Starting phenix.real_space_refine on Tue May 27 17:47:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8psk_17854/05_2025/8psk_17854.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psk_17854/05_2025/8psk_17854.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8psk_17854/05_2025/8psk_17854.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psk_17854/05_2025/8psk_17854.map" model { file = "/net/cci-nas-00/data/ceres_data/8psk_17854/05_2025/8psk_17854.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psk_17854/05_2025/8psk_17854.cif" } resolution = 2.8 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= -0.002 sd= 0.012 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 18867 2.51 5 N 4954 2.21 5 O 5676 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.43s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29604 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: 16004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16004 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Chain: "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: 15.06, per 1000 atoms: 0.51 Number of scatterers: 29604 At special positions: 0 Unit cell: (183.57, 182.515, 176.185, 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 5676 8.00 N 4954 7.00 C 18867 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=2.21 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: 6.73 Conformation dependent library (CDL) restraints added in 3.6 seconds 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7026 Finding SS restraints... Secondary structure from input PDB file: 171 helices and 30 sheets defined 51.6% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.60 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.729A pdb=" N PHE A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 51 through 65 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 382 Processing helix chain 'A' and resid 383 through 390 Processing helix chain 'A' and resid 395 through 399 Processing helix chain 'A' and resid 404 through 422 removed outlier: 4.086A 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 Processing helix chain 'A' and resid 459 through 462 Processing helix chain 'A' and resid 463 through 483 Processing helix chain 'A' and resid 521 through 532 Processing helix chain 'A' and resid 608 through 615 Processing helix chain 'A' and resid 652 through 670 Processing helix chain 'A' and resid 687 through 699 removed outlier: 3.559A pdb=" N GLU A 691 " --> pdb=" O SER A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 726 Processing helix chain 'A' and resid 741 through 754 Processing helix chain 'A' and resid 780 through 784 Processing helix chain 'A' and resid 785 through 796 Processing helix chain 'A' and resid 796 through 813 Processing helix chain 'A' and resid 838 through 846 Processing helix chain 'A' and resid 848 through 856 removed outlier: 4.748A pdb=" N HIS A 854 " --> pdb=" O PHE A 850 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 890 Processing helix chain 'A' and resid 898 through 908 removed outlier: 3.571A pdb=" N LEU A 908 " --> pdb=" O ASN A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 920 Processing helix chain 'A' and resid 929 through 933 removed outlier: 3.583A pdb=" N VAL A 933 " --> pdb=" O LEU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 970 Processing helix chain 'A' and resid 997 through 1005 removed outlier: 3.839A pdb=" N GLN A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ILE A1004 " --> pdb=" O GLN A1000 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA A1005 " --> pdb=" O VAL A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.782A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1032 through 1043 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1087 through 1100 removed outlier: 4.597A pdb=" N ALA A1091 " --> pdb=" O LYS A1087 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1198 Processing helix chain 'A' and resid 1201 through 1208 removed outlier: 3.570A pdb=" N GLN A1207 " --> pdb=" O ASP A1203 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1226 removed outlier: 3.813A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1262 Processing helix chain 'A' and resid 1275 through 1280 removed outlier: 6.303A pdb=" N ILE A1280 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1291 Processing helix chain 'A' and resid 1303 through 1305 No H-bonds generated for 'chain 'A' and resid 1303 through 1305' Processing helix chain 'A' and resid 1306 through 1321 Processing helix chain 'A' and resid 1336 through 1346 Processing helix chain 'A' and resid 1351 through 1358 Processing helix chain 'A' and resid 1361 through 1365 Processing helix chain 'A' and resid 1390 through 1397 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1444 through 1475 removed outlier: 3.672A pdb=" N GLU A1475 " --> pdb=" O LYS A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1509 removed outlier: 4.321A pdb=" N ASN A1483 " --> pdb=" O SER A1479 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N GLU A1484 " --> pdb=" O GLU A1480 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU A1492 " --> pdb=" O GLU A1488 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.538A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1536 Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.769A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1601 Processing helix chain 'A' and resid 1615 through 1621 removed outlier: 3.665A pdb=" N GLN A1620 " --> pdb=" O ILE A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 4.014A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A1663 " --> pdb=" O ASP A1659 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1658 through 1663' Processing helix chain 'A' and resid 1666 through 1694 Processing helix chain 'A' and resid 1710 through 1717 Processing helix chain 'A' and resid 1734 through 1738 Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 4.152A 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: 3.574A pdb=" N ILE A1787 " --> pdb=" O ASN A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1792 through 1801 removed outlier: 3.666A pdb=" N ALA A1801 " --> pdb=" O GLU A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1853 through 1862 removed outlier: 3.847A pdb=" N LYS A1857 " --> pdb=" O GLY A1853 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A1860 " --> pdb=" O LYS A1856 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA A1862 " --> pdb=" O ALA A1858 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 160 Processing helix chain 'B' and resid 171 through 176 Processing helix chain 'B' and resid 179 through 195 removed outlier: 3.536A pdb=" N GLN B 183 " --> pdb=" O LYS B 179 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 removed outlier: 3.712A pdb=" N LEU B 209 " --> pdb=" O PRO B 205 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 237 Processing helix chain 'B' and resid 242 through 254 Processing helix chain 'B' and resid 257 through 271 Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 26 through 41 Processing helix chain 'G' and resid 56 through 72 removed outlier: 3.753A pdb=" N LEU G 71 " --> pdb=" O TYR G 67 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 96 Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.611A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 Processing helix chain 'G' and resid 143 through 151 Processing helix chain 'G' and resid 168 through 180 removed outlier: 3.935A pdb=" N GLU G 172 " --> pdb=" O ASP G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.797A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (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 255 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 275 through 284 removed outlier: 4.112A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 314 removed outlier: 3.993A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG G 297 " --> pdb=" O PHE G 293 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 Processing helix chain 'G' and resid 345 through 360 removed outlier: 4.072A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) removed outlier: 3.611A 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 397 removed outlier: 3.539A pdb=" N THR G 392 " --> pdb=" O GLY G 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 434 Proline residue: G 434 - end of helix Processing helix chain 'G' and resid 435 through 445 removed outlier: 3.838A pdb=" N LYS G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 467 through 471 Processing helix chain 'G' and resid 474 through 485 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 507 through 510 Processing helix chain 'G' and resid 511 through 521 removed outlier: 3.714A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.899A pdb=" N PHE G 548 " --> pdb=" O LYS G 544 " (cutoff:3.500A) Processing helix chain 'G' and resid 551 through 555 Processing helix chain 'G' and resid 560 through 565 Processing helix chain 'G' and resid 581 through 588 removed outlier: 3.777A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 612 Processing helix chain 'G' and resid 622 through 624 No H-bonds generated for 'chain 'G' and resid 622 through 624' Processing helix chain 'G' and resid 626 through 641 Processing helix chain 'G' and resid 655 through 672 Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 Processing helix chain 'G' and resid 709 through 723 Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.388A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 773 through 783 removed outlier: 3.816A pdb=" N THR G 777 " --> pdb=" O SER G 773 " (cutoff:3.500A) Proline residue: G 779 - end of helix Processing helix chain 'G' and resid 784 through 788 removed outlier: 3.838A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 808 removed outlier: 4.342A pdb=" N ILE G 807 " --> pdb=" O ARG G 804 " (cutoff:3.500A) Processing helix chain 'G' and resid 814 through 823 Processing helix chain 'G' and resid 831 through 837 Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 876 through 899 removed outlier: 4.600A pdb=" N VAL G 881 " --> pdb=" O LYS G 877 " (cutoff:3.500A) Proline residue: G 882 - end of helix removed outlier: 5.206A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 removed outlier: 3.605A pdb=" N ALA G 979 " --> pdb=" O LYS G 975 " (cutoff:3.500A) Processing helix chain 'G' and resid 988 through 992 Processing helix chain 'G' and resid 996 through 1007 Processing helix chain 'G' and resid 1024 through 1031 Processing helix chain 'G' and resid 1035 through 1043 removed outlier: 4.653A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 Processing helix chain 'G' and resid 1093 through 1097 removed outlier: 3.551A pdb=" N ILE G1097 " --> pdb=" O GLU G1094 " (cutoff:3.500A) Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1174 Processing helix chain 'G' and resid 1189 through 1192 Processing helix chain 'G' and resid 1257 through 1271 Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1324 through 1337 removed outlier: 4.058A pdb=" N VAL G1328 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA G1337 " --> pdb=" O ALA G1333 " (cutoff:3.500A) Processing helix chain 'G' and resid 1346 through 1348 No H-bonds generated for 'chain 'G' and resid 1346 through 1348' Processing helix chain 'G' and resid 1418 through 1422 Processing helix chain 'G' and resid 1437 through 1447 removed outlier: 3.886A pdb=" N ILE G1441 " --> pdb=" O THR G1437 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS G1447 " --> pdb=" O VAL G1443 " (cutoff:3.500A) Processing helix chain 'G' and resid 1514 through 1524 Processing helix chain 'G' and resid 1550 through 1558 Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 Processing helix chain 'G' and resid 1601 through 1603 No H-bonds generated for 'chain 'G' and resid 1601 through 1603' Processing helix chain 'G' and resid 1677 through 1682 Processing helix chain 'G' and resid 1684 through 1703 Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 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 1818 removed outlier: 3.939A pdb=" N ALA G1813 " --> pdb=" O LEU G1809 " (cutoff:3.500A) Processing helix chain 'G' and resid 1823 through 1841 Processing helix chain 'G' and resid 1858 through 1863 removed outlier: 4.036A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1882 Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 3.593A pdb=" N ASP G1908 " --> pdb=" O LEU G1904 " (cutoff:3.500A) Processing helix chain 'G' and resid 1924 through 1930 removed outlier: 3.510A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1952 removed outlier: 3.987A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G1947 " --> pdb=" O ILE G1943 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS G1950 " --> pdb=" O GLU G1946 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1983 removed outlier: 4.002A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1994 removed outlier: 3.624A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER G1990 " --> pdb=" O LYS G1986 " (cutoff:3.500A) Processing helix chain 'G' and resid 1997 through 2001 Processing helix chain 'G' and resid 2022 through 2033 Processing helix chain 'G' and resid 2035 through 2044 Processing helix chain 'G' and resid 2044 through 2050 removed outlier: 3.782A pdb=" N GLN G2050 " --> pdb=" O GLU G2046 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 removed outlier: 6.692A pdb=" N VAL G1899 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N TYR G1891 " --> pdb=" O GLN G1897 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N GLN G1897 " --> pdb=" O TYR G1891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.654A pdb=" N ARG A 43 " --> pdb=" O THR G1663 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL G1665 " --> pdb=" O ARG A 43 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N VAL A 45 " --> pdb=" O VAL G1665 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.528A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE G1664 " --> pdb=" O ALA G1805 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 400 through 402 removed outlier: 6.606A pdb=" N VAL A 678 " --> pdb=" O VAL A 704 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N THR A 706 " --> pdb=" O VAL A 678 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE A 680 " --> pdb=" O THR A 706 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N MET A 923 " --> pdb=" O ARG A 641 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 497 through 503 Processing sheet with id=AA5, first strand: chain 'A' and resid 872 through 873 Processing sheet with id=AA6, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA7, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.520A pdb=" N GLY A1023 " --> pdb=" O ILE A1386 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LYS A1649 " --> pdb=" O GLY A1645 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1060 through 1067 removed outlier: 3.803A pdb=" N ARG A1070 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB1, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB2, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB3, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB4, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB5, first strand: chain 'A' and resid 1768 through 1775 removed outlier: 3.619A pdb=" N ASP A1866 " --> pdb=" O THR A1885 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB7, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.843A pdb=" N VAL G 22 " --> pdb=" O ARG G 7 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 459 through 460 removed outlier: 7.554A pdb=" N ALA G 270 " --> pdb=" O TYR G 460 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N THR G 271 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ALA G 158 " --> pdb=" O THR G 271 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL G 527 " --> pdb=" O GLY G 542 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 417 through 420 removed outlier: 6.081A pdb=" N SER G 380 " --> pdb=" O ILE G 368 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE G 368 " --> pdb=" O SER G 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC2, first strand: chain 'G' and resid 592 through 594 removed outlier: 3.906A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU G 703 " --> pdb=" O ALA G 729 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N GLN G 731 " --> pdb=" O LEU G 703 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU G 705 " --> pdb=" O GLN G 731 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR G 733 " --> pdb=" O LEU G 705 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.666A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC5, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC6, first strand: chain 'G' and resid 1126 through 1128 removed outlier: 6.406A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) removed outlier: 7.503A pdb=" N PHE G1158 " --> pdb=" O ILE G1251 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N GLU G1253 " --> pdb=" O PHE G1158 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N THR G1160 " --> pdb=" O GLU G1253 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 1285 through 1286 Processing sheet with id=AC8, first strand: chain 'G' and resid 1285 through 1286 removed outlier: 5.200A pdb=" N THR G1374 " --> pdb=" O SER G1397 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N SER G1397 " --> pdb=" O THR G1374 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ALA G1376 " --> pdb=" O THR G1395 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N THR G1395 " --> pdb=" O ALA G1376 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N ILE G1378 " --> pdb=" O VAL G1393 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL G1393 " --> pdb=" O ILE G1378 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N VAL G1403 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N MET G1359 " --> pdb=" O VAL G1403 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU G1405 " --> pdb=" O TYR G1357 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N TYR G1357 " --> pdb=" O GLU G1405 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N THR G1407 " --> pdb=" O ASN G1355 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASN G1355 " --> pdb=" O THR G1407 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER G1409 " --> pdb=" O LEU G1353 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU G1656 " --> pdb=" O ARG G1606 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TYR G1608 " --> pdb=" O GLU G1654 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLU G1654 " --> pdb=" O TYR G1608 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS G1610 " --> pdb=" O THR G1652 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR G1652 " --> pdb=" O CYS G1610 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N PHE G1612 " --> pdb=" O VAL G1650 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N VAL G1650 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) removed outlier: 14.288A pdb=" N ILE G1632 " --> pdb=" O GLU G1534 " (cutoff:3.500A) removed outlier: 14.547A pdb=" N GLU G1534 " --> pdb=" O ILE G1632 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 6.598A pdb=" N CYS G1485 " --> pdb=" O ASP G1505 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP G1505 " --> pdb=" O CYS G1485 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N GLY G1487 " --> pdb=" O ILE G1503 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ILE G1503 " --> pdb=" O GLY G1487 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ILE G1489 " --> pdb=" O ILE G1501 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1424 through 1427 removed outlier: 5.076A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS G1462 " --> pdb=" O ILE G1435 " (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 1740 through 1741 removed outlier: 3.848A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) 1511 hydrogen bonds defined for protein. 4209 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: 15.36 Time building geometry restraints manager: 7.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 5070 1.31 - 1.44: 7640 1.44 - 1.58: 17324 1.58 - 1.72: 1 1.72 - 1.86: 187 Bond restraints: 30222 Sorted by residual: bond pdb=" C PRO A1627 " pdb=" O PRO A1627 " ideal model delta sigma weight residual 1.234 1.172 0.062 1.14e-02 7.69e+03 2.96e+01 bond pdb=" C PRO A1362 " pdb=" O PRO A1362 " ideal model delta sigma weight residual 1.237 1.171 0.067 1.26e-02 6.30e+03 2.80e+01 bond pdb=" C PRO A 736 " pdb=" O PRO A 736 " ideal model delta sigma weight residual 1.234 1.173 0.060 1.14e-02 7.69e+03 2.79e+01 bond pdb=" C PRO A1190 " pdb=" O PRO A1190 " ideal model delta sigma weight residual 1.233 1.173 0.060 1.16e-02 7.43e+03 2.63e+01 bond pdb=" C GLY A1248 " pdb=" O GLY A1248 " ideal model delta sigma weight residual 1.233 1.185 0.048 9.80e-03 1.04e+04 2.44e+01 ... (remaining 30217 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 30963 2.15 - 4.30: 9129 4.30 - 6.46: 809 6.46 - 8.61: 31 8.61 - 10.76: 4 Bond angle restraints: 40936 Sorted by residual: angle pdb=" C SER A1417 " pdb=" N VAL A1418 " pdb=" CA VAL A1418 " ideal model delta sigma weight residual 120.24 124.76 -4.52 6.30e-01 2.52e+00 5.15e+01 angle pdb=" N GLY B 240 " pdb=" CA GLY B 240 " pdb=" C GLY B 240 " ideal model delta sigma weight residual 114.69 106.29 8.40 1.19e+00 7.06e-01 4.99e+01 angle pdb=" C ILE A1189 " pdb=" CA ILE A1189 " pdb=" CB ILE A1189 " ideal model delta sigma weight residual 110.88 117.14 -6.26 9.80e-01 1.04e+00 4.08e+01 angle pdb=" C TRP G 661 " pdb=" N GLY G 662 " pdb=" CA GLY G 662 " ideal model delta sigma weight residual 119.94 126.78 -6.84 1.09e+00 8.42e-01 3.94e+01 angle pdb=" CB GLU G1309 " pdb=" CG GLU G1309 " pdb=" CD GLU G1309 " ideal model delta sigma weight residual 112.60 123.20 -10.60 1.70e+00 3.46e-01 3.89e+01 ... (remaining 40931 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 16519 17.67 - 35.34: 1372 35.34 - 53.01: 255 53.01 - 70.68: 58 70.68 - 88.35: 44 Dihedral angle restraints: 18248 sinusoidal: 7339 harmonic: 10909 Sorted by residual: dihedral pdb=" CB CYS A1246 " pdb=" SG CYS A1246 " pdb=" SG CYS A1327 " pdb=" CB CYS A1327 " ideal model delta sinusoidal sigma weight residual 93.00 17.54 75.46 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CA ASP G 974 " pdb=" C ASP G 974 " pdb=" N LYS G 975 " pdb=" CA LYS G 975 " ideal model delta harmonic sigma weight residual 180.00 154.46 25.54 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA PHE A 896 " pdb=" C PHE A 896 " pdb=" N SER A 897 " pdb=" CA SER A 897 " ideal model delta harmonic sigma weight residual 180.00 155.30 24.70 0 5.00e+00 4.00e-02 2.44e+01 ... (remaining 18245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2172 0.061 - 0.122: 1694 0.122 - 0.183: 611 0.183 - 0.244: 109 0.244 - 0.306: 16 Chirality restraints: 4602 Sorted by residual: chirality pdb=" CA SER B 235 " pdb=" N SER B 235 " pdb=" C SER B 235 " pdb=" CB SER B 235 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA ILE G1751 " pdb=" N ILE G1751 " pdb=" C ILE G1751 " pdb=" CB ILE G1751 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.14e+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 2.72 -0.29 2.00e-01 2.50e+01 2.13e+00 ... (remaining 4599 not shown) Planarity restraints: 5285 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.019 2.00e-02 2.50e+03 3.63e-02 5.94e+01 pdb=" C10 FMN G2101 " 0.026 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.050 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.040 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.060 2.00e-02 2.50e+03 pdb=" C6 FMN G2101 " 0.024 2.00e-02 2.50e+03 pdb=" C7 FMN G2101 " -0.013 2.00e-02 2.50e+03 pdb=" C7M FMN G2101 " -0.069 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.031 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.027 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " -0.003 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.041 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.016 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.039 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.038 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.043 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.074 2.00e-02 2.50e+03 3.82e-02 2.92e+01 pdb=" CG TYR A 722 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.018 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1529 " 0.068 2.00e-02 2.50e+03 3.52e-02 2.48e+01 pdb=" CG TYR A1529 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A1529 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A1529 " -0.031 2.00e-02 2.50e+03 pdb=" CE1 TYR A1529 " -0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A1529 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A1529 " 0.016 2.00e-02 2.50e+03 pdb=" OH TYR A1529 " 0.035 2.00e-02 2.50e+03 ... (remaining 5282 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 711 2.69 - 3.25: 28877 3.25 - 3.80: 46398 3.80 - 4.35: 65492 4.35 - 4.90: 106406 Nonbonded interactions: 247884 Sorted by model distance: nonbonded pdb=" OD1 ASP G 287 " pdb=" OG SER G 291 " model vdw 2.142 3.040 nonbonded pdb=" O LEU B 221 " pdb=" OG SER B 225 " model vdw 2.213 3.040 nonbonded pdb=" OE1 GLU G1811 " pdb=" OH TYR G2010 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR G 615 " pdb=" OD1 ASP G1075 " model vdw 2.240 3.040 nonbonded pdb=" O LYS G 355 " pdb=" OG SER G 358 " model vdw 2.248 3.040 ... (remaining 247879 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.230 Set scattering table: 0.260 Process input model: 66.210 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:11.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.184 30223 Z= 1.002 Angle : 1.823 19.046 40938 Z= 1.340 Chirality : 0.088 0.306 4602 Planarity : 0.007 0.038 5285 Dihedral : 14.420 88.350 11219 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.52 % Favored : 95.21 % Rotamer: Outliers : 0.25 % Allowed : 3.21 % Favored : 96.55 % 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: -2.78 (0.12), residues: 3760 helix: -2.33 (0.10), residues: 1664 sheet: -1.39 (0.20), residues: 500 loop : -1.19 (0.14), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.009 TRP G1449 HIS 0.015 0.004 HIS G1564 PHE 0.054 0.007 PHE G1300 TYR 0.074 0.008 TYR A 722 ARG 0.017 0.002 ARG A 396 Details of bonding type rmsd hydrogen bonds : bond 0.20648 ( 1503) hydrogen bonds : angle 8.55991 ( 4209) SS BOND : bond 0.18385 ( 1) SS BOND : angle 16.54408 ( 2) covalent geometry : bond 0.01340 (30222) covalent geometry : angle 1.81964 (40936) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 387 time to evaluate : 3.607 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8926 (tp30) cc_final: 0.8396 (tp30) REVERT: A 340 ARG cc_start: 0.6764 (mmt180) cc_final: 0.6233 (mpt180) REVERT: A 364 GLU cc_start: 0.5576 (tt0) cc_final: 0.5361 (tt0) REVERT: A 529 MET cc_start: 0.8806 (mmp) cc_final: 0.8236 (mmp) REVERT: A 537 LYS cc_start: 0.7557 (tptt) cc_final: 0.7336 (mttm) REVERT: A 612 GLU cc_start: 0.8289 (tp30) cc_final: 0.7978 (tp30) REVERT: A 944 ARG cc_start: 0.8605 (ttm110) cc_final: 0.8396 (ttp80) REVERT: A 1162 GLU cc_start: 0.7960 (mp0) cc_final: 0.7345 (mp0) REVERT: A 1180 ARG cc_start: 0.7269 (mpt180) cc_final: 0.6799 (mpt90) REVERT: A 1260 MET cc_start: 0.9154 (ptp) cc_final: 0.8913 (ptm) REVERT: A 1496 GLU cc_start: 0.6696 (tt0) cc_final: 0.6462 (tt0) REVERT: B 168 MET cc_start: 0.6459 (mmm) cc_final: 0.5996 (tpp) REVERT: B 179 LYS cc_start: 0.8313 (mppt) cc_final: 0.7740 (mptt) REVERT: B 183 GLN cc_start: 0.8311 (tp-100) cc_final: 0.7908 (tp40) REVERT: B 192 LYS cc_start: 0.8280 (pptt) cc_final: 0.8077 (ptmt) REVERT: B 237 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7454 (tpp) REVERT: B 261 GLN cc_start: 0.7962 (mt0) cc_final: 0.7541 (mt0) REVERT: B 271 ASN cc_start: 0.8370 (m110) cc_final: 0.8042 (m-40) REVERT: G 64 PHE cc_start: 0.8347 (t80) cc_final: 0.7985 (t80) REVERT: G 81 ASP cc_start: 0.7600 (m-30) cc_final: 0.7241 (m-30) REVERT: G 132 MET cc_start: 0.8609 (mmp) cc_final: 0.8216 (mpm) REVERT: G 217 GLU cc_start: 0.8342 (tp30) cc_final: 0.7861 (tp30) REVERT: G 221 ASN cc_start: 0.8470 (m110) cc_final: 0.7949 (m110) REVERT: G 325 GLU cc_start: 0.8530 (tp30) cc_final: 0.8076 (tp30) REVERT: G 329 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7861 (mt-10) REVERT: G 387 TYR cc_start: 0.8318 (t80) cc_final: 0.7928 (t80) REVERT: G 447 ASN cc_start: 0.8350 (t0) cc_final: 0.7577 (p0) REVERT: G 553 ASN cc_start: 0.8168 (m110) cc_final: 0.7948 (m-40) REVERT: G 881 VAL cc_start: 0.8911 (t) cc_final: 0.8704 (t) REVERT: G 1309 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6780 (mm-30) REVERT: G 1401 LYS cc_start: 0.8144 (pptt) cc_final: 0.7816 (pmtt) REVERT: G 1500 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7965 (tm-30) REVERT: G 1673 GLU cc_start: 0.8094 (pm20) cc_final: 0.7864 (pm20) REVERT: G 1784 MET cc_start: 0.8730 (tmm) cc_final: 0.8292 (tmt) REVERT: G 1962 ARG cc_start: 0.6707 (tmt-80) cc_final: 0.6437 (tmt-80) REVERT: G 2015 THR cc_start: 0.8505 (m) cc_final: 0.8261 (p) outliers start: 8 outliers final: 4 residues processed: 393 average time/residue: 1.7385 time to fit residues: 781.1584 Evaluate side-chains 272 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 3.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1327 CYS Chi-restraints excluded: chain B residue 237 MET Chi-restraints excluded: chain G residue 1381 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 5.9990 chunk 284 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 chunk 192 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 294 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 179 optimal weight: 9.9990 chunk 219 optimal weight: 0.8980 chunk 341 optimal weight: 4.9990 overall best weight: 2.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 379 ASN A 524 GLN A 904 ASN A 989 GLN A1380 GLN A1494 HIS A1495 ASN A1563 HIS A1780 ASN A1877 GLN G 93 ASN G 102 HIS G 221 ASN G 346 GLN G 354 ASN G 440 ASN G 715 GLN G 718 ASN G 747 HIS G 908 ASN G 993 GLN G1178 GLN G1217 ASN G1241 ASN G1341 ASN G1399 ASN G1595 ASN G1851 ASN G1890 ASN G1897 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.079948 restraints weight = 52774.151| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.10 r_work: 0.2856 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30223 Z= 0.153 Angle : 0.576 12.006 40938 Z= 0.307 Chirality : 0.044 0.190 4602 Planarity : 0.004 0.033 5285 Dihedral : 4.989 58.545 4036 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.60 % Favored : 98.32 % Rotamer: Outliers : 1.51 % Allowed : 8.79 % Favored : 89.70 % 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: -0.06 (0.13), residues: 3760 helix: 0.59 (0.12), residues: 1679 sheet: -0.83 (0.20), residues: 532 loop : -0.27 (0.16), residues: 1549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 661 HIS 0.010 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.018 0.002 TYR A 417 ARG 0.005 0.001 ARG G1881 Details of bonding type rmsd hydrogen bonds : bond 0.04507 ( 1503) hydrogen bonds : angle 5.11678 ( 4209) SS BOND : bond 0.00288 ( 1) SS BOND : angle 5.26183 ( 2) covalent geometry : bond 0.00348 (30222) covalent geometry : angle 0.57508 (40936) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 3.320 Fit side-chains REVERT: A 16 GLU cc_start: 0.8541 (tp30) cc_final: 0.8192 (tp30) REVERT: A 59 ARG cc_start: 0.7853 (ptp-110) cc_final: 0.7649 (mtp85) REVERT: A 340 ARG cc_start: 0.6837 (mmt180) cc_final: 0.6270 (mmt180) REVERT: A 612 GLU cc_start: 0.8076 (tp30) cc_final: 0.7561 (tp30) REVERT: A 944 ARG cc_start: 0.8510 (ttm110) cc_final: 0.8234 (ttp80) REVERT: A 1044 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: A 1162 GLU cc_start: 0.7602 (mp0) cc_final: 0.7248 (mp0) REVERT: A 1180 ARG cc_start: 0.7056 (mpt180) cc_final: 0.6341 (mpt90) REVERT: A 1260 MET cc_start: 0.9128 (ptp) cc_final: 0.8859 (ptm) REVERT: A 1491 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7924 (tmt170) REVERT: A 1496 GLU cc_start: 0.6275 (tt0) cc_final: 0.6012 (tt0) REVERT: A 1498 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7972 (tm-30) REVERT: B 168 MET cc_start: 0.5976 (mmm) cc_final: 0.5656 (tpp) REVERT: B 183 GLN cc_start: 0.8245 (tp-100) cc_final: 0.8024 (tp40) REVERT: B 193 GLU cc_start: 0.7623 (tp30) cc_final: 0.7142 (tm-30) REVERT: B 202 GLU cc_start: 0.7506 (pm20) cc_final: 0.6755 (pm20) REVERT: B 261 GLN cc_start: 0.7694 (mt0) cc_final: 0.7360 (mt0) REVERT: B 272 GLU cc_start: 0.7820 (tt0) cc_final: 0.7614 (tt0) REVERT: G 81 ASP cc_start: 0.7600 (m-30) cc_final: 0.7280 (m-30) REVERT: G 97 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7452 (pt0) REVERT: G 132 MET cc_start: 0.8241 (mmp) cc_final: 0.7834 (mpm) REVERT: G 167 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7906 (p0) REVERT: G 325 GLU cc_start: 0.8390 (tp30) cc_final: 0.7838 (tp30) REVERT: G 329 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7470 (mt-10) REVERT: G 387 TYR cc_start: 0.8271 (t80) cc_final: 0.7936 (t80) REVERT: G 447 ASN cc_start: 0.8366 (t0) cc_final: 0.7745 (p0) REVERT: G 696 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: G 1309 GLU cc_start: 0.6653 (mm-30) cc_final: 0.6409 (mm-30) outliers start: 49 outliers final: 17 residues processed: 319 average time/residue: 1.6021 time to fit residues: 592.0273 Evaluate side-chains 275 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 252 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1491 ARG Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1904 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 25 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 220 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 129 optimal weight: 5.9990 chunk 142 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 chunk 322 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 318 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A 904 ASN A1494 HIS A1806 GLN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN G 221 ASN G 650 ASN G1355 ASN G1399 ASN G1421 ASN ** G1564 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.107462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.078498 restraints weight = 53345.835| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 2.13 r_work: 0.2845 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30223 Z= 0.217 Angle : 0.596 11.799 40938 Z= 0.313 Chirality : 0.045 0.187 4602 Planarity : 0.004 0.041 5285 Dihedral : 4.804 59.619 4031 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.58 % Favored : 97.37 % Rotamer: Outliers : 2.13 % Allowed : 10.42 % Favored : 87.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.14), residues: 3760 helix: 1.18 (0.12), residues: 1687 sheet: -0.66 (0.20), residues: 532 loop : -0.11 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 865 HIS 0.010 0.001 HIS A1689 PHE 0.023 0.002 PHE A 35 TYR 0.021 0.002 TYR A 722 ARG 0.007 0.001 ARG G1956 Details of bonding type rmsd hydrogen bonds : bond 0.04615 ( 1503) hydrogen bonds : angle 4.95694 ( 4209) SS BOND : bond 0.03057 ( 1) SS BOND : angle 9.85791 ( 2) covalent geometry : bond 0.00513 (30222) covalent geometry : angle 0.59198 (40936) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 258 time to evaluate : 3.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8453 (tp30) cc_final: 0.8096 (tp30) REVERT: A 20 TYR cc_start: 0.8452 (m-80) cc_final: 0.8227 (m-80) REVERT: A 59 ARG cc_start: 0.7907 (ptp-110) cc_final: 0.7670 (mtp85) REVERT: A 340 ARG cc_start: 0.6703 (mmt180) cc_final: 0.5539 (mpt180) REVERT: A 517 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.6971 (mm-30) REVERT: A 529 MET cc_start: 0.8949 (mmp) cc_final: 0.8413 (mmp) REVERT: A 612 GLU cc_start: 0.8188 (tp30) cc_final: 0.7763 (tp30) REVERT: A 1044 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: A 1159 GLU cc_start: 0.8014 (mp0) cc_final: 0.7661 (pm20) REVERT: A 1162 GLU cc_start: 0.7551 (mp0) cc_final: 0.7150 (mp0) REVERT: A 1180 ARG cc_start: 0.6997 (mpt180) cc_final: 0.6206 (mpt90) REVERT: A 1260 MET cc_start: 0.9223 (ptp) cc_final: 0.8952 (ptm) REVERT: B 168 MET cc_start: 0.6019 (mmm) cc_final: 0.5655 (tpp) REVERT: B 183 GLN cc_start: 0.8247 (tp-100) cc_final: 0.8020 (tp40) REVERT: B 193 GLU cc_start: 0.7603 (tp30) cc_final: 0.7210 (tm-30) REVERT: B 202 GLU cc_start: 0.7491 (pm20) cc_final: 0.6741 (pm20) REVERT: B 224 GLN cc_start: 0.8191 (mm-40) cc_final: 0.7899 (mm-40) REVERT: B 261 GLN cc_start: 0.7753 (mt0) cc_final: 0.7446 (mt0) REVERT: G 81 ASP cc_start: 0.7565 (m-30) cc_final: 0.7232 (m-30) REVERT: G 97 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7337 (pt0) REVERT: G 132 MET cc_start: 0.8221 (mmp) cc_final: 0.7883 (mpm) REVERT: G 167 ASP cc_start: 0.8204 (OUTLIER) cc_final: 0.7797 (p0) REVERT: G 325 GLU cc_start: 0.8476 (tp30) cc_final: 0.7858 (tp30) REVERT: G 329 GLU cc_start: 0.7772 (mt-10) cc_final: 0.7448 (mt-10) REVERT: G 387 TYR cc_start: 0.8372 (t80) cc_final: 0.7957 (t80) REVERT: G 696 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: G 831 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8329 (mtmm) REVERT: G 1309 GLU cc_start: 0.6573 (mm-30) cc_final: 0.6339 (mm-30) REVERT: G 1319 MET cc_start: 0.8791 (ttt) cc_final: 0.8541 (ttt) REVERT: G 1784 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8808 (tmt) REVERT: G 1801 ASP cc_start: 0.7668 (OUTLIER) cc_final: 0.7335 (p0) outliers start: 69 outliers final: 21 residues processed: 306 average time/residue: 1.6005 time to fit residues: 570.9284 Evaluate side-chains 274 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 3.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1203 ASP Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 306 ILE Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 843 ILE Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 268 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 247 optimal weight: 9.9990 chunk 221 optimal weight: 0.0870 chunk 120 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 316 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 265 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A1494 HIS A1495 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 752 GLN G1367 GLN G1399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.108314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.079666 restraints weight = 53363.415| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.00 r_work: 0.2871 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30223 Z= 0.164 Angle : 0.537 10.691 40938 Z= 0.282 Chirality : 0.043 0.169 4602 Planarity : 0.004 0.037 5285 Dihedral : 4.622 59.144 4030 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.21 % Favored : 97.77 % Rotamer: Outliers : 2.40 % Allowed : 11.19 % Favored : 86.41 % 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: 0.79 (0.14), residues: 3760 helix: 1.45 (0.13), residues: 1688 sheet: -0.51 (0.21), residues: 533 loop : -0.01 (0.16), residues: 1539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 661 HIS 0.008 0.001 HIS A1689 PHE 0.024 0.002 PHE G 28 TYR 0.015 0.002 TYR A 722 ARG 0.006 0.000 ARG A1489 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 1503) hydrogen bonds : angle 4.80845 ( 4209) SS BOND : bond 0.02066 ( 1) SS BOND : angle 7.06389 ( 2) covalent geometry : bond 0.00383 (30222) covalent geometry : angle 0.53444 (40936) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 259 time to evaluate : 3.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8473 (tp30) cc_final: 0.8140 (tp30) REVERT: A 20 TYR cc_start: 0.8409 (m-80) cc_final: 0.8177 (m-80) REVERT: A 340 ARG cc_start: 0.6654 (mmt180) cc_final: 0.5481 (mpt180) REVERT: A 517 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6874 (mm-30) REVERT: A 612 GLU cc_start: 0.8162 (tp30) cc_final: 0.7787 (tp30) REVERT: A 958 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.7993 (m) REVERT: A 1044 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7851 (pm20) REVERT: A 1159 GLU cc_start: 0.8016 (mp0) cc_final: 0.7662 (pm20) REVERT: A 1162 GLU cc_start: 0.7461 (mp0) cc_final: 0.7110 (mp0) REVERT: A 1167 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8737 (mp) REVERT: A 1180 ARG cc_start: 0.7209 (mpt180) cc_final: 0.6411 (mpt90) REVERT: A 1260 MET cc_start: 0.9171 (ptp) cc_final: 0.8865 (ptm) REVERT: A 1491 ARG cc_start: 0.8432 (tpt90) cc_final: 0.7975 (tpp80) REVERT: A 1806 GLN cc_start: 0.7083 (tt0) cc_final: 0.6806 (tp40) REVERT: B 168 MET cc_start: 0.6037 (mmm) cc_final: 0.5691 (tpp) REVERT: B 183 GLN cc_start: 0.8276 (tp-100) cc_final: 0.8052 (tp40) REVERT: B 193 GLU cc_start: 0.7547 (tp30) cc_final: 0.7235 (tm-30) REVERT: B 194 PHE cc_start: 0.8081 (m-10) cc_final: 0.7641 (m-10) REVERT: B 202 GLU cc_start: 0.7361 (pm20) cc_final: 0.6596 (pm20) REVERT: B 224 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7853 (mm-40) REVERT: B 261 GLN cc_start: 0.7850 (mt0) cc_final: 0.7553 (mt0) REVERT: G 67 TYR cc_start: 0.8122 (t80) cc_final: 0.7642 (t80) REVERT: G 81 ASP cc_start: 0.7506 (m-30) cc_final: 0.7173 (m-30) REVERT: G 97 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: G 121 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8224 (mt-10) REVERT: G 132 MET cc_start: 0.8206 (mmp) cc_final: 0.7784 (mpm) REVERT: G 167 ASP cc_start: 0.8195 (p0) cc_final: 0.7774 (p0) REVERT: G 325 GLU cc_start: 0.8494 (tp30) cc_final: 0.7878 (tp30) REVERT: G 329 GLU cc_start: 0.7736 (mt-10) cc_final: 0.7406 (mt-10) REVERT: G 387 TYR cc_start: 0.8373 (t80) cc_final: 0.7943 (t80) REVERT: G 1309 GLU cc_start: 0.6530 (mm-30) cc_final: 0.6324 (mm-30) REVERT: G 1319 MET cc_start: 0.8786 (ttt) cc_final: 0.8560 (ttt) REVERT: G 1467 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8118 (mp0) REVERT: G 1784 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8780 (tmt) REVERT: G 1838 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8027 (mtp) REVERT: G 1849 ARG cc_start: 0.6451 (ttp-110) cc_final: 0.6115 (ttp-110) outliers start: 78 outliers final: 32 residues processed: 317 average time/residue: 1.4721 time to fit residues: 547.0249 Evaluate side-chains 287 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 247 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1173 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1838 MET Chi-restraints excluded: chain G residue 1904 LEU Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 93 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 273 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 295 optimal weight: 5.9990 chunk 37 optimal weight: 0.2980 chunk 143 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 overall best weight: 3.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A1494 HIS A1783 ASN ** B 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 418 ASN G1399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.079858 restraints weight = 53259.469| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 1.96 r_work: 0.2873 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2759 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 30223 Z= 0.176 Angle : 0.545 10.288 40938 Z= 0.284 Chirality : 0.043 0.168 4602 Planarity : 0.004 0.041 5285 Dihedral : 4.601 59.472 4030 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.66 % Favored : 97.29 % Rotamer: Outliers : 2.22 % Allowed : 12.36 % Favored : 85.42 % 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: 0.88 (0.14), residues: 3760 helix: 1.51 (0.13), residues: 1685 sheet: -0.45 (0.21), residues: 521 loop : 0.04 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 865 HIS 0.008 0.001 HIS A1689 PHE 0.026 0.002 PHE G 28 TYR 0.017 0.002 TYR A 722 ARG 0.007 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 1503) hydrogen bonds : angle 4.78311 ( 4209) SS BOND : bond 0.03106 ( 1) SS BOND : angle 6.08186 ( 2) covalent geometry : bond 0.00412 (30222) covalent geometry : angle 0.54285 (40936) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 260 time to evaluate : 3.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8459 (tp30) cc_final: 0.8118 (tp30) REVERT: A 340 ARG cc_start: 0.6694 (mmt180) cc_final: 0.5534 (mpt180) REVERT: A 517 GLU cc_start: 0.7153 (OUTLIER) cc_final: 0.6809 (mm-30) REVERT: A 529 MET cc_start: 0.8927 (mmp) cc_final: 0.8480 (mmp) REVERT: A 612 GLU cc_start: 0.8168 (tp30) cc_final: 0.7808 (tp30) REVERT: A 958 SER cc_start: 0.8366 (OUTLIER) cc_final: 0.8011 (m) REVERT: A 1044 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7850 (pm20) REVERT: A 1159 GLU cc_start: 0.8032 (mp0) cc_final: 0.7673 (pm20) REVERT: A 1162 GLU cc_start: 0.7486 (mp0) cc_final: 0.7102 (mp0) REVERT: A 1167 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8736 (mp) REVERT: A 1180 ARG cc_start: 0.7245 (mpt180) cc_final: 0.6415 (mpt90) REVERT: A 1209 ASP cc_start: 0.8468 (t70) cc_final: 0.8166 (t70) REVERT: A 1298 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8608 (tp) REVERT: A 1498 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7049 (tm-30) REVERT: A 1806 GLN cc_start: 0.6951 (tt0) cc_final: 0.6656 (tp40) REVERT: B 168 MET cc_start: 0.5983 (mmm) cc_final: 0.5633 (tpp) REVERT: B 193 GLU cc_start: 0.7574 (tp30) cc_final: 0.7184 (tm-30) REVERT: B 194 PHE cc_start: 0.8094 (m-10) cc_final: 0.7644 (m-10) REVERT: G 67 TYR cc_start: 0.8161 (t80) cc_final: 0.7619 (t80) REVERT: G 81 ASP cc_start: 0.7507 (m-30) cc_final: 0.7168 (m-30) REVERT: G 97 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: G 121 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8206 (mt-10) REVERT: G 132 MET cc_start: 0.8170 (mmp) cc_final: 0.7693 (mpm) REVERT: G 167 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7758 (p0) REVERT: G 325 GLU cc_start: 0.8497 (tp30) cc_final: 0.7879 (tp30) REVERT: G 329 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7383 (mt-10) REVERT: G 346 GLN cc_start: 0.8480 (tt0) cc_final: 0.8221 (tt0) REVERT: G 387 TYR cc_start: 0.8395 (t80) cc_final: 0.7986 (t80) REVERT: G 1309 GLU cc_start: 0.6564 (mm-30) cc_final: 0.6348 (mm-30) REVERT: G 1319 MET cc_start: 0.8798 (ttt) cc_final: 0.8591 (ttt) REVERT: G 1467 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8103 (mp0) REVERT: G 1500 GLU cc_start: 0.7576 (tm-30) cc_final: 0.7287 (tm-30) REVERT: G 1650 VAL cc_start: 0.9218 (OUTLIER) cc_final: 0.8833 (m) REVERT: G 1784 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8784 (tmt) REVERT: G 1801 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7173 (p0) REVERT: G 1849 ARG cc_start: 0.6533 (ttp-110) cc_final: 0.6252 (ttp80) outliers start: 72 outliers final: 32 residues processed: 312 average time/residue: 1.5059 time to fit residues: 548.2016 Evaluate side-chains 294 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 3.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 297 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 418 ASN Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1689 ASP Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 18 optimal weight: 3.9990 chunk 249 optimal weight: 6.9990 chunk 172 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 316 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 301 optimal weight: 8.9990 chunk 354 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 904 ASN A1494 HIS B 261 GLN G 181 HIS G 418 ASN G 715 GLN G1399 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.106807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.078456 restraints weight = 53468.779| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.97 r_work: 0.2860 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 30223 Z= 0.218 Angle : 0.568 10.706 40938 Z= 0.297 Chirality : 0.045 0.178 4602 Planarity : 0.004 0.037 5285 Dihedral : 4.674 59.863 4030 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.69 % Favored : 97.26 % Rotamer: Outliers : 2.37 % Allowed : 13.04 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.79 (0.14), residues: 3760 helix: 1.41 (0.13), residues: 1693 sheet: -0.42 (0.21), residues: 509 loop : -0.01 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 865 HIS 0.009 0.001 HIS A1689 PHE 0.027 0.002 PHE G 28 TYR 0.018 0.002 TYR A 722 ARG 0.006 0.001 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 1503) hydrogen bonds : angle 4.83019 ( 4209) SS BOND : bond 0.03191 ( 1) SS BOND : angle 8.31492 ( 2) covalent geometry : bond 0.00514 (30222) covalent geometry : angle 0.56504 (40936) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 253 time to evaluate : 3.530 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8448 (tp30) cc_final: 0.8104 (tp30) REVERT: A 340 ARG cc_start: 0.6721 (mmt180) cc_final: 0.5879 (mpt180) REVERT: A 517 GLU cc_start: 0.7166 (OUTLIER) cc_final: 0.6822 (mm-30) REVERT: A 529 MET cc_start: 0.8911 (mmp) cc_final: 0.8655 (mmp) REVERT: A 612 GLU cc_start: 0.8158 (tp30) cc_final: 0.7814 (tp30) REVERT: A 958 SER cc_start: 0.8372 (OUTLIER) cc_final: 0.8008 (m) REVERT: A 1044 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7911 (pm20) REVERT: A 1142 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8179 (mt-10) REVERT: A 1159 GLU cc_start: 0.8065 (mp0) cc_final: 0.7673 (pm20) REVERT: A 1162 GLU cc_start: 0.7554 (mp0) cc_final: 0.7124 (mp0) REVERT: A 1167 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8745 (mp) REVERT: A 1180 ARG cc_start: 0.7217 (mpt180) cc_final: 0.6387 (mpt90) REVERT: A 1209 ASP cc_start: 0.8514 (t70) cc_final: 0.8199 (t70) REVERT: A 1260 MET cc_start: 0.9074 (ptp) cc_final: 0.8834 (ptm) REVERT: A 1298 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8633 (tp) REVERT: A 1498 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: A 1806 GLN cc_start: 0.6955 (tt0) cc_final: 0.6670 (tp40) REVERT: B 168 MET cc_start: 0.6025 (mmm) cc_final: 0.5642 (tpp) REVERT: G 67 TYR cc_start: 0.8157 (t80) cc_final: 0.7629 (t80) REVERT: G 81 ASP cc_start: 0.7518 (m-30) cc_final: 0.7182 (m-30) REVERT: G 97 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7323 (pt0) REVERT: G 121 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8223 (mt-10) REVERT: G 132 MET cc_start: 0.8184 (mmp) cc_final: 0.7743 (mpm) REVERT: G 167 ASP cc_start: 0.8192 (OUTLIER) cc_final: 0.7773 (p0) REVERT: G 325 GLU cc_start: 0.8503 (tp30) cc_final: 0.7869 (tp30) REVERT: G 329 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7358 (mt-10) REVERT: G 387 TYR cc_start: 0.8388 (t80) cc_final: 0.8012 (t80) REVERT: G 659 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8414 (mp) REVERT: G 696 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7629 (mp0) REVERT: G 831 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8343 (mtmm) REVERT: G 1467 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: G 1500 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7312 (tm-30) REVERT: G 1650 VAL cc_start: 0.9221 (OUTLIER) cc_final: 0.8846 (m) REVERT: G 1784 MET cc_start: 0.9119 (OUTLIER) cc_final: 0.8801 (tmt) REVERT: G 1801 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7171 (p0) REVERT: G 1849 ARG cc_start: 0.6520 (ttp-110) cc_final: 0.6049 (ttp80) REVERT: G 1986 LYS cc_start: 0.6947 (ttmt) cc_final: 0.6710 (ttpt) outliers start: 77 outliers final: 36 residues processed: 309 average time/residue: 1.5368 time to fit residues: 558.0248 Evaluate side-chains 297 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 246 time to evaluate : 3.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1044 GLU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 328 LEU Chi-restraints excluded: chain G residue 334 VAL Chi-restraints excluded: chain G residue 447 ASN Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 630 MET Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 696 GLU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 850 MET Chi-restraints excluded: chain G residue 880 LEU Chi-restraints excluded: chain G residue 1190 SER Chi-restraints excluded: chain G residue 1348 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1382 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1689 ASP Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1801 ASP Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 27 optimal weight: 0.8980 chunk 333 optimal weight: 8.9990 chunk 90 optimal weight: 0.4980 chunk 357 optimal weight: 20.0000 chunk 109 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 274 optimal weight: 5.9990 chunk 181 optimal weight: 3.9990 chunk 235 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 373 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 904 ASN A1494 HIS G1008 GLN G1399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.110468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.082399 restraints weight = 53010.712| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.96 r_work: 0.2922 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 30223 Z= 0.100 Angle : 0.490 9.675 40938 Z= 0.257 Chirality : 0.041 0.160 4602 Planarity : 0.003 0.037 5285 Dihedral : 4.284 58.314 4030 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.77 % Rotamer: Outliers : 1.60 % Allowed : 14.03 % Favored : 84.37 % 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: 1.10 (0.14), residues: 3760 helix: 1.69 (0.13), residues: 1695 sheet: -0.27 (0.22), residues: 505 loop : 0.13 (0.16), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.026 0.001 PHE G 28 TYR 0.023 0.001 TYR B 294 ARG 0.009 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 1503) hydrogen bonds : angle 4.58176 ( 4209) SS BOND : bond 0.01334 ( 1) SS BOND : angle 4.33557 ( 2) covalent geometry : bond 0.00222 (30222) covalent geometry : angle 0.48894 (40936) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 3.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8489 (tp30) cc_final: 0.8183 (tp30) REVERT: A 20 TYR cc_start: 0.8329 (m-80) cc_final: 0.8048 (m-80) REVERT: A 340 ARG cc_start: 0.6662 (mmt180) cc_final: 0.5770 (mpt180) REVERT: A 529 MET cc_start: 0.8893 (mmp) cc_final: 0.8519 (mmp) REVERT: A 612 GLU cc_start: 0.8184 (tp30) cc_final: 0.7848 (tp30) REVERT: A 1159 GLU cc_start: 0.7963 (mp0) cc_final: 0.7632 (pm20) REVERT: A 1162 GLU cc_start: 0.7493 (mp0) cc_final: 0.7122 (mp0) REVERT: A 1180 ARG cc_start: 0.7188 (mpt180) cc_final: 0.6495 (mpt90) REVERT: A 1209 ASP cc_start: 0.8435 (t70) cc_final: 0.8196 (t70) REVERT: A 1496 GLU cc_start: 0.6179 (tt0) cc_final: 0.5921 (tt0) REVERT: A 1498 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.6987 (tm-30) REVERT: A 1757 GLU cc_start: 0.5262 (tt0) cc_final: 0.5015 (pt0) REVERT: A 1806 GLN cc_start: 0.6972 (tt0) cc_final: 0.6701 (tp40) REVERT: B 168 MET cc_start: 0.5971 (mmm) cc_final: 0.5591 (tpp) REVERT: B 224 GLN cc_start: 0.8408 (tp40) cc_final: 0.7879 (mm-40) REVERT: G 67 TYR cc_start: 0.8045 (t80) cc_final: 0.7645 (t80) REVERT: G 81 ASP cc_start: 0.7472 (m-30) cc_final: 0.7146 (m-30) REVERT: G 97 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7264 (pt0) REVERT: G 132 MET cc_start: 0.8145 (mmp) cc_final: 0.7679 (mpm) REVERT: G 167 ASP cc_start: 0.8105 (OUTLIER) cc_final: 0.7667 (p0) REVERT: G 325 GLU cc_start: 0.8483 (tp30) cc_final: 0.7879 (tp30) REVERT: G 329 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7295 (mt-10) REVERT: G 346 GLN cc_start: 0.8358 (tt0) cc_final: 0.8028 (tt0) REVERT: G 387 TYR cc_start: 0.8421 (t80) cc_final: 0.8040 (t80) REVERT: G 659 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8333 (mp) REVERT: G 831 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8357 (mtmm) REVERT: G 1319 MET cc_start: 0.8791 (ttt) cc_final: 0.8495 (ttt) REVERT: G 1467 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8060 (pm20) REVERT: G 1784 MET cc_start: 0.9083 (ppp) cc_final: 0.8738 (tmt) REVERT: G 1836 MET cc_start: 0.8765 (mmm) cc_final: 0.8481 (mmp) REVERT: G 1849 ARG cc_start: 0.6693 (ttp-110) cc_final: 0.6399 (ttp80) REVERT: G 1986 LYS cc_start: 0.7011 (ttmt) cc_final: 0.6786 (ttpt) REVERT: G 2045 TRP cc_start: 0.7820 (t-100) cc_final: 0.6935 (t-100) outliers start: 52 outliers final: 18 residues processed: 316 average time/residue: 1.5574 time to fit residues: 581.3376 Evaluate side-chains 278 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 167 ASP Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 135 optimal weight: 8.9990 chunk 349 optimal weight: 5.9990 chunk 40 optimal weight: 6.9990 chunk 310 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 chunk 139 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 375 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A1494 HIS G1352 HIS G1399 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.109270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081325 restraints weight = 53718.305| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.96 r_work: 0.2912 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 30223 Z= 0.114 Angle : 0.500 9.522 40938 Z= 0.261 Chirality : 0.042 0.196 4602 Planarity : 0.004 0.040 5285 Dihedral : 4.256 59.067 4030 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Rotamer: Outliers : 1.51 % Allowed : 14.89 % Favored : 83.60 % 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: 1.21 (0.14), residues: 3760 helix: 1.78 (0.13), residues: 1682 sheet: -0.21 (0.22), residues: 499 loop : 0.19 (0.16), residues: 1579 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.027 0.001 PHE G 28 TYR 0.017 0.001 TYR B 294 ARG 0.009 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 1503) hydrogen bonds : angle 4.56561 ( 4209) SS BOND : bond 0.02136 ( 1) SS BOND : angle 3.83793 ( 2) covalent geometry : bond 0.00260 (30222) covalent geometry : angle 0.49890 (40936) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8512 (tp30) cc_final: 0.8190 (tp30) REVERT: A 340 ARG cc_start: 0.6641 (mmt180) cc_final: 0.5745 (mpt180) REVERT: A 517 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6866 (mm-30) REVERT: A 612 GLU cc_start: 0.8164 (tp30) cc_final: 0.7845 (tp30) REVERT: A 1142 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 1159 GLU cc_start: 0.7988 (mp0) cc_final: 0.7694 (pm20) REVERT: A 1162 GLU cc_start: 0.7306 (mp0) cc_final: 0.6896 (mp0) REVERT: A 1180 ARG cc_start: 0.7198 (mpt180) cc_final: 0.6519 (mpt90) REVERT: A 1209 ASP cc_start: 0.8447 (t70) cc_final: 0.8126 (t70) REVERT: A 1498 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7041 (tm-30) REVERT: A 1757 GLU cc_start: 0.5021 (tt0) cc_final: 0.4785 (pt0) REVERT: A 1806 GLN cc_start: 0.6871 (tt0) cc_final: 0.6601 (tp40) REVERT: B 168 MET cc_start: 0.5947 (mmm) cc_final: 0.5551 (tpp) REVERT: B 224 GLN cc_start: 0.8385 (tp40) cc_final: 0.7827 (mm-40) REVERT: G 67 TYR cc_start: 0.8079 (t80) cc_final: 0.7659 (t80) REVERT: G 81 ASP cc_start: 0.7489 (m-30) cc_final: 0.7151 (m-30) REVERT: G 97 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7257 (pt0) REVERT: G 111 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7964 (mt-10) REVERT: G 132 MET cc_start: 0.8170 (mmp) cc_final: 0.7670 (mpm) REVERT: G 167 ASP cc_start: 0.8146 (p0) cc_final: 0.7785 (p0) REVERT: G 325 GLU cc_start: 0.8494 (tp30) cc_final: 0.7880 (tp30) REVERT: G 329 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7391 (mt-10) REVERT: G 387 TYR cc_start: 0.8418 (t80) cc_final: 0.7985 (t80) REVERT: G 497 LYS cc_start: 0.7599 (mmtm) cc_final: 0.7334 (mmtt) REVERT: G 659 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8329 (mp) REVERT: G 694 TYR cc_start: 0.8504 (m-10) cc_final: 0.8107 (m-10) REVERT: G 831 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8386 (mtmm) REVERT: G 1252 SER cc_start: 0.8765 (p) cc_final: 0.8448 (t) REVERT: G 1319 MET cc_start: 0.8781 (ttt) cc_final: 0.8494 (ttt) REVERT: G 1467 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8074 (pm20) REVERT: G 1784 MET cc_start: 0.9089 (OUTLIER) cc_final: 0.8744 (tmt) REVERT: G 1836 MET cc_start: 0.8760 (mmm) cc_final: 0.8415 (mmp) REVERT: G 1849 ARG cc_start: 0.6616 (ttp-110) cc_final: 0.6340 (ttp80) REVERT: G 1986 LYS cc_start: 0.7010 (ttmt) cc_final: 0.6791 (ttpt) REVERT: G 2045 TRP cc_start: 0.7856 (t-100) cc_final: 0.6943 (t-100) outliers start: 49 outliers final: 26 residues processed: 303 average time/residue: 1.4619 time to fit residues: 518.1130 Evaluate side-chains 290 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 257 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1127 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1689 ASP Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 261 optimal weight: 6.9990 chunk 252 optimal weight: 8.9990 chunk 296 optimal weight: 9.9990 chunk 177 optimal weight: 0.1980 chunk 140 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 273 optimal weight: 0.8980 chunk 148 optimal weight: 5.9990 chunk 231 optimal weight: 0.5980 chunk 292 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A1494 HIS A1877 GLN B 271 ASN G 346 GLN G1399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.108455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.080884 restraints weight = 53247.529| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.88 r_work: 0.2905 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30223 Z= 0.136 Angle : 0.518 9.567 40938 Z= 0.269 Chirality : 0.042 0.189 4602 Planarity : 0.004 0.043 5285 Dihedral : 4.322 59.896 4030 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.21 % Favored : 97.74 % Rotamer: Outliers : 1.54 % Allowed : 15.14 % Favored : 83.32 % 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: 1.19 (0.14), residues: 3760 helix: 1.74 (0.13), residues: 1688 sheet: -0.19 (0.22), residues: 499 loop : 0.20 (0.16), residues: 1573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 661 HIS 0.007 0.001 HIS A1689 PHE 0.028 0.001 PHE G 28 TYR 0.020 0.001 TYR B 294 ARG 0.010 0.000 ARG A 709 Details of bonding type rmsd hydrogen bonds : bond 0.03689 ( 1503) hydrogen bonds : angle 4.58117 ( 4209) SS BOND : bond 0.02370 ( 1) SS BOND : angle 4.75393 ( 2) covalent geometry : bond 0.00315 (30222) covalent geometry : angle 0.51660 (40936) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 259 time to evaluate : 3.417 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8443 (tp30) cc_final: 0.8122 (tp30) REVERT: A 20 TYR cc_start: 0.8356 (m-80) cc_final: 0.8121 (m-80) REVERT: A 340 ARG cc_start: 0.6650 (mmt180) cc_final: 0.5821 (mpt180) REVERT: A 517 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6833 (mm-30) REVERT: A 529 MET cc_start: 0.8888 (mmp) cc_final: 0.8418 (mmp) REVERT: A 612 GLU cc_start: 0.8187 (tp30) cc_final: 0.7880 (tp30) REVERT: A 1142 GLU cc_start: 0.8479 (mt-10) cc_final: 0.8154 (mt-10) REVERT: A 1162 GLU cc_start: 0.7321 (mp0) cc_final: 0.6889 (mp0) REVERT: A 1180 ARG cc_start: 0.7263 (mpt180) cc_final: 0.6584 (mpt90) REVERT: A 1209 ASP cc_start: 0.8461 (t70) cc_final: 0.8125 (t70) REVERT: A 1298 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8530 (tp) REVERT: A 1498 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.6927 (tm-30) REVERT: A 1757 GLU cc_start: 0.5050 (tt0) cc_final: 0.4821 (pt0) REVERT: A 1806 GLN cc_start: 0.6968 (tt0) cc_final: 0.6683 (tp40) REVERT: B 168 MET cc_start: 0.5956 (mmm) cc_final: 0.5584 (tpp) REVERT: B 224 GLN cc_start: 0.8397 (tp40) cc_final: 0.7823 (mm-40) REVERT: G 67 TYR cc_start: 0.8076 (t80) cc_final: 0.7649 (t80) REVERT: G 81 ASP cc_start: 0.7566 (m-30) cc_final: 0.7238 (m-30) REVERT: G 97 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7260 (pt0) REVERT: G 111 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7970 (mt-10) REVERT: G 121 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8207 (mt-10) REVERT: G 132 MET cc_start: 0.8043 (mmp) cc_final: 0.7614 (mpm) REVERT: G 167 ASP cc_start: 0.8129 (p0) cc_final: 0.7813 (p0) REVERT: G 325 GLU cc_start: 0.8485 (tp30) cc_final: 0.7879 (tp30) REVERT: G 329 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7311 (mt-10) REVERT: G 387 TYR cc_start: 0.8403 (t80) cc_final: 0.8035 (t80) REVERT: G 447 ASN cc_start: 0.8621 (t0) cc_final: 0.7817 (p0) REVERT: G 659 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8314 (mp) REVERT: G 694 TYR cc_start: 0.8501 (m-10) cc_final: 0.8259 (m-10) REVERT: G 831 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8374 (mtmm) REVERT: G 1252 SER cc_start: 0.8754 (p) cc_final: 0.8450 (t) REVERT: G 1319 MET cc_start: 0.8781 (ttt) cc_final: 0.8490 (ttt) REVERT: G 1349 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.8221 (mtpm) REVERT: G 1467 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: G 1784 MET cc_start: 0.9092 (OUTLIER) cc_final: 0.8744 (tmt) REVERT: G 1836 MET cc_start: 0.8746 (mmm) cc_final: 0.8391 (mmp) REVERT: G 1986 LYS cc_start: 0.7054 (ttmt) cc_final: 0.6804 (ttpt) REVERT: G 2045 TRP cc_start: 0.7849 (t-100) cc_final: 0.6929 (t-100) outliers start: 50 outliers final: 28 residues processed: 297 average time/residue: 1.5209 time to fit residues: 532.8699 Evaluate side-chains 290 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 1096 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1298 ILE Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1560 MET Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 510 SER Chi-restraints excluded: chain G residue 658 MET Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 827 VAL Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 1349 LYS Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1689 ASP Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1753 LYS Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 20 optimal weight: 3.9990 chunk 255 optimal weight: 0.0060 chunk 210 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 109 optimal weight: 0.8980 chunk 347 optimal weight: 6.9990 chunk 330 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 328 optimal weight: 2.9990 chunk 155 optimal weight: 20.0000 chunk 106 optimal weight: 0.0770 overall best weight: 1.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A1482 GLN A1494 HIS A1495 ASN G1399 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.082654 restraints weight = 53479.378| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.88 r_work: 0.2934 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 30223 Z= 0.104 Angle : 0.501 9.467 40938 Z= 0.260 Chirality : 0.042 0.191 4602 Planarity : 0.004 0.044 5285 Dihedral : 4.213 59.237 4030 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.05 % Favored : 97.90 % Rotamer: Outliers : 1.26 % Allowed : 15.38 % Favored : 83.35 % 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: 1.27 (0.14), residues: 3760 helix: 1.78 (0.13), residues: 1694 sheet: -0.08 (0.22), residues: 505 loop : 0.24 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 661 HIS 0.005 0.001 HIS A1689 PHE 0.025 0.001 PHE A 35 TYR 0.019 0.001 TYR B 294 ARG 0.018 0.000 ARG G1849 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 1503) hydrogen bonds : angle 4.50651 ( 4209) SS BOND : bond 0.01809 ( 1) SS BOND : angle 3.88478 ( 2) covalent geometry : bond 0.00234 (30222) covalent geometry : angle 0.50059 (40936) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.8491 (tp30) cc_final: 0.8174 (tp30) REVERT: A 340 ARG cc_start: 0.6616 (mmt180) cc_final: 0.5720 (mpt180) REVERT: A 517 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.6816 (mm-30) REVERT: A 529 MET cc_start: 0.8860 (mmp) cc_final: 0.8454 (mmp) REVERT: A 612 GLU cc_start: 0.8134 (tp30) cc_final: 0.7828 (tp30) REVERT: A 1142 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8133 (mt-10) REVERT: A 1159 GLU cc_start: 0.7915 (mp0) cc_final: 0.7621 (pm20) REVERT: A 1162 GLU cc_start: 0.7310 (mp0) cc_final: 0.6906 (mp0) REVERT: A 1180 ARG cc_start: 0.7229 (mpt180) cc_final: 0.6554 (mpt90) REVERT: A 1209 ASP cc_start: 0.8416 (t70) cc_final: 0.8170 (t70) REVERT: A 1498 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6960 (tm-30) REVERT: A 1757 GLU cc_start: 0.4985 (tt0) cc_final: 0.4758 (pt0) REVERT: A 1806 GLN cc_start: 0.6946 (tt0) cc_final: 0.6734 (tp40) REVERT: B 168 MET cc_start: 0.5885 (mmm) cc_final: 0.5514 (tpp) REVERT: B 237 MET cc_start: 0.8322 (mmp) cc_final: 0.7921 (mpm) REVERT: B 262 ASP cc_start: 0.8297 (m-30) cc_final: 0.8031 (m-30) REVERT: B 271 ASN cc_start: 0.7911 (m110) cc_final: 0.7503 (m110) REVERT: B 272 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7339 (tm-30) REVERT: G 67 TYR cc_start: 0.8094 (t80) cc_final: 0.7684 (t80) REVERT: G 81 ASP cc_start: 0.7587 (m-30) cc_final: 0.7262 (m-30) REVERT: G 95 TYR cc_start: 0.6773 (m-80) cc_final: 0.6553 (m-80) REVERT: G 97 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7251 (pt0) REVERT: G 111 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7921 (mt-10) REVERT: G 132 MET cc_start: 0.8161 (mmp) cc_final: 0.7695 (mpm) REVERT: G 167 ASP cc_start: 0.8105 (p0) cc_final: 0.7802 (p0) REVERT: G 387 TYR cc_start: 0.8390 (t80) cc_final: 0.8012 (t80) REVERT: G 447 ASN cc_start: 0.8589 (t0) cc_final: 0.7834 (p0) REVERT: G 497 LYS cc_start: 0.7567 (mmtm) cc_final: 0.7302 (mmtt) REVERT: G 659 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8316 (mp) REVERT: G 694 TYR cc_start: 0.8432 (m-10) cc_final: 0.8034 (m-10) REVERT: G 831 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8363 (mtmm) REVERT: G 1252 SER cc_start: 0.8685 (p) cc_final: 0.8402 (t) REVERT: G 1319 MET cc_start: 0.8758 (ttt) cc_final: 0.8466 (ttt) REVERT: G 1467 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8099 (pm20) REVERT: G 1784 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8725 (tmt) REVERT: G 1836 MET cc_start: 0.8742 (mmm) cc_final: 0.8344 (mmp) REVERT: G 1849 ARG cc_start: 0.6397 (ttp-110) cc_final: 0.6113 (ttp80) REVERT: G 1986 LYS cc_start: 0.7044 (ttmt) cc_final: 0.6819 (ttpt) REVERT: G 2045 TRP cc_start: 0.7847 (t-100) cc_final: 0.6922 (t-100) outliers start: 41 outliers final: 23 residues processed: 291 average time/residue: 1.5129 time to fit residues: 515.2580 Evaluate side-chains 281 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 250 time to evaluate : 3.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 517 GLU Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1179 LEU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1395 LYS Chi-restraints excluded: chain A residue 1445 MET Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1785 THR Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 272 GLU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 41 LEU Chi-restraints excluded: chain G residue 97 GLU Chi-restraints excluded: chain G residue 659 LEU Chi-restraints excluded: chain G residue 688 LEU Chi-restraints excluded: chain G residue 831 LYS Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1467 GLU Chi-restraints excluded: chain G residue 1472 VAL Chi-restraints excluded: chain G residue 1585 SER Chi-restraints excluded: chain G residue 1586 SER Chi-restraints excluded: chain G residue 1616 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1689 ASP Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1760 THR Chi-restraints excluded: chain G residue 1784 MET Chi-restraints excluded: chain G residue 1936 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 352 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 286 optimal weight: 0.9990 chunk 217 optimal weight: 0.0040 chunk 102 optimal weight: 8.9990 chunk 119 optimal weight: 6.9990 chunk 24 optimal weight: 4.9990 chunk 312 optimal weight: 10.0000 overall best weight: 1.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN A 758 ASN A1494 HIS A1877 GLN B 271 ASN G1399 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.108947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.081314 restraints weight = 53517.389| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.07 r_work: 0.2910 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30223 Z= 0.125 Angle : 0.509 9.487 40938 Z= 0.263 Chirality : 0.042 0.186 4602 Planarity : 0.004 0.038 5285 Dihedral : 4.247 59.789 4030 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.29 % Favored : 97.66 % Rotamer: Outliers : 1.29 % Allowed : 15.63 % Favored : 83.08 % 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: 1.30 (0.14), residues: 3760 helix: 1.80 (0.13), residues: 1687 sheet: -0.10 (0.22), residues: 515 loop : 0.29 (0.16), residues: 1558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 661 HIS 0.006 0.001 HIS A1689 PHE 0.024 0.001 PHE A 35 TYR 0.019 0.001 TYR B 294 ARG 0.008 0.000 ARG A 632 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 1503) hydrogen bonds : angle 4.52751 ( 4209) SS BOND : bond 0.02185 ( 1) SS BOND : angle 4.61857 ( 2) covalent geometry : bond 0.00289 (30222) covalent geometry : angle 0.50792 (40936) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24957.89 seconds wall clock time: 430 minutes 9.53 seconds (25809.53 seconds total)