Starting phenix.real_space_refine on Sun Jul 5 17:16:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.cif Found real_map, /net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.cif" model { file = "/net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8psf_17851/07_2026/8psf_17851.map" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 104 5.16 5 C 18578 2.51 5 N 4914 2.21 5 O 5606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29204 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 12346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1579, 12346 Classifications: {'peptide': 1579} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 61, 'TRANS': 1517} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 802 Classifications: {'peptide': 163} Incomplete info: {'truncation_to_alanine': 134} Link IDs: {'PTRANS': 8, 'TRANS': 154} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 440 Unresolved non-hydrogen angles: 556 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 11, 'HIS:plan': 2, 'GLN:plan1': 6, 'ASN:plan1': 2, 'PHE:plan': 5, 'ARG:plan': 5, 'TYR:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 189 Chain: "G" Number of atoms: 16004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2034, 16004 Classifications: {'peptide': 2034} Link IDs: {'PCIS': 1, 'PTRANS': 108, 'TRANS': 1924} Chain breaks: 1 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'PNS': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.76, per 1000 atoms: 0.20 Number of scatterers: 29204 At special positions: 0 Unit cell: (181.46, 183.57, 175.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 104 16.00 P 2 15.00 O 5606 8.00 N 4914 7.00 C 18578 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=2.18 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.17 Conformation dependent library (CDL) restraints added in 1.2 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: 178 helices and 30 sheets defined 51.8% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 2 through 22 removed outlier: 3.748A 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 52 through 65 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 84 through 90 Processing helix chain 'A' and resid 329 through 351 Processing helix chain 'A' and resid 355 through 383 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: 4.116A 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 457 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 removed outlier: 3.719A pdb=" N GLY A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) 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: 3.581A 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: 4.592A 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 907 Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 929 through 933 Processing helix chain 'A' and resid 935 through 970 removed outlier: 4.094A pdb=" N THR A 950 " --> pdb=" O GLU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1002 Processing helix chain 'A' and resid 1006 through 1010 removed outlier: 3.855A pdb=" N GLU A1010 " --> pdb=" O ALA A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1017 Processing helix chain 'A' and resid 1032 through 1042 Processing helix chain 'A' and resid 1046 through 1057 Processing helix chain 'A' and resid 1085 through 1087 No H-bonds generated for 'chain 'A' and resid 1085 through 1087' Processing helix chain 'A' and resid 1088 through 1100 removed outlier: 5.983A pdb=" N THR A1095 " --> pdb=" O ALA A1091 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N SER A1096 " --> pdb=" O LYS A1092 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1111 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1194 through 1199 Processing helix chain 'A' and resid 1201 through 1208 Processing helix chain 'A' and resid 1209 through 1225 removed outlier: 3.769A pdb=" N LEU A1213 " --> pdb=" O ASP A1209 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A1214 " --> pdb=" O PRO A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1237 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1253 through 1262 Processing helix chain 'A' and resid 1271 through 1275 removed outlier: 4.604A pdb=" N LEU A1275 " --> pdb=" O ASN A1272 " (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 1468 removed outlier: 3.527A pdb=" N ARG A1448 " --> pdb=" O ASN A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1477 removed outlier: 3.813A pdb=" N LEU A1472 " --> pdb=" O GLU A1468 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A1476 " --> pdb=" O LEU A1472 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A1477 " --> pdb=" O GLU A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1481 through 1509 Processing helix chain 'A' and resid 1520 through 1528 removed outlier: 3.680A pdb=" N LEU A1526 " --> pdb=" O LEU A1522 " (cutoff:3.500A) Processing helix chain 'A' and resid 1532 through 1534 No H-bonds generated for 'chain 'A' and resid 1532 through 1534' Processing helix chain 'A' and resid 1546 through 1564 removed outlier: 3.896A pdb=" N LYS A1551 " --> pdb=" O LYS A1547 " (cutoff:3.500A) Processing helix chain 'A' and resid 1577 through 1582 removed outlier: 3.577A pdb=" N THR A1581 " --> pdb=" O GLN A1577 " (cutoff:3.500A) Processing helix chain 'A' and resid 1584 through 1586 No H-bonds generated for 'chain 'A' and resid 1584 through 1586' Processing helix chain 'A' and resid 1587 through 1601 Processing helix chain 'A' and resid 1615 through 1621 Processing helix chain 'A' and resid 1658 through 1663 removed outlier: 4.125A pdb=" N TYR A1662 " --> pdb=" O PRO A1658 " (cutoff:3.500A) removed outlier: 3.962A 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 removed outlier: 3.799A pdb=" N ILE A1738 " --> pdb=" O SER A1735 " (cutoff:3.500A) Processing helix chain 'A' and resid 1740 through 1745 removed outlier: 3.957A pdb=" N TYR A1744 " --> pdb=" O SER A1740 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1760 Processing helix chain 'A' and resid 1777 through 1779 No H-bonds generated for 'chain 'A' and resid 1777 through 1779' Processing helix chain 'A' and resid 1783 through 1791 Processing helix chain 'A' and resid 1792 through 1802 removed outlier: 3.554A pdb=" N GLN A1802 " --> pdb=" O TYR A1798 " (cutoff:3.500A) Processing helix chain 'A' and resid 1804 through 1824 Processing helix chain 'A' and resid 1853 through 1862 Processing helix chain 'B' and resid 146 through 160 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.722A pdb=" N ASN B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 removed outlier: 3.648A pdb=" N GLU B 203 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 204 " --> pdb=" O PRO B 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 200 through 204' Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 224 through 234 Processing helix chain 'B' and resid 242 through 253 Processing helix chain 'B' and resid 257 through 271 removed outlier: 3.926A pdb=" N GLY B 263 " --> pdb=" O GLY B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 299 Processing helix chain 'G' and resid 26 through 41 removed outlier: 3.519A pdb=" N GLN G 32 " --> pdb=" O PHE G 28 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU G 33 " --> pdb=" O ILE G 29 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 34 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 70 Processing helix chain 'G' and resid 80 through 95 removed outlier: 3.622A pdb=" N LEU G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 111 removed outlier: 3.668A pdb=" N GLN G 110 " --> pdb=" O ALA G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 133 removed outlier: 3.720A pdb=" N THR G 119 " --> pdb=" O THR G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 143 through 152 Processing helix chain 'G' and resid 169 through 180 removed outlier: 3.521A pdb=" N LEU G 173 " --> pdb=" O TYR G 169 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 202 removed outlier: 5.197A pdb=" N ASP G 186 " --> pdb=" O VAL G 182 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU G 187 " --> pdb=" O LEU G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 209 removed outlier: 3.885A pdb=" N VAL G 208 " --> pdb=" O ASP G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 214 through 221 Processing helix chain 'G' and resid 222 through 225 Processing helix chain 'G' and resid 227 through 233 Processing helix chain 'G' and resid 233 through 256 Proline residue: G 239 - end of helix Processing helix chain 'G' and resid 259 through 266 Processing helix chain 'G' and resid 275 through 286 removed outlier: 3.975A pdb=" N THR G 279 " --> pdb=" O GLN G 275 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA G 284 " --> pdb=" O ALA G 280 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR G 286 " --> pdb=" O ALA G 282 " (cutoff:3.500A) Processing helix chain 'G' and resid 291 through 312 removed outlier: 4.217A pdb=" N SER G 295 " --> pdb=" O SER G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 320 through 330 Processing helix chain 'G' and resid 345 through 360 removed outlier: 4.019A pdb=" N HIS G 359 " --> pdb=" O LYS G 355 " (cutoff:3.500A) Processing helix chain 'G' and resid 361 through 365 Processing helix chain 'G' and resid 382 through 396 removed outlier: 3.536A pdb=" N ALA G 396 " --> pdb=" O THR G 392 " (cutoff:3.500A) Processing helix chain 'G' and resid 408 through 412 Processing helix chain 'G' and resid 429 through 433 Processing helix chain 'G' and resid 434 through 444 removed outlier: 4.273A pdb=" N LEU G 438 " --> pdb=" O PRO G 434 " (cutoff:3.500A) Processing helix chain 'G' and resid 451 through 455 Processing helix chain 'G' and resid 474 through 485 removed outlier: 3.547A pdb=" N ARG G 478 " --> pdb=" O SER G 474 " (cutoff:3.500A) 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 519 removed outlier: 3.638A pdb=" N LEU G 515 " --> pdb=" O GLY G 511 " (cutoff:3.500A) Processing helix chain 'G' and resid 544 through 549 removed outlier: 3.818A 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: 3.695A pdb=" N LEU G 586 " --> pdb=" O LYS G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 603 through 613 removed outlier: 3.517A pdb=" N VAL G 607 " --> pdb=" O SER G 603 " (cutoff:3.500A) 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 639 Processing helix chain 'G' and resid 655 through 672 removed outlier: 3.710A pdb=" N TRP G 661 " --> pdb=" O PHE G 657 " (cutoff:3.500A) Proline residue: G 664 - end of helix Processing helix chain 'G' and resid 687 through 698 removed outlier: 3.596A pdb=" N LEU G 698 " --> pdb=" O TYR G 694 " (cutoff:3.500A) Processing helix chain 'G' and resid 709 through 722 Processing helix chain 'G' and resid 747 through 759 removed outlier: 5.238A pdb=" N SER G 755 " --> pdb=" O LEU G 751 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LYS G 756 " --> pdb=" O GLN G 752 " (cutoff:3.500A) Processing helix chain 'G' and resid 777 through 782 Processing helix chain 'G' and resid 783 through 788 removed outlier: 3.840A pdb=" N LYS G 788 " --> pdb=" O TRP G 785 " (cutoff:3.500A) Processing helix chain 'G' and resid 802 through 808 removed outlier: 4.327A 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 removed outlier: 3.523A pdb=" N TYR G 836 " --> pdb=" O GLU G 833 " (cutoff:3.500A) Processing helix chain 'G' and resid 859 through 872 Processing helix chain 'G' and resid 879 through 898 removed outlier: 5.205A pdb=" N ASP G 889 " --> pdb=" O GLU G 885 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N TYR G 890 " --> pdb=" O ALA G 886 " (cutoff:3.500A) Processing helix chain 'G' and resid 913 through 917 Processing helix chain 'G' and resid 918 through 930 Processing helix chain 'G' and resid 940 through 959 Processing helix chain 'G' and resid 969 through 974 Processing helix chain 'G' and resid 975 through 987 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 1034 through 1043 removed outlier: 3.823A pdb=" N SER G1037 " --> pdb=" O LEU G1034 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LEU G1040 " --> pdb=" O SER G1037 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU G1041 " --> pdb=" O GLU G1038 " (cutoff:3.500A) Processing helix chain 'G' and resid 1047 through 1051 Processing helix chain 'G' and resid 1058 through 1062 Processing helix chain 'G' and resid 1069 through 1090 Processing helix chain 'G' and resid 1093 through 1097 Processing helix chain 'G' and resid 1134 through 1144 Processing helix chain 'G' and resid 1148 through 1156 Processing helix chain 'G' and resid 1168 through 1174 Processing helix chain 'G' and resid 1257 through 1271 Processing helix chain 'G' and resid 1293 through 1305 Processing helix chain 'G' and resid 1308 through 1312 Processing helix chain 'G' and resid 1324 through 1337 removed outlier: 4.171A pdb=" N VAL G1328 " --> pdb=" O ASP G1324 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ARG G1332 " --> pdb=" O VAL G1328 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA G1333 " --> pdb=" O VAL G1329 " (cutoff:3.500A) Processing helix chain 'G' and resid 1338 through 1339 No H-bonds generated for 'chain 'G' and resid 1338 through 1339' Processing helix chain 'G' and resid 1340 through 1344 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 1438 through 1447 Processing helix chain 'G' and resid 1514 through 1524 Processing helix chain 'G' and resid 1550 through 1558 removed outlier: 3.540A pdb=" N VAL G1556 " --> pdb=" O PRO G1552 " (cutoff:3.500A) Processing helix chain 'G' and resid 1561 through 1565 Processing helix chain 'G' and resid 1566 through 1573 Processing helix chain 'G' and resid 1581 through 1597 Processing helix chain 'G' and resid 1601 through 1603 No H-bonds generated for 'chain 'G' and resid 1601 through 1603' Processing helix chain 'G' and resid 1677 through 1684 removed outlier: 3.801A pdb=" N THR G1683 " --> pdb=" O ASP G1679 " (cutoff:3.500A) Processing helix chain 'G' and resid 1684 through 1703 removed outlier: 3.612A pdb=" N GLN G1688 " --> pdb=" O SER G1684 " (cutoff:3.500A) Processing helix chain 'G' and resid 1705 through 1713 Processing helix chain 'G' and resid 1722 through 1735 Processing helix chain 'G' and resid 1773 through 1795 Proline residue: G1779 - end of helix Processing helix chain 'G' and resid 1809 through 1819 removed outlier: 3.824A 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: 3.778A pdb=" N VAL G1862 " --> pdb=" O ASN G1858 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA G1863 " --> pdb=" O PRO G1859 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 1858 through 1863' Processing helix chain 'G' and resid 1867 through 1883 Processing helix chain 'G' and resid 1904 through 1921 removed outlier: 3.505A pdb=" N ASP G1908 " --> pdb=" O LEU G1904 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS G1918 " --> pdb=" O LEU G1914 " (cutoff:3.500A) Processing helix chain 'G' and resid 1923 through 1931 removed outlier: 3.538A pdb=" N LYS G1929 " --> pdb=" O ILE G1925 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU G1931 " --> pdb=" O LEU G1927 " (cutoff:3.500A) Processing helix chain 'G' and resid 1935 through 1953 removed outlier: 3.587A pdb=" N GLU G1942 " --> pdb=" O GLY G1938 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE G1943 " --> pdb=" O HIS G1939 " (cutoff:3.500A) Processing helix chain 'G' and resid 1979 through 1983 removed outlier: 4.025A pdb=" N ASN G1983 " --> pdb=" O TYR G1980 " (cutoff:3.500A) Processing helix chain 'G' and resid 1984 through 1996 removed outlier: 3.538A pdb=" N PHE G1988 " --> pdb=" O GLY G1984 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN G1995 " --> pdb=" O PHE G1991 " (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: 3.793A 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: 7.699A pdb=" N GLU G1887 " --> pdb=" O ASP G1903 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ASP G1903 " --> pdb=" O GLU G1887 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL G1889 " --> pdb=" O ALA G1901 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ALA G1901 " --> pdb=" O VAL G1889 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR G1891 " --> pdb=" O VAL G1899 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL G1899 " --> pdb=" O TYR G1891 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 77 through 80 removed outlier: 6.708A pdb=" N THR G1662 " --> pdb=" O THR G1803 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALA G1805 " --> pdb=" O THR G1662 " (cutoff:3.500A) removed outlier: 6.313A 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: 6.443A pdb=" N TYR A 677 " --> pdb=" O ALA A 767 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE A 769 " --> pdb=" O TYR A 677 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU A 679 " --> pdb=" O ILE A 769 " (cutoff:3.500A) removed outlier: 9.538A pdb=" N VAL A 922 " --> pdb=" O LEU A 862 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 864 " --> pdb=" O VAL A 922 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ALA A 924 " --> pdb=" O VAL A 864 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLY A 866 " --> pdb=" O ALA A 924 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N LEU A 926 " --> pdb=" O GLY A 866 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE A 868 " --> pdb=" O LEU A 926 " (cutoff:3.500A) removed outlier: 4.449A 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 Processing sheet with id=AA8, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 6.769A pdb=" N MET A1388 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N VAL A1021 " --> pdb=" O MET A1388 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ILE A1019 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A1402 " --> pdb=" O VAL A1021 " (cutoff:3.500A) removed outlier: 5.697A pdb=" N VAL A1404 " --> pdb=" O VAL A1656 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A1656 " --> pdb=" O VAL A1404 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A1406 " --> pdb=" O ILE A1654 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ALA A1638 " --> pdb=" O LEU A1536 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A1538 " --> pdb=" O ALA A1638 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1060 through 1066 removed outlier: 4.062A pdb=" N TRP A1075 " --> pdb=" O VAL A1084 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1103 through 1105 Processing sheet with id=AB2, first strand: chain 'A' and resid 1119 through 1126 Processing sheet with id=AB3, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id=AB4, first strand: chain 'A' and resid 1604 through 1605 Processing sheet with id=AB5, first strand: chain 'A' and resid 1723 through 1724 Processing sheet with id=AB6, first strand: chain 'A' and resid 1768 through 1775 Processing sheet with id=AB7, first strand: chain 'A' and resid 1837 through 1840 Processing sheet with id=AB8, first strand: chain 'G' and resid 6 through 13 removed outlier: 3.673A pdb=" N LEU G 16 " --> pdb=" O HIS G 13 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 267 through 272 removed outlier: 7.527A pdb=" N LEU G 156 " --> pdb=" O LYS G 268 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ALA G 270 " --> pdb=" O LEU G 156 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA G 158 " --> pdb=" O ALA G 270 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N GLY G 272 " --> pdb=" O ALA G 158 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE G 160 " --> pdb=" O GLY G 272 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL G 157 " --> pdb=" O LEU G 502 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE G 501 " --> pdb=" O ILE G 528 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'G' and resid 419 through 420 removed outlier: 7.357A pdb=" N ASN G 376 " --> pdb=" O VAL G 371 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N VAL G 371 " --> pdb=" O ASN G 376 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL G 378 " --> pdb=" O SER G 369 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 568 through 571 Processing sheet with id=AC3, first strand: chain 'G' and resid 592 through 594 removed outlier: 3.910A pdb=" N THR G 616 " --> pdb=" O LEU G 592 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N PHE G 647 " --> pdb=" O PHE G 678 " (cutoff:3.500A) removed outlier: 8.562A pdb=" N THR G 680 " --> pdb=" O PHE G 647 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE G 649 " --> pdb=" O THR G 680 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLY G 682 " --> pdb=" O ILE G 649 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU G 651 " --> pdb=" O GLY G 682 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLN G 677 " --> pdb=" O TYR G 702 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLY G 704 " --> pdb=" O GLN G 677 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU G 679 " --> pdb=" O GLY G 704 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLY G 798 " --> pdb=" O LEU G 765 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 739 through 740 removed outlier: 3.567A pdb=" N GLY G 739 " --> pdb=" O HIS G 855 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 906 through 907 Processing sheet with id=AC6, first strand: chain 'G' and resid 931 through 932 Processing sheet with id=AC7, first strand: chain 'G' and resid 1125 through 1128 removed outlier: 3.548A pdb=" N VAL G1209 " --> pdb=" O LEU G1197 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLU G1199 " --> pdb=" O PRO G1207 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N THR G1208 " --> pdb=" O ILE G1224 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE G1218 " --> pdb=" O LEU G1214 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU G1238 " --> pdb=" O MET G1221 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N PHE G1158 " --> pdb=" O ILE G1251 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLU G1253 " --> pdb=" O PHE G1158 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR G1160 " --> pdb=" O GLU G1253 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 1290 through 1291 removed outlier: 6.823A pdb=" N ASP G1391 " --> pdb=" O GLU G1379 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL G1381 " --> pdb=" O ILE G1389 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE G1389 " --> pdb=" O VAL G1381 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN G1383 " --> pdb=" O GLY G1387 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLY G1387 " --> pdb=" O ASN G1383 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG G1398 " --> pdb=" O PRO G1402 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL G1403 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N MET G1359 " --> pdb=" O VAL G1403 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLU G1405 " --> pdb=" O TYR G1357 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N TYR G1357 " --> pdb=" O GLU G1405 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR G1407 " --> pdb=" O ASN G1355 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASN G1355 " --> pdb=" O THR G1407 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N SER G1409 " --> pdb=" O LEU G1353 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N LEU G1353 " --> pdb=" O PHE G1612 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARG G1606 " --> pdb=" O MET G1359 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL G1605 " --> pdb=" O GLU G1658 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLU G1658 " --> pdb=" O VAL G1605 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG G1635 " --> pdb=" O MET G1631 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N MET G1631 " --> pdb=" O ARG G1635 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU G1637 " --> pdb=" O VAL G1629 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA G1540 " --> pdb=" O ILE G1626 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS G1628 " --> pdb=" O PRO G1538 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N GLY G1630 " --> pdb=" O PRO G1536 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 1423 through 1427 removed outlier: 3.725A pdb=" N GLY G1487 " --> pdb=" O VAL G1504 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY G1502 " --> pdb=" O ILE G1489 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL G1491 " --> pdb=" O GLU G1500 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU G1500 " --> pdb=" O VAL G1491 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 1423 through 1427 removed outlier: 5.090A pdb=" N THR G1463 " --> pdb=" O GLU G1492 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL G1430 " --> pdb=" O LEU G1527 " (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 1739 through 1741 removed outlier: 3.832A pdb=" N THR G1740 " --> pdb=" O LYS G1747 " (cutoff:3.500A) 1509 hydrogen bonds defined for protein. 4194 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.24 Time building geometry restraints manager: 2.94 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: 5048 1.31 - 1.45: 7516 1.45 - 1.59: 17054 1.59 - 1.72: 2 1.72 - 1.86: 182 Bond restraints: 29802 Sorted by residual: bond pdb=" C MET A1388 " pdb=" O MET A1388 " ideal model delta sigma weight residual 1.233 1.172 0.061 1.17e-02 7.31e+03 2.72e+01 bond pdb=" C PHE A1688 " pdb=" O PHE A1688 " ideal model delta sigma weight residual 1.236 1.177 0.060 1.15e-02 7.56e+03 2.71e+01 bond pdb=" N ILE A1157 " pdb=" CA ILE A1157 " ideal model delta sigma weight residual 1.460 1.495 -0.034 7.30e-03 1.88e+04 2.21e+01 bond pdb=" C PRO A1029 " pdb=" O PRO A1029 " ideal model delta sigma weight residual 1.237 1.175 0.062 1.32e-02 5.74e+03 2.20e+01 bond pdb=" N ILE G1501 " pdb=" CA ILE G1501 " ideal model delta sigma weight residual 1.457 1.500 -0.044 9.30e-03 1.16e+04 2.19e+01 ... (remaining 29797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 28271 1.92 - 3.83: 10469 3.83 - 5.75: 1530 5.75 - 7.67: 119 7.67 - 9.58: 9 Bond angle restraints: 40398 Sorted by residual: angle pdb=" CA GLY A 383 " pdb=" C GLY A 383 " pdb=" O GLY A 383 " ideal model delta sigma weight residual 122.23 117.91 4.32 6.90e-01 2.10e+00 3.92e+01 angle pdb=" CA THR A1282 " pdb=" CB THR A1282 " pdb=" OG1 THR A1282 " ideal model delta sigma weight residual 109.60 100.56 9.04 1.50e+00 4.44e-01 3.63e+01 angle pdb=" CA ASP G1316 " pdb=" CB ASP G1316 " pdb=" CG ASP G1316 " ideal model delta sigma weight residual 112.60 118.32 -5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N PRO G 599 " pdb=" CA PRO G 599 " pdb=" CB PRO G 599 " ideal model delta sigma weight residual 102.60 96.61 5.99 1.10e+00 8.26e-01 2.97e+01 angle pdb=" CA GLY A1375 " pdb=" C GLY A1375 " pdb=" O GLY A1375 " ideal model delta sigma weight residual 122.22 118.69 3.53 6.50e-01 2.37e+00 2.95e+01 ... (remaining 40393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.76: 16953 23.76 - 47.52: 844 47.52 - 71.27: 117 71.27 - 95.03: 33 95.03 - 118.79: 1 Dihedral angle restraints: 17948 sinusoidal: 7041 harmonic: 10907 Sorted by residual: dihedral pdb=" C5' FMN G2101 " pdb=" O5' FMN G2101 " pdb=" P FMN G2101 " pdb=" O1P FMN G2101 " ideal model delta sinusoidal sigma weight residual 75.26 -165.95 -118.79 1 2.00e+01 2.50e-03 3.56e+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 180.00 153.64 26.36 0 5.00e+00 4.00e-02 2.78e+01 dihedral pdb=" CA ILE G1503 " pdb=" C ILE G1503 " pdb=" N VAL G1504 " pdb=" CA VAL G1504 " ideal model delta harmonic sigma weight residual 180.00 155.17 24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 17945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 2140 0.062 - 0.124: 1670 0.124 - 0.187: 597 0.187 - 0.249: 129 0.249 - 0.311: 17 Chirality restraints: 4553 Sorted by residual: chirality pdb=" CA VAL A 893 " pdb=" N VAL A 893 " pdb=" C VAL A 893 " pdb=" CB VAL A 893 " both_signs ideal model delta sigma weight residual False 2.44 2.75 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" CA GLN A1389 " pdb=" N GLN A1389 " pdb=" C GLN A1389 " pdb=" CB GLN A1389 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" CA ILE A1326 " pdb=" N ILE A1326 " pdb=" C ILE A1326 " pdb=" CB ILE A1326 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 4550 not shown) Planarity restraints: 5235 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G2101 " 0.014 2.00e-02 2.50e+03 3.52e-02 5.90e+01 pdb=" C10 FMN G2101 " 0.027 2.00e-02 2.50e+03 pdb=" C2 FMN G2101 " -0.051 2.00e-02 2.50e+03 pdb=" C4 FMN G2101 " 0.001 2.00e-02 2.50e+03 pdb=" C4A FMN G2101 " 0.042 2.00e-02 2.50e+03 pdb=" C5A FMN G2101 " 0.049 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 " -0.064 2.00e-02 2.50e+03 pdb=" C8 FMN G2101 " -0.025 2.00e-02 2.50e+03 pdb=" C8M FMN G2101 " -0.039 2.00e-02 2.50e+03 pdb=" C9 FMN G2101 " 0.004 2.00e-02 2.50e+03 pdb=" C9A FMN G2101 " 0.044 2.00e-02 2.50e+03 pdb=" N1 FMN G2101 " -0.010 2.00e-02 2.50e+03 pdb=" N10 FMN G2101 " 0.038 2.00e-02 2.50e+03 pdb=" N3 FMN G2101 " -0.044 2.00e-02 2.50e+03 pdb=" N5 FMN G2101 " 0.047 2.00e-02 2.50e+03 pdb=" O2 FMN G2101 " -0.030 2.00e-02 2.50e+03 pdb=" O4 FMN G2101 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 PNS B1901 " -0.061 2.00e-02 2.50e+03 6.08e-02 4.62e+01 pdb=" C34 PNS B1901 " 0.039 2.00e-02 2.50e+03 pdb=" C37 PNS B1901 " -0.073 2.00e-02 2.50e+03 pdb=" N36 PNS B1901 " 0.089 2.00e-02 2.50e+03 pdb=" O35 PNS B1901 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 722 " 0.073 2.00e-02 2.50e+03 3.93e-02 3.09e+01 pdb=" CG TYR A 722 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR A 722 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A 722 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 722 " -0.032 2.00e-02 2.50e+03 pdb=" CZ TYR A 722 " 0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 722 " 0.051 2.00e-02 2.50e+03 ... (remaining 5232 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1523 2.74 - 3.28: 29948 3.28 - 3.82: 45766 3.82 - 4.36: 63710 4.36 - 4.90: 102081 Nonbonded interactions: 243028 Sorted by model distance: nonbonded pdb=" O LYS G 355 " pdb=" OG SER G 358 " model vdw 2.200 3.040 nonbonded pdb=" OH TYR A 81 " pdb=" OH TYR A 89 " model vdw 2.261 3.040 nonbonded pdb=" NH1 ARG G 894 " pdb=" OD2 ASP G 898 " model vdw 2.286 3.120 nonbonded pdb=" O VAL G1048 " pdb=" OG1 THR G1051 " model vdw 2.286 3.040 nonbonded pdb=" OH TYR A1694 " pdb=" OD2 ASP G1001 " model vdw 2.292 3.040 ... (remaining 243023 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.150 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.148 29804 Z= 1.005 Angle : 1.853 20.937 40400 Z= 1.357 Chirality : 0.090 0.311 4553 Planarity : 0.007 0.061 5235 Dihedral : 14.528 118.791 10919 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.68 % Favored : 95.03 % Rotamer: Outliers : 0.71 % Allowed : 3.76 % Favored : 95.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.14 (0.11), residues: 3760 helix: -2.59 (0.09), residues: 1666 sheet: -1.75 (0.20), residues: 512 loop : -1.35 (0.14), residues: 1582 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A1036 TYR 0.073 0.007 TYR A 722 PHE 0.061 0.007 PHE A1376 TRP 0.043 0.009 TRP G1449 HIS 0.018 0.004 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.01347 / 1.00 (29802) covalent geometry : angle 1.84961 / 1.36 (40398) SS BOND : bond 0.14841 / 7.81 ( 1) SS BOND : angle 16.69006 / 9.61 ( 2) hydrogen bonds : bond 0.21702 / 14.21 ( 1501) hydrogen bonds : angle 8.74526 / 6.23 ( 4194) Misc. bond : bond 0.06775 / 3.57 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 253 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 MET cc_start: 0.8644 (mmp) cc_final: 0.8359 (mmp) REVERT: A 1121 MET cc_start: 0.8804 (mtp) cc_final: 0.8551 (tpt) REVERT: A 1150 ASP cc_start: 0.8928 (p0) cc_final: 0.8705 (p0) REVERT: A 1515 ARG cc_start: 0.8996 (mtp85) cc_final: 0.8309 (ptt180) REVERT: A 1755 MET cc_start: 0.8833 (mtp) cc_final: 0.8626 (mtp) REVERT: A 1841 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7753 (mtp180) REVERT: G 599 PRO cc_start: 0.9089 (OUTLIER) cc_final: 0.8797 (Cg_endo) REVERT: G 908 ASN cc_start: 0.9088 (m-40) cc_final: 0.8886 (p0) REVERT: G 1872 GLN cc_start: 0.9329 (tp40) cc_final: 0.8890 (tp-100) REVERT: G 1964 PHE cc_start: 0.8204 (m-10) cc_final: 0.7920 (m-10) outliers start: 22 outliers final: 5 residues processed: 271 average time/residue: 0.8038 time to fit residues: 248.4552 Evaluate side-chains 189 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 183 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 599 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 21 GLN A 63 ASN A 356 ASN A 379 ASN A 618 ASN A 971 ASN A1380 GLN A1549 ASN A1620 GLN A1695 ASN A1703 HIS G 36 GLN ** G 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 GLN G 273 HIS G 440 ASN G 456 GLN G 718 ASN G 723 HIS G 747 HIS G 752 GLN G 993 GLN G1217 ASN G1241 ASN G1352 HIS G1432 GLN G1529 GLN G1535 ASN G1595 ASN G1839 GLN G1890 ASN G1912 ASN G1977 HIS G2013 ASN G2020 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.067164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.047887 restraints weight = 87653.680| |-----------------------------------------------------------------------------| r_work (start): 0.2722 rms_B_bonded: 2.84 r_work: 0.2584 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2461 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9037 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29804 Z= 0.135 Angle : 0.578 10.334 40400 Z= 0.308 Chirality : 0.043 0.182 4553 Planarity : 0.004 0.035 5235 Dihedral : 5.549 106.015 4038 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Rotamer: Outliers : 1.09 % Allowed : 7.59 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.13), residues: 3760 helix: 0.45 (0.12), residues: 1692 sheet: -1.19 (0.21), residues: 527 loop : -0.21 (0.16), residues: 1541 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G1765 TYR 0.014 0.001 TYR A 417 PHE 0.023 0.001 PHE A 35 TRP 0.014 0.001 TRP G1138 HIS 0.006 0.001 HIS G1939 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (29802) covalent geometry : angle 0.57662 / 0.31 (40398) SS BOND : bond 0.00278 / 0.15 ( 1) SS BOND : angle 4.89897 / 2.85 ( 2) hydrogen bonds : bond 0.04707 / 3.09 ( 1501) hydrogen bonds : angle 5.13647 / 3.60 ( 4194) Misc. bond : bond 0.00026 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 GLU cc_start: 0.6887 (pp20) cc_final: 0.6669 (pp20) REVERT: A 492 ASP cc_start: 0.8506 (t0) cc_final: 0.8285 (t0) REVERT: A 529 MET cc_start: 0.9437 (mmp) cc_final: 0.9208 (mmp) REVERT: A 1070 ARG cc_start: 0.8239 (ttp-110) cc_final: 0.8027 (tmm160) REVERT: A 1121 MET cc_start: 0.9356 (mtp) cc_final: 0.8369 (tpt) REVERT: A 1150 ASP cc_start: 0.9346 (p0) cc_final: 0.9120 (p0) REVERT: A 1354 GLU cc_start: 0.9011 (mp0) cc_final: 0.8795 (mp0) REVERT: A 1498 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: A 1789 ARG cc_start: 0.8324 (tmt170) cc_final: 0.8032 (tmt170) REVERT: A 1813 TRP cc_start: 0.8968 (t-100) cc_final: 0.8719 (t-100) REVERT: A 1834 LEU cc_start: 0.8716 (mt) cc_final: 0.8165 (pp) REVERT: G 111 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8292 (mp0) REVERT: G 908 ASN cc_start: 0.9255 (m-40) cc_final: 0.8835 (p0) REVERT: G 1164 MET cc_start: 0.9002 (mmp) cc_final: 0.8456 (mmm) outliers start: 34 outliers final: 11 residues processed: 220 average time/residue: 0.7698 time to fit residues: 195.1976 Evaluate side-chains 192 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 648 ASP Chi-restraints excluded: chain A residue 1142 GLU Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1498 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 35 GLU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 304 optimal weight: 1.9990 chunk 290 optimal weight: 0.3980 chunk 107 optimal weight: 4.9990 chunk 128 optimal weight: 4.9990 chunk 255 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 258 optimal weight: 0.3980 chunk 250 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 342 GLN A 475 GLN A 506 ASN A 971 ASN G 38 ASN G 102 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1302 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.067155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.047863 restraints weight = 88290.190| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 2.85 r_work: 0.2594 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 29804 Z= 0.138 Angle : 0.518 9.599 40400 Z= 0.272 Chirality : 0.042 0.162 4553 Planarity : 0.003 0.043 5235 Dihedral : 5.088 98.736 4032 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 1.00 % Allowed : 8.84 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.14), residues: 3760 helix: 1.33 (0.13), residues: 1706 sheet: -0.81 (0.21), residues: 529 loop : 0.10 (0.17), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 709 TYR 0.013 0.001 TYR A 722 PHE 0.024 0.001 PHE A 35 TRP 0.013 0.001 TRP A1813 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (29802) covalent geometry : angle 0.51676 / 0.27 (40398) SS BOND : bond 0.00376 / 0.20 ( 1) SS BOND : angle 4.84018 / 2.79 ( 2) hydrogen bonds : bond 0.03992 / 2.62 ( 1501) hydrogen bonds : angle 4.69926 / 3.28 ( 4194) Misc. bond : bond 0.00005 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.6986 (mmt180) cc_final: 0.6778 (mmp-170) REVERT: A 492 ASP cc_start: 0.8492 (t0) cc_final: 0.8276 (t0) REVERT: A 529 MET cc_start: 0.9445 (mmp) cc_final: 0.9029 (mmp) REVERT: A 841 GLU cc_start: 0.8769 (mp0) cc_final: 0.8347 (tp30) REVERT: A 1070 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7954 (tmm160) REVERT: A 1121 MET cc_start: 0.9350 (mtp) cc_final: 0.8339 (tpt) REVERT: A 1135 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8751 (tm-30) REVERT: A 1354 GLU cc_start: 0.9002 (mp0) cc_final: 0.8776 (mp0) REVERT: A 1789 ARG cc_start: 0.8376 (tmt170) cc_final: 0.8166 (tmt170) REVERT: A 1813 TRP cc_start: 0.8945 (t-100) cc_final: 0.8596 (t-100) REVERT: A 1834 LEU cc_start: 0.8766 (mt) cc_final: 0.8224 (pp) REVERT: A 1841 ARG cc_start: 0.7349 (mtp180) cc_final: 0.7013 (mtp180) REVERT: G 111 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8617 (mt-10) REVERT: G 329 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8313 (pp20) REVERT: G 908 ASN cc_start: 0.9250 (m-40) cc_final: 0.8828 (p0) REVERT: G 1164 MET cc_start: 0.9029 (mmp) cc_final: 0.8460 (mmm) REVERT: G 1323 MET cc_start: 0.8996 (ptp) cc_final: 0.8708 (ttm) outliers start: 31 outliers final: 16 residues processed: 210 average time/residue: 0.7483 time to fit residues: 181.3501 Evaluate side-chains 190 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 1023 ARG Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1925 ILE Chi-restraints excluded: chain G residue 1946 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 114 optimal weight: 4.9990 chunk 157 optimal weight: 50.0000 chunk 5 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 chunk 291 optimal weight: 10.0000 chunk 60 optimal weight: 7.9990 chunk 302 optimal weight: 10.0000 chunk 220 optimal weight: 6.9990 chunk 257 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 527 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.066057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.047146 restraints weight = 88999.118| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.82 r_work: 0.2563 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2440 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29804 Z= 0.237 Angle : 0.551 9.804 40400 Z= 0.287 Chirality : 0.044 0.185 4553 Planarity : 0.004 0.044 5235 Dihedral : 4.962 92.568 4028 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.45 % Favored : 97.53 % Rotamer: Outliers : 1.48 % Allowed : 9.74 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.14), residues: 3760 helix: 1.51 (0.13), residues: 1703 sheet: -0.65 (0.21), residues: 536 loop : 0.24 (0.17), residues: 1521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 709 TYR 0.014 0.001 TYR A 722 PHE 0.022 0.002 PHE A1376 TRP 0.013 0.001 TRP A1030 HIS 0.008 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (29802) covalent geometry : angle 0.54926 / 0.29 (40398) SS BOND : bond 0.00505 / 0.27 ( 1) SS BOND : angle 5.41856 / 3.12 ( 2) hydrogen bonds : bond 0.04195 / 2.75 ( 1501) hydrogen bonds : angle 4.65228 / 3.24 ( 4194) Misc. bond : bond 0.00019 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 182 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 ARG cc_start: 0.7401 (mmt180) cc_final: 0.7088 (mmp-170) REVERT: A 492 ASP cc_start: 0.8560 (t0) cc_final: 0.8249 (t0) REVERT: A 529 MET cc_start: 0.9449 (mmp) cc_final: 0.9016 (mmp) REVERT: A 841 GLU cc_start: 0.8946 (mp0) cc_final: 0.8377 (tp30) REVERT: A 1070 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7907 (tmm160) REVERT: A 1121 MET cc_start: 0.9320 (mtp) cc_final: 0.8292 (tpt) REVERT: A 1135 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8783 (tm-30) REVERT: A 1354 GLU cc_start: 0.9053 (mp0) cc_final: 0.8827 (mp0) REVERT: A 1672 GLU cc_start: 0.9036 (tt0) cc_final: 0.8751 (tp30) REVERT: A 1789 ARG cc_start: 0.8370 (tmt170) cc_final: 0.8120 (tmt170) REVERT: A 1813 TRP cc_start: 0.8918 (t-100) cc_final: 0.8529 (t-100) REVERT: A 1834 LEU cc_start: 0.8815 (mt) cc_final: 0.8228 (pp) REVERT: A 1841 ARG cc_start: 0.7462 (mtp180) cc_final: 0.7066 (mtp180) REVERT: G 111 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8314 (mp0) REVERT: G 168 ASP cc_start: 0.8711 (t0) cc_final: 0.8506 (t0) REVERT: G 329 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8417 (pp20) REVERT: G 908 ASN cc_start: 0.9284 (m-40) cc_final: 0.8857 (p0) REVERT: G 1164 MET cc_start: 0.9032 (mmp) cc_final: 0.8479 (mmm) REVERT: G 1323 MET cc_start: 0.9048 (ptp) cc_final: 0.8820 (ttm) outliers start: 46 outliers final: 25 residues processed: 215 average time/residue: 0.7192 time to fit residues: 179.6971 Evaluate side-chains 200 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1135 GLU Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 1023 ARG Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Chi-restraints excluded: chain G residue 1946 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 164 optimal weight: 9.9990 chunk 312 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 221 optimal weight: 0.0970 chunk 103 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 274 optimal weight: 2.9990 chunk 104 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 285 optimal weight: 10.0000 chunk 160 optimal weight: 50.0000 overall best weight: 4.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1652 GLN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.065925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.047078 restraints weight = 88898.487| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.79 r_work: 0.2562 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2441 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29804 Z= 0.227 Angle : 0.542 9.781 40400 Z= 0.282 Chirality : 0.044 0.182 4553 Planarity : 0.004 0.065 5235 Dihedral : 4.905 90.859 4027 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.48 % Allowed : 10.45 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.14), residues: 3760 helix: 1.63 (0.13), residues: 1697 sheet: -0.57 (0.21), residues: 526 loop : 0.34 (0.17), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 632 TYR 0.014 0.001 TYR A 722 PHE 0.022 0.001 PHE A1376 TRP 0.011 0.001 TRP A1030 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.23 (29802) covalent geometry : angle 0.54075 / 0.28 (40398) SS BOND : bond 0.00635 / 0.33 ( 1) SS BOND : angle 5.37132 / 3.08 ( 2) hydrogen bonds : bond 0.04088 / 2.68 ( 1501) hydrogen bonds : angle 4.59136 / 3.20 ( 4194) Misc. bond : bond 0.00046 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ASP cc_start: 0.8598 (t0) cc_final: 0.8244 (t0) REVERT: A 522 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8548 (tp) REVERT: A 529 MET cc_start: 0.9448 (mmp) cc_final: 0.9029 (mmp) REVERT: A 841 GLU cc_start: 0.9024 (mp0) cc_final: 0.8443 (tp30) REVERT: A 1070 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7916 (tmm160) REVERT: A 1121 MET cc_start: 0.9304 (mtp) cc_final: 0.8249 (tpt) REVERT: A 1354 GLU cc_start: 0.9058 (OUTLIER) cc_final: 0.8825 (mp0) REVERT: A 1515 ARG cc_start: 0.9233 (mtp85) cc_final: 0.8201 (ptt180) REVERT: A 1672 GLU cc_start: 0.9053 (tt0) cc_final: 0.8768 (tp30) REVERT: A 1789 ARG cc_start: 0.8428 (tmt170) cc_final: 0.8183 (tmt170) REVERT: A 1841 ARG cc_start: 0.7475 (mtp180) cc_final: 0.7029 (mtp180) REVERT: G 111 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8288 (mp0) REVERT: G 168 ASP cc_start: 0.8652 (t0) cc_final: 0.8382 (t0) REVERT: G 329 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8461 (pp20) REVERT: G 908 ASN cc_start: 0.9304 (m-40) cc_final: 0.8855 (p0) REVERT: G 1164 MET cc_start: 0.9038 (mmp) cc_final: 0.8488 (mmm) outliers start: 46 outliers final: 27 residues processed: 214 average time/residue: 0.7103 time to fit residues: 176.4131 Evaluate side-chains 201 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 522 LEU Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 128 optimal weight: 10.0000 chunk 301 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 292 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 167 optimal weight: 9.9990 chunk 151 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1780 ASN G 181 HIS ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1619 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.065826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.047073 restraints weight = 88748.764| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 2.76 r_work: 0.2563 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 29804 Z= 0.228 Angle : 0.543 9.677 40400 Z= 0.282 Chirality : 0.044 0.183 4553 Planarity : 0.004 0.045 5235 Dihedral : 4.877 90.363 4027 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.45 % Allowed : 11.03 % Favored : 87.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.14), residues: 3760 helix: 1.68 (0.13), residues: 1697 sheet: -0.48 (0.21), residues: 526 loop : 0.38 (0.17), residues: 1537 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 709 TYR 0.013 0.001 TYR A 722 PHE 0.022 0.001 PHE A 35 TRP 0.016 0.001 TRP A1813 HIS 0.007 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.23 (29802) covalent geometry : angle 0.54222 / 0.28 (40398) SS BOND : bond 0.00665 / 0.35 ( 1) SS BOND : angle 5.29981 / 3.04 ( 2) hydrogen bonds : bond 0.04059 / 2.66 ( 1501) hydrogen bonds : angle 4.57340 / 3.18 ( 4194) Misc. bond : bond 0.00003 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 180 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ASP cc_start: 0.8584 (t0) cc_final: 0.8225 (t0) REVERT: A 522 LEU cc_start: 0.8845 (mt) cc_final: 0.8563 (tp) REVERT: A 529 MET cc_start: 0.9449 (mmp) cc_final: 0.9015 (mmp) REVERT: A 1070 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7909 (tmm160) REVERT: A 1121 MET cc_start: 0.9290 (mtp) cc_final: 0.8109 (tpt) REVERT: A 1124 GLU cc_start: 0.9287 (tt0) cc_final: 0.8876 (tm-30) REVERT: A 1354 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8793 (mp0) REVERT: A 1672 GLU cc_start: 0.9065 (tt0) cc_final: 0.8761 (tp30) REVERT: A 1789 ARG cc_start: 0.8406 (tmt170) cc_final: 0.8190 (tmt170) REVERT: A 1813 TRP cc_start: 0.8924 (t-100) cc_final: 0.8559 (t-100) REVERT: A 1834 LEU cc_start: 0.8724 (mt) cc_final: 0.8298 (pp) REVERT: A 1841 ARG cc_start: 0.7498 (mtp180) cc_final: 0.7022 (mtp180) REVERT: G 111 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8538 (mt-10) REVERT: G 168 ASP cc_start: 0.8605 (t0) cc_final: 0.8303 (t0) REVERT: G 329 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8499 (pp20) REVERT: G 908 ASN cc_start: 0.9310 (m-40) cc_final: 0.8846 (p0) REVERT: G 1164 MET cc_start: 0.9019 (mmp) cc_final: 0.8497 (mmm) outliers start: 45 outliers final: 29 residues processed: 212 average time/residue: 0.6802 time to fit residues: 167.7644 Evaluate side-chains 205 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 173 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1260 MET Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1851 LEU Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 320 optimal weight: 5.9990 chunk 364 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 240 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 303 optimal weight: 9.9990 chunk 221 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 135 optimal weight: 0.0980 chunk 144 optimal weight: 20.0000 chunk 227 optimal weight: 0.9990 overall best weight: 2.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.066819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.048070 restraints weight = 88265.644| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.79 r_work: 0.2593 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2472 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29804 Z= 0.143 Angle : 0.518 10.476 40400 Z= 0.268 Chirality : 0.042 0.187 4553 Planarity : 0.003 0.055 5235 Dihedral : 4.742 88.264 4027 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.35 % Allowed : 11.61 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.14), residues: 3760 helix: 1.81 (0.13), residues: 1697 sheet: -0.44 (0.22), residues: 534 loop : 0.45 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 632 TYR 0.013 0.001 TYR G1553 PHE 0.024 0.001 PHE A 35 TRP 0.014 0.001 TRP A1813 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (29802) covalent geometry : angle 0.51699 / 0.27 (40398) SS BOND : bond 0.00339 / 0.18 ( 1) SS BOND : angle 4.43021 / 2.54 ( 2) hydrogen bonds : bond 0.03704 / 2.43 ( 1501) hydrogen bonds : angle 4.46866 / 3.11 ( 4194) Misc. bond : bond 0.00011 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 180 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ASP cc_start: 0.8570 (t0) cc_final: 0.8263 (t0) REVERT: A 529 MET cc_start: 0.9426 (mmp) cc_final: 0.8997 (mmp) REVERT: A 841 GLU cc_start: 0.8746 (mp0) cc_final: 0.8351 (tp30) REVERT: A 1070 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7892 (tmm160) REVERT: A 1121 MET cc_start: 0.9274 (mtp) cc_final: 0.8104 (tpt) REVERT: A 1124 GLU cc_start: 0.9303 (tt0) cc_final: 0.8885 (tm-30) REVERT: A 1251 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.9031 (mtm) REVERT: A 1354 GLU cc_start: 0.9064 (OUTLIER) cc_final: 0.8834 (mp0) REVERT: A 1515 ARG cc_start: 0.9175 (mtp85) cc_final: 0.8179 (ptt180) REVERT: A 1789 ARG cc_start: 0.8475 (tmt170) cc_final: 0.8217 (tmt170) REVERT: A 1813 TRP cc_start: 0.8896 (t-100) cc_final: 0.8512 (t-100) REVERT: A 1834 LEU cc_start: 0.8793 (mt) cc_final: 0.8191 (pp) REVERT: A 1841 ARG cc_start: 0.7510 (mtp180) cc_final: 0.6993 (mtp180) REVERT: G 111 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8604 (mt-10) REVERT: G 168 ASP cc_start: 0.8585 (t0) cc_final: 0.8276 (t0) REVERT: G 329 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8483 (pp20) REVERT: G 908 ASN cc_start: 0.9296 (m-40) cc_final: 0.8810 (p0) REVERT: G 1164 MET cc_start: 0.9026 (mmp) cc_final: 0.8498 (mmm) outliers start: 42 outliers final: 26 residues processed: 212 average time/residue: 0.7026 time to fit residues: 173.9273 Evaluate side-chains 202 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 754 ASP Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1650 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 287 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 360 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1535 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.066882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.048246 restraints weight = 88540.663| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 2.78 r_work: 0.2599 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2479 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29804 Z= 0.148 Angle : 0.528 11.608 40400 Z= 0.269 Chirality : 0.042 0.173 4553 Planarity : 0.003 0.048 5235 Dihedral : 4.688 86.569 4027 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.35 % Allowed : 11.99 % Favored : 86.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3760 helix: 1.86 (0.13), residues: 1697 sheet: -0.35 (0.22), residues: 533 loop : 0.48 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 709 TYR 0.014 0.001 TYR G1553 PHE 0.024 0.001 PHE A 35 TRP 0.013 0.001 TRP A1813 HIS 0.006 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (29802) covalent geometry : angle 0.52677 / 0.27 (40398) SS BOND : bond 0.00398 / 0.21 ( 1) SS BOND : angle 4.49855 / 2.58 ( 2) hydrogen bonds : bond 0.03658 / 2.40 ( 1501) hydrogen bonds : angle 4.43209 / 3.08 ( 4194) Misc. bond : bond 0.00008 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 342 GLN cc_start: 0.9301 (mt0) cc_final: 0.9092 (mt0) REVERT: A 492 ASP cc_start: 0.8567 (t0) cc_final: 0.8258 (t0) REVERT: A 529 MET cc_start: 0.9430 (mmp) cc_final: 0.8997 (mmp) REVERT: A 841 GLU cc_start: 0.8744 (mp0) cc_final: 0.8345 (tp30) REVERT: A 1070 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7878 (tmm160) REVERT: A 1121 MET cc_start: 0.9296 (mtp) cc_final: 0.8146 (tpt) REVERT: A 1124 GLU cc_start: 0.9297 (tt0) cc_final: 0.8879 (tm-30) REVERT: A 1129 GLU cc_start: 0.5733 (OUTLIER) cc_final: 0.5146 (pt0) REVERT: A 1251 MET cc_start: 0.9360 (OUTLIER) cc_final: 0.9012 (mtm) REVERT: A 1354 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8813 (mp0) REVERT: A 1515 ARG cc_start: 0.9164 (mtp85) cc_final: 0.8175 (ptt180) REVERT: A 1789 ARG cc_start: 0.8464 (tmt170) cc_final: 0.8188 (tmt170) REVERT: A 1813 TRP cc_start: 0.8901 (t-100) cc_final: 0.8502 (t-100) REVERT: A 1834 LEU cc_start: 0.8790 (mt) cc_final: 0.8186 (pp) REVERT: A 1841 ARG cc_start: 0.7515 (mtp180) cc_final: 0.7009 (mtp180) REVERT: G 111 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8355 (mp0) REVERT: G 168 ASP cc_start: 0.8658 (t0) cc_final: 0.8321 (t0) REVERT: G 329 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8501 (pp20) REVERT: G 908 ASN cc_start: 0.9321 (m-40) cc_final: 0.8807 (p0) REVERT: G 1164 MET cc_start: 0.9026 (mmp) cc_final: 0.8491 (mmm) outliers start: 42 outliers final: 26 residues processed: 210 average time/residue: 0.7164 time to fit residues: 175.6607 Evaluate side-chains 202 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 451 MET Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 951 SER Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1251 MET Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1677 VAL Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1777 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1470 THR Chi-restraints excluded: chain G residue 1565 VAL Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 198 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 360 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 233 optimal weight: 0.8980 chunk 251 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1601 ASN ** G1055 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1434 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.067600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.048843 restraints weight = 88480.918| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 2.83 r_work: 0.2630 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 29804 Z= 0.107 Angle : 0.516 11.851 40400 Z= 0.262 Chirality : 0.042 0.163 4553 Planarity : 0.003 0.059 5235 Dihedral : 4.550 81.564 4027 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.96 % Allowed : 12.35 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.14), residues: 3760 helix: 1.95 (0.13), residues: 1702 sheet: -0.12 (0.22), residues: 526 loop : 0.49 (0.17), residues: 1532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG A 632 TYR 0.013 0.001 TYR G1553 PHE 0.026 0.001 PHE A 35 TRP 0.015 0.001 TRP A1813 HIS 0.004 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (29802) covalent geometry : angle 0.51506 / 0.26 (40398) SS BOND : bond 0.00137 / 0.07 ( 1) SS BOND : angle 3.85113 / 2.20 ( 2) hydrogen bonds : bond 0.03370 / 2.21 ( 1501) hydrogen bonds : angle 4.34145 / 3.02 ( 4194) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ASP cc_start: 0.8535 (t0) cc_final: 0.8236 (t0) REVERT: A 529 MET cc_start: 0.9401 (mmp) cc_final: 0.8957 (mmp) REVERT: A 841 GLU cc_start: 0.8787 (mp0) cc_final: 0.8297 (tp30) REVERT: A 1070 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7893 (tmm160) REVERT: A 1121 MET cc_start: 0.9240 (mtp) cc_final: 0.8057 (tpt) REVERT: A 1124 GLU cc_start: 0.9294 (tt0) cc_final: 0.8879 (tm-30) REVERT: A 1129 GLU cc_start: 0.5804 (OUTLIER) cc_final: 0.5179 (pt0) REVERT: A 1354 GLU cc_start: 0.9041 (OUTLIER) cc_final: 0.8833 (mp0) REVERT: A 1515 ARG cc_start: 0.9171 (mtp85) cc_final: 0.8177 (ptt180) REVERT: A 1789 ARG cc_start: 0.8456 (tmt170) cc_final: 0.8171 (tmt170) REVERT: A 1813 TRP cc_start: 0.8897 (t-100) cc_final: 0.8483 (t-100) REVERT: A 1834 LEU cc_start: 0.8826 (mt) cc_final: 0.8239 (pp) REVERT: A 1841 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6931 (mtp180) REVERT: G 168 ASP cc_start: 0.8630 (t0) cc_final: 0.8319 (t0) REVERT: G 329 GLU cc_start: 0.8807 (tm-30) cc_final: 0.8502 (pp20) REVERT: G 908 ASN cc_start: 0.9297 (m-40) cc_final: 0.8769 (p0) REVERT: G 1164 MET cc_start: 0.9027 (mmp) cc_final: 0.8493 (mmm) outliers start: 30 outliers final: 19 residues processed: 208 average time/residue: 0.7004 time to fit residues: 168.9325 Evaluate side-chains 191 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 105 optimal weight: 5.9990 chunk 165 optimal weight: 6.9990 chunk 59 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 111 optimal weight: 0.0970 chunk 201 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 329 optimal weight: 4.9990 chunk 216 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 250 optimal weight: 0.7980 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1652 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1478 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.067026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.048404 restraints weight = 88912.013| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 2.83 r_work: 0.2608 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2490 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9021 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29804 Z= 0.149 Angle : 0.533 12.420 40400 Z= 0.269 Chirality : 0.042 0.168 4553 Planarity : 0.003 0.056 5235 Dihedral : 4.565 79.802 4027 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.90 % Allowed : 12.96 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.14), residues: 3760 helix: 1.94 (0.13), residues: 1703 sheet: -0.08 (0.22), residues: 527 loop : 0.52 (0.17), residues: 1530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 709 TYR 0.014 0.001 TYR G1553 PHE 0.024 0.001 PHE A 35 TRP 0.013 0.001 TRP A1813 HIS 0.005 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (29802) covalent geometry : angle 0.53196 / 0.27 (40398) SS BOND : bond 0.00408 / 0.21 ( 1) SS BOND : angle 4.36036 / 2.49 ( 2) hydrogen bonds : bond 0.03569 / 2.33 ( 1501) hydrogen bonds : angle 4.37319 / 3.04 ( 4194) Misc. bond : bond 0.00009 / 0.00 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7520 Ramachandran restraints generated. 3760 Oldfield, 0 Emsley, 3760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 492 ASP cc_start: 0.8573 (t0) cc_final: 0.8266 (t0) REVERT: A 841 GLU cc_start: 0.8770 (mp0) cc_final: 0.8247 (tp30) REVERT: A 1070 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7896 (tmm160) REVERT: A 1121 MET cc_start: 0.9263 (mtp) cc_final: 0.8099 (tpt) REVERT: A 1124 GLU cc_start: 0.9316 (tt0) cc_final: 0.8894 (tm-30) REVERT: A 1129 GLU cc_start: 0.5630 (OUTLIER) cc_final: 0.4996 (pt0) REVERT: A 1354 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8774 (mp0) REVERT: A 1515 ARG cc_start: 0.9152 (mtp85) cc_final: 0.8159 (ptt180) REVERT: A 1789 ARG cc_start: 0.8446 (tmt170) cc_final: 0.8150 (tmt170) REVERT: A 1813 TRP cc_start: 0.8879 (t-100) cc_final: 0.8463 (t-100) REVERT: A 1834 LEU cc_start: 0.8815 (mt) cc_final: 0.8218 (pp) REVERT: A 1841 ARG cc_start: 0.7531 (mtp180) cc_final: 0.7036 (mtp180) REVERT: G 168 ASP cc_start: 0.8713 (t0) cc_final: 0.8364 (t0) REVERT: G 329 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8496 (pp20) REVERT: G 668 GLU cc_start: 0.9295 (tt0) cc_final: 0.9032 (tm-30) REVERT: G 908 ASN cc_start: 0.9373 (m-40) cc_final: 0.8807 (p0) REVERT: G 1011 MET cc_start: 0.9191 (mmm) cc_final: 0.8966 (mpp) REVERT: G 1164 MET cc_start: 0.8971 (mmp) cc_final: 0.8413 (mmm) outliers start: 28 outliers final: 21 residues processed: 194 average time/residue: 0.6817 time to fit residues: 153.7764 Evaluate side-chains 190 residues out of total 3245 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 LYS Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 1001 VAL Chi-restraints excluded: chain A residue 1010 GLU Chi-restraints excluded: chain A residue 1070 ARG Chi-restraints excluded: chain A residue 1129 GLU Chi-restraints excluded: chain A residue 1305 CYS Chi-restraints excluded: chain A residue 1332 TYR Chi-restraints excluded: chain A residue 1333 ASP Chi-restraints excluded: chain A residue 1354 GLU Chi-restraints excluded: chain A residue 1540 SER Chi-restraints excluded: chain A residue 1642 THR Chi-restraints excluded: chain A residue 1776 ILE Chi-restraints excluded: chain A residue 1861 GLU Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 425 SER Chi-restraints excluded: chain G residue 971 SER Chi-restraints excluded: chain G residue 995 LEU Chi-restraints excluded: chain G residue 1381 VAL Chi-restraints excluded: chain G residue 1386 THR Chi-restraints excluded: chain G residue 1679 ASP Chi-restraints excluded: chain G residue 1708 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 267 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 259 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 357 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 205 optimal weight: 4.9990 chunk 166 optimal weight: 40.0000 chunk 147 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 364 optimal weight: 0.0000 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 11 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.049525 restraints weight = 88961.181| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.84 r_work: 0.2640 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9002 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29804 Z= 0.100 Angle : 0.512 12.426 40400 Z= 0.258 Chirality : 0.041 0.163 4553 Planarity : 0.003 0.068 5235 Dihedral : 4.442 74.389 4027 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.15 % Favored : 97.82 % Rotamer: Outliers : 0.84 % Allowed : 13.05 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.62 (0.14), residues: 3760 helix: 2.00 (0.13), residues: 1700 sheet: 0.02 (0.22), residues: 531 loop : 0.55 (0.17), residues: 1529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG A 632 TYR 0.011 0.001 TYR A 417 PHE 0.026 0.001 PHE A 35 TRP 0.015 0.001 TRP A1813 HIS 0.004 0.001 HIS A1689 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (29802) covalent geometry : angle 0.51107 / 0.26 (40398) SS BOND : bond 0.00202 / 0.11 ( 1) SS BOND : angle 3.62291 / 2.06 ( 2) hydrogen bonds : bond 0.03269 / 2.14 ( 1501) hydrogen bonds : angle 4.29221 / 2.98 ( 4194) Misc. bond : bond 0.00011 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11125.19 seconds wall clock time: 189 minutes 48.45 seconds (11388.45 seconds total)