = 64900.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064201 restraints weight = 33940.817| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30229 Z= 0.098 Angle : 0.524 8.879 40946 Z= 0.266 Chirality : 0.041 0.184 4603 Planarity : 0.004 0.054 5286 Dihedral : 4.389 57.990 4033 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 1.23 % Allowed : 13.41 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.14), residues: 3761 helix: 1.29 (0.13), residues: 1696 sheet: -1.19 (0.22), residues: 488 loop : -0.27 (0.16), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 PHE 0.013 0.001 PHE G1519 TYR 0.028 0.001 TYR G1762 ARG 0.007 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03160 ( 1288) hydrogen bonds : angle 4.39981 ( 3597) SS BOND : bond 0.00714 ( 1) SS BOND : angle 2.82687 ( 2) covalent geometry : bond 0.00215 (30228) covalent geometry : angle 0.52330 (40944) *********************** 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 263 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 223 time to evaluate : 3.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8318 (ttp) cc_final: 0.8106 (ttt) REVERT: A 1121 MET cc_start: 0.2472 (tpt) cc_final: 0.1421 (tpt) REVERT: A 1313 ASP cc_start: 0.8197 (t70) cc_final: 0.7997 (t70) REVERT: B 168 MET cc_start: 0.7781 (tpp) cc_final: 0.7213 (tpp) REVERT: B 229 LEU cc_start: 0.8539 (mt) cc_final: 0.8208 (pp) REVERT: B 237 MET cc_start: 0.8225 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: B 292 GLN cc_start: 0.8600 (pp30) cc_final: 0.7820 (mm110) REVERT: G 714 SER cc_start: 0.8920 (OUTLIER) cc_final: 0.8583 (p) REVERT: G 764 MET cc_start: 0.8541 (mtm) cc_final: 0.8202 (mtm) REVERT: G 1136 GLU cc_start: 0.9049 (mp0) cc_final: 0.8717 (mp0) outliers start: 40 outliers final: 26 residues processed: 251 average time/residue: 0.3988 time to fit residues: 165.1167 Evaluate side-chains 234 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 206 time to evaluate : 3.237 ------------------------------------------------------------------------------- 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 16 GLU Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 909 LEU Chi-restraints excluded: chain A residue 1275 LEU 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 154 LEU Chi-restraints excluded: chain B residue 185 GLU Chi-restraints excluded: chain B residue 211 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 237 MET 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 666 ILE Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS 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 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 348 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 312 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 245 optimal weight: 4.9990 chunk 222 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 266 optimal weight: 10.0000 chunk 309 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- 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 = 0.3632 r_free = 0.3632 target = 0.082136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.061107 restraints weight = 128705.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.061517 restraints weight = 61336.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061952 restraints weight = 42397.237| |-----------------------------------------------------------------------------| r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30229 Z= 0.207 Angle : 0.587 9.405 40946 Z= 0.301 Chirality : 0.043 0.222 4603 Planarity : 0.004 0.051 5286 Dihedral : 4.587 59.668 4033 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 1.33 % Allowed : 13.59 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.14), residues: 3761 helix: 1.17 (0.13), residues: 1708 sheet: -1.22 (0.23), residues: 459 loop : -0.39 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP G 661 HIS 0.004 0.001 HIS A 639 PHE 0.021 0.002 PHE G1158 TYR 0.017 0.002 TYR G1833 ARG 0.007 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 1288) hydrogen bonds : angle 4.60742 ( 3597) SS BOND : bond 0.01363 ( 1) SS BOND : angle 3.93179 ( 2) covalent geometry : bond 0.00464 (30228) covalent geometry : angle 0.58667 (40944) *********************** 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 251 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 208 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8419 (ttp) cc_final: 0.8176 (ttt) REVERT: A 440 MET cc_start: 0.8682 (mmt) cc_final: 0.8399 (mmt) REVERT: A 1121 MET cc_start: 0.2695 (tpt) cc_final: 0.1644 (tpt) REVERT: A 1313 ASP cc_start: 0.8273 (t70) cc_final: 0.8057 (t70) REVERT: A 1561 MET cc_start: 0.8329 (mmm) cc_final: 0.7828 (mmm) REVERT: B 203 GLU cc_start: 0.8459 (tp30) cc_final: 0.8253 (tp30) REVERT: B 229 LEU cc_start: 0.8523 (mt) cc_final: 0.8184 (pp) REVERT: B 292 GLN cc_start: 0.8616 (pp30) cc_final: 0.7800 (mm110) REVERT: G 714 SER cc_start: 0.8925 (OUTLIER) cc_final: 0.8563 (p) REVERT: G 1136 GLU cc_start: 0.9045 (mp0) cc_final: 0.8718 (mp0) REVERT: G 1265 MET cc_start: 0.8639 (tmm) cc_final: 0.8266 (ppp) REVERT: G 1859 PRO cc_start: 0.5058 (Cg_exo) cc_final: 0.4733 (Cg_endo) outliers start: 43 outliers final: 31 residues processed: 235 average time/residue: 0.3956 time to fit residues: 154.0637 Evaluate side-chains 233 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 3.093 ------------------------------------------------------------------------------- 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 1275 LEU 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 211 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 454 ASP Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 666 ILE 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 1481 SER Chi-restraints excluded: chain G residue 1497 GLU Chi-restraints excluded: chain G residue 1499 VAL 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 2035 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 351 optimal weight: 0.0870 chunk 302 optimal weight: 20.0000 chunk 360 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 210 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 146 optimal weight: 0.0770 chunk 3 optimal weight: 40.0000 overall best weight: 3.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.082867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.061854 restraints weight = 127591.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062411 restraints weight = 62235.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.062658 restraints weight = 42107.389| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30229 Z= 0.147 Angle : 0.566 11.110 40946 Z= 0.287 Chirality : 0.042 0.326 4603 Planarity : 0.004 0.051 5286 Dihedral : 4.508 59.010 4033 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.00 % Favored : 96.94 % Rotamer: Outliers : 1.20 % Allowed : 13.99 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3761 helix: 1.21 (0.13), residues: 1705 sheet: -1.07 (0.23), residues: 464 loop : -0.32 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 661 HIS 0.004 0.001 HIS A 454 PHE 0.016 0.001 PHE G1158 TYR 0.017 0.001 TYR G1833 ARG 0.007 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 1288) hydrogen bonds : angle 4.54278 ( 3597) SS BOND : bond 0.01081 ( 1) SS BOND : angle 3.46372 ( 2) covalent geometry : bond 0.00331 (30228) covalent geometry : angle 0.56553 (40944) *********************** 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 248 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 3.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8412 (ttp) cc_final: 0.8153 (ttt) REVERT: A 1121 MET cc_start: 0.2621 (tpt) cc_final: 0.1630 (tpt) REVERT: A 1313 ASP cc_start: 0.8228 (t70) cc_final: 0.8019 (t70) REVERT: A 1561 MET cc_start: 0.8420 (mmm) cc_final: 0.8006 (mmm) REVERT: B 229 LEU cc_start: 0.8527 (mt) cc_final: 0.8196 (pp) REVERT: B 237 MET cc_start: 0.8033 (mmm) cc_final: 0.7453 (mmm) REVERT: B 292 GLN cc_start: 0.8624 (pp30) cc_final: 0.7843 (mm110) REVERT: G 714 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8607 (p) REVERT: G 1136 GLU cc_start: 0.9068 (mp0) cc_final: 0.8702 (mp0) REVERT: G 1221 MET cc_start: 0.7942 (tmm) cc_final: 0.6898 (tmm) REVERT: G 1265 MET cc_start: 0.8675 (tmm) cc_final: 0.8225 (ppp) outliers start: 39 outliers final: 29 residues processed: 236 average time/residue: 0.3934 time to fit residues: 155.6785 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 : 3.799 ------------------------------------------------------------------------------- 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 16 GLU 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 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 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 211 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 666 ILE 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 1481 SER Chi-restraints excluded: chain G residue 1499 VAL 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 2035 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 123 optimal weight: 0.3980 chunk 307 optimal weight: 10.0000 chunk 362 optimal weight: 9.9990 chunk 314 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 247 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 chunk 223 optimal weight: 0.0670 chunk 118 optimal weight: 0.0980 chunk 317 optimal weight: 8.9990 overall best weight: 1.5122 ------------------------------------------------------------------------------- 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** G2027 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.083886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.062058 restraints weight = 127726.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.063761 restraints weight = 65222.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064200 restraints weight = 34337.954| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 30229 Z= 0.106 Angle : 0.558 11.515 40946 Z= 0.281 Chirality : 0.042 0.278 4603 Planarity : 0.004 0.053 5286 Dihedral : 4.346 58.357 4032 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.66 % Favored : 97.31 % Rotamer: Outliers : 0.92 % Allowed : 14.42 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.14), residues: 3761 helix: 1.27 (0.13), residues: 1700 sheet: -0.98 (0.23), residues: 480 loop : -0.21 (0.16), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 661 HIS 0.004 0.001 HIS A 639 PHE 0.018 0.001 PHE B 286 TYR 0.020 0.001 TYR G2030 ARG 0.008 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 1288) hydrogen bonds : angle 4.45422 ( 3597) SS BOND : bond 0.00759 ( 1) SS BOND : angle 2.96616 ( 2) covalent geometry : bond 0.00237 (30228) covalent geometry : angle 0.55798 (40944) ********************** 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 247 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 217 time to evaluate : 3.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 MET cc_start: 0.8296 (ttp) cc_final: 0.7924 (ttt) REVERT: A 1121 MET cc_start: 0.2439 (tpt) cc_final: 0.1510 (tpt) REVERT: A 1313 ASP cc_start: 0.8234 (t70) cc_final: 0.8014 (t70) REVERT: A 1561 MET cc_start: 0.8463 (mmm) cc_final: 0.8085 (mmm) REVERT: B 203 GLU cc_start: 0.8337 (tp30) cc_final: 0.8131 (tp30) REVERT: B 229 LEU cc_start: 0.8532 (mt) cc_final: 0.8207 (pp) REVERT: B 237 MET cc_start: 0.8118 (mmm) cc_final: 0.7471 (mmm) REVERT: B 292 GLN cc_start: 0.8629 (pp30) cc_final: 0.7877 (mm110) REVERT: G 67 TYR cc_start: 0.8353 (t80) cc_final: 0.8150 (t80) REVERT: G 714 SER cc_start: 0.8933 (OUTLIER) cc_final: 0.8523 (p) REVERT: G 1136 GLU cc_start: 0.9057 (mp0) cc_final: 0.8737 (mp0) REVERT: G 1265 MET cc_start: 0.8623 (tmm) cc_final: 0.8228 (ppp) REVERT: G 1727 LYS cc_start: 0.8773 (mmtp) cc_final: 0.8521 (mtmm) REVERT: G 1822 MET cc_start: 0.6389 (pmm) cc_final: 0.5826 (pmm) REVERT: G 1836 MET cc_start: 0.8352 (mmm) cc_final: 0.8095 (mmm) outliers start: 30 outliers final: 23 residues processed: 236 average time/residue: 0.4215 time to fit residues: 165.6922 Evaluate side-chains 232 residues out of total 3246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 208 time to evaluate : 3.337 ------------------------------------------------------------------------------- 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 1275 LEU 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 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 666 ILE Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 855 HIS Chi-restraints excluded: chain G residue 1481 SER Chi-restraints excluded: chain G residue 1499 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1609 THR 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 6 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 239 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 233 optimal weight: 1.9990 chunk 350 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 251 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 346 optimal weight: 0.8980 chunk 366 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 ASN A 798 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.084005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.062635 restraints weight = 127423.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.063669 restraints weight = 62637.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.064033 restraints weight = 36998.632| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30229 Z= 0.109 Angle : 0.560 12.251 40946 Z= 0.282 Chirality : 0.042 0.255 4603 Planarity : 0.004 0.052 5286 Dihedral : 4.264 58.493 4032 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.77 % Favored : 97.21 % Rotamer: Outliers : 0.99 % Allowed : 14.58 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.14), residues: 3761 helix: 1.34 (0.13), residues: 1697 sheet: -0.94 (0.23), residues: 485 loop : -0.16 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 661 HIS 0.004 0.001 HIS A 454 PHE 0.026 0.001 PHE B 286 TYR 0.016 0.001 TYR G2030 ARG 0.007 0.000 ARG G1023 Details of bonding type rmsd hydrogen bonds : bond 0.03156 ( 1288) hydrogen bonds : angle 4.43034 ( 3597) SS BOND : bond 0.00793 ( 1) SS BOND : angle 2.94678 ( 2) covalent geometry : bond 0.00247 (30228) covalent geometry : angle 0.55984 (40944) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8345.38 seconds wall clock time: 148 minutes 31.48 seconds (8911.48 seconds total)