Starting phenix.real_space_refine on Thu Aug 6 08:05:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbz_62235/08_2026/9kbz_62235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbz_62235/08_2026/9kbz_62235.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kbz_62235/08_2026/9kbz_62235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbz_62235/08_2026/9kbz_62235.map" model { file = "/net/cci-nas-00/data/ceres_data/9kbz_62235/08_2026/9kbz_62235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbz_62235/08_2026/9kbz_62235.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.061 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: 6 Type Number sf(0) Gaussians P 103 5.49 5 Mg 3 5.21 5 S 73 5.16 5 C 8438 2.51 5 N 2379 2.21 5 O 2862 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13858 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1423, 11290 Classifications: {'peptide': 1423} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1365} Chain breaks: 9 Chain: "B" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 379 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "C" Number of atoms: 1102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1102 Classifications: {'RNA': 52} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 25, 'rna3p_pyr': 26} Link IDs: {'rna2p': 1, 'rna3p': 50} Chain: "D" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1084 Classifications: {'RNA': 51} Modifications used: {'p5*END': 1, 'rna3p_pur': 27, 'rna3p_pyr': 24} Link IDs: {'rna3p': 50} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.37, per 1000 atoms: 0.17 Number of scatterers: 13858 At special positions: 0 Unit cell: (88.92, 112.005, 183.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 73 16.00 P 103 15.00 Mg 3 11.99 O 2862 8.00 N 2379 7.00 C 8438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.08 Conformation dependent library (CDL) restraints added in 563.0 milliseconds 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 10 sheets defined 44.6% alpha, 11.4% beta 47 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 126 through 135 removed outlier: 3.784A pdb=" N GLU A 130 " --> pdb=" O ARG A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 161 Processing helix chain 'A' and resid 161 through 166 removed outlier: 4.274A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 194 removed outlier: 3.510A pdb=" N VAL A 194 " --> pdb=" O ILE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.580A pdb=" N HIS A 237 " --> pdb=" O HIS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 243 No H-bonds generated for 'chain 'A' and resid 241 through 243' Processing helix chain 'A' and resid 253 through 256 Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 299 through 313 removed outlier: 3.589A pdb=" N LYS A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 removed outlier: 3.533A pdb=" N GLY A 327 " --> pdb=" O VAL A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 370 removed outlier: 3.627A pdb=" N LEU A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 401 removed outlier: 4.417A pdb=" N SER A 382 " --> pdb=" O GLN A 378 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N MET A 383 " --> pdb=" O THR A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 415 Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 470 through 483 removed outlier: 3.561A pdb=" N GLN A 475 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 480 " --> pdb=" O LEU A 476 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N VAL A 482 " --> pdb=" O LYS A 478 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE A 483 " --> pdb=" O ILE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 510 removed outlier: 3.670A pdb=" N ALA A 501 " --> pdb=" O ARG A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 546 removed outlier: 3.552A pdb=" N THR A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 544 " --> pdb=" O ILE A 540 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER A 546 " --> pdb=" O LYS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 584 Processing helix chain 'A' and resid 604 through 609 Processing helix chain 'A' and resid 609 through 627 removed outlier: 3.636A pdb=" N LYS A 615 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU A 623 " --> pdb=" O ASP A 619 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR A 626 " --> pdb=" O ASN A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 664 removed outlier: 4.228A pdb=" N SER A 658 " --> pdb=" O GLY A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 716 through 731 removed outlier: 3.507A pdb=" N CYS A 721 " --> pdb=" O LYS A 717 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A 722 " --> pdb=" O LYS A 718 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N VAL A 725 " --> pdb=" O CYS A 721 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 730 " --> pdb=" O HIS A 726 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 731 " --> pdb=" O GLU A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 824 removed outlier: 3.544A pdb=" N GLU A 824 " --> pdb=" O VAL A 821 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 871 removed outlier: 3.582A pdb=" N PHE A 861 " --> pdb=" O LEU A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 872 through 876 Processing helix chain 'A' and resid 913 through 921 removed outlier: 3.706A pdb=" N ILE A 917 " --> pdb=" O ASP A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 957 removed outlier: 3.541A pdb=" N LYS A 957 " --> pdb=" O ILE A 953 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 953 through 957' Processing helix chain 'A' and resid 992 through 1001 Processing helix chain 'A' and resid 1058 through 1066 removed outlier: 3.713A pdb=" N SER A1066 " --> pdb=" O GLY A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1067 through 1088 removed outlier: 3.594A pdb=" N VAL A1080 " --> pdb=" O GLU A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1089 through 1091 No H-bonds generated for 'chain 'A' and resid 1089 through 1091' Processing helix chain 'A' and resid 1092 through 1098 Processing helix chain 'A' and resid 1099 through 1106 removed outlier: 3.531A pdb=" N GLU A1105 " --> pdb=" O HIS A1101 " (cutoff:3.500A) Processing helix chain 'A' and resid 1119 through 1141 removed outlier: 3.980A pdb=" N VAL A1123 " --> pdb=" O GLU A1119 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A1124 " --> pdb=" O ARG A1120 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL A1133 " --> pdb=" O LEU A1129 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS A1136 " --> pdb=" O ALA A1132 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LEU A1139 " --> pdb=" O ARG A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1155 Processing helix chain 'A' and resid 1158 through 1169 removed outlier: 3.564A pdb=" N LYS A1169 " --> pdb=" O LEU A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1250 removed outlier: 4.005A pdb=" N ILE A1235 " --> pdb=" O TYR A1231 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A1240 " --> pdb=" O ALA A1236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N PHE A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A1248 " --> pdb=" O GLY A1244 " (cutoff:3.500A) Processing helix chain 'A' and resid 1251 through 1263 Processing helix chain 'A' and resid 1269 through 1279 removed outlier: 4.051A pdb=" N VAL A1273 " --> pdb=" O GLU A1269 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N CYS A1277 " --> pdb=" O VAL A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1280 through 1290 removed outlier: 3.844A pdb=" N TYR A1283 " --> pdb=" O SER A1280 " (cutoff:3.500A) Proline residue: A1285 - end of helix removed outlier: 4.210A pdb=" N THR A1288 " --> pdb=" O PRO A1285 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN A1290 " --> pdb=" O THR A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1299 removed outlier: 3.677A pdb=" N GLN A1298 " --> pdb=" O THR A1294 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1312 removed outlier: 3.561A pdb=" N VAL A1310 " --> pdb=" O LYS A1306 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLN A1311 " --> pdb=" O GLY A1307 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A1312 " --> pdb=" O LEU A1308 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1306 through 1312' Processing helix chain 'A' and resid 1326 through 1349 removed outlier: 3.870A pdb=" N ALA A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU A1337 " --> pdb=" O GLY A1333 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR A1347 " --> pdb=" O SER A1343 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A1349 " --> pdb=" O PHE A1345 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1363 Processing helix chain 'A' and resid 1366 through 1378 removed outlier: 4.093A pdb=" N ASN A1372 " --> pdb=" O GLU A1368 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A1373 " --> pdb=" O ALA A1369 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A1375 " --> pdb=" O ALA A1371 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER A1376 " --> pdb=" O ASN A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1403 removed outlier: 3.633A pdb=" N GLU A1395 " --> pdb=" O HIS A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1418 through 1435 removed outlier: 4.329A pdb=" N VAL A1424 " --> pdb=" O LEU A1420 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLN A1425 " --> pdb=" O GLY A1421 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A1431 " --> pdb=" O CYS A1427 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A1433 " --> pdb=" O GLY A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1438 through 1449 removed outlier: 3.560A pdb=" N VAL A1442 " --> pdb=" O ASN A1438 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A1444 " --> pdb=" O ASN A1440 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE A1449 " --> pdb=" O MET A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1475 Processing helix chain 'A' and resid 1510 through 1528 removed outlier: 3.931A pdb=" N LYS A1516 " --> pdb=" O ARG A1512 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS A1517 " --> pdb=" O GLU A1513 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A1518 " --> pdb=" O GLY A1514 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A1521 " --> pdb=" O LYS A1517 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR A1524 " --> pdb=" O GLN A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1621 through 1633 removed outlier: 3.596A pdb=" N CYS A1630 " --> pdb=" O LEU A1626 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL A1631 " --> pdb=" O HIS A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1679 through 1698 removed outlier: 3.617A pdb=" N HIS A1697 " --> pdb=" O TRP A1693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 201 removed outlier: 3.534A pdb=" N HIS A 201 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL A 172 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU A 247 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET A 285 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A 140 " --> pdb=" O ILE A 282 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 333 through 335 Processing sheet with id=AA3, first strand: chain 'A' and resid 338 through 339 Processing sheet with id=AA4, first strand: chain 'A' and resid 679 through 683 removed outlier: 3.555A pdb=" N ILE A 691 " --> pdb=" O LYS A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 770 through 771 Processing sheet with id=AA6, first strand: chain 'A' and resid 811 through 812 removed outlier: 4.147A pdb=" N PHE A 811 " --> pdb=" O ILE A 797 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL A 790 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N GLU A 849 " --> pdb=" O VAL A 790 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU A 792 " --> pdb=" O VAL A 847 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N VAL A 847 " --> pdb=" O LEU A 792 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 794 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 841 " --> pdb=" O MET A 798 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 839 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 836 " --> pdb=" O LEU A 832 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 943 through 946 Processing sheet with id=AA8, first strand: chain 'A' and resid 1043 through 1045 removed outlier: 7.394A pdb=" N LEU A1012 " --> pdb=" O ILE A 975 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE A 975 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ARG A1014 " --> pdb=" O ALA A 973 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN A 968 " --> pdb=" O THR A 963 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 972 " --> pdb=" O SER A 959 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N SER A 959 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A1054 " --> pdb=" O LEU A 960 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N PHE A 962 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N LEU A1052 " --> pdb=" O PHE A 962 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1479 through 1485 Processing sheet with id=AB1, first strand: chain 'A' and resid 1640 through 1645 removed outlier: 3.672A pdb=" N TYR A1673 " --> pdb=" O CYS B 325 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE B 342 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ARG B 351 " --> pdb=" O MET B 340 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET B 340 " --> pdb=" O ARG B 351 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG B 343 " --> pdb=" O ILE B 309 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 228 hydrogen bond angles 0 basepair planarities 47 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 3.08 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4005 1.34 - 1.46: 2862 1.46 - 1.58: 7176 1.58 - 1.70: 206 1.70 - 1.82: 101 Bond restraints: 14350 Sorted by residual: bond pdb=" P A D 1 " pdb=" OP3 A D 1 " ideal model delta sigma weight residual 1.480 1.601 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" CA GLU A1040 " pdb=" C GLU A1040 " ideal model delta sigma weight residual 1.522 1.551 -0.029 1.20e-02 6.94e+03 5.93e+00 bond pdb=" N PHE A1188 " pdb=" CA PHE A1188 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.53e+00 bond pdb=" O3' C D 2 " pdb=" P A D 3 " ideal model delta sigma weight residual 1.607 1.586 0.021 1.20e-02 6.94e+03 3.00e+00 bond pdb=" C1' G C 54 " pdb=" N9 G C 54 " ideal model delta sigma weight residual 1.483 1.457 0.026 1.50e-02 4.44e+03 3.00e+00 ... (remaining 14345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 19355 1.99 - 3.99: 506 3.99 - 5.98: 23 5.98 - 7.98: 6 7.98 - 9.97: 6 Bond angle restraints: 19896 Sorted by residual: angle pdb=" O5' U D 35 " pdb=" C5' U D 35 " pdb=" C4' U D 35 " ideal model delta sigma weight residual 109.40 113.34 -3.94 8.00e-01 1.56e+00 2.43e+01 angle pdb=" N GLU A1040 " pdb=" CA GLU A1040 " pdb=" C GLU A1040 " ideal model delta sigma weight residual 108.07 115.56 -7.49 1.59e+00 3.96e-01 2.22e+01 angle pdb=" N ILE A1045 " pdb=" CA ILE A1045 " pdb=" C ILE A1045 " ideal model delta sigma weight residual 109.19 112.98 -3.79 8.20e-01 1.49e+00 2.13e+01 angle pdb=" N PHE A1188 " pdb=" CA PHE A1188 " pdb=" C PHE A1188 " ideal model delta sigma weight residual 110.80 119.36 -8.56 2.13e+00 2.20e-01 1.62e+01 angle pdb=" N GLY A1189 " pdb=" CA GLY A1189 " pdb=" C GLY A1189 " ideal model delta sigma weight residual 113.18 104.12 9.06 2.37e+00 1.78e-01 1.46e+01 ... (remaining 19891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.63: 7424 18.63 - 37.27: 928 37.27 - 55.90: 279 55.90 - 74.54: 143 74.54 - 93.17: 19 Dihedral angle restraints: 8793 sinusoidal: 4491 harmonic: 4302 Sorted by residual: dihedral pdb=" CA LEU A1450 " pdb=" C LEU A1450 " pdb=" N ASP A1451 " pdb=" CA ASP A1451 " ideal model delta harmonic sigma weight residual -180.00 -150.01 -29.99 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA LYS A 530 " pdb=" C LYS A 530 " pdb=" N SER A 531 " pdb=" CA SER A 531 " ideal model delta harmonic sigma weight residual 180.00 153.86 26.14 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA HIS A 802 " pdb=" C HIS A 802 " pdb=" N PRO A 803 " pdb=" CA PRO A 803 " ideal model delta harmonic sigma weight residual 180.00 -155.75 -24.25 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 8790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1818 0.045 - 0.090: 338 0.090 - 0.135: 150 0.135 - 0.180: 47 0.180 - 0.225: 2 Chirality restraints: 2355 Sorted by residual: chirality pdb=" C3' C D 2 " pdb=" C4' C D 2 " pdb=" O3' C D 2 " pdb=" C2' C D 2 " both_signs ideal model delta sigma weight residual False -2.48 -2.70 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ASP A1451 " pdb=" N ASP A1451 " pdb=" C ASP A1451 " pdb=" CB ASP A1451 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" C3' G C 54 " pdb=" C4' G C 54 " pdb=" O3' G C 54 " pdb=" C2' G C 54 " both_signs ideal model delta sigma weight residual False -2.48 -2.65 0.17 2.00e-01 2.50e+01 7.56e-01 ... (remaining 2352 not shown) Planarity restraints: 2144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 802 " -0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO A 803 " 0.205 5.00e-02 4.00e+02 pdb=" CA PRO A 803 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO A 803 " -0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A1190 " 0.053 5.00e-02 4.00e+02 8.06e-02 1.04e+01 pdb=" N PRO A1191 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO A1191 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A1191 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A1450 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C LEU A1450 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU A1450 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A1451 " -0.017 2.00e-02 2.50e+03 ... (remaining 2141 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 88 2.56 - 3.14: 10226 3.14 - 3.73: 21645 3.73 - 4.31: 29678 4.31 - 4.90: 46650 Nonbonded interactions: 108287 Sorted by model distance: nonbonded pdb=" OE2 GLU A1330 " pdb="MG MG A1802 " model vdw 1.974 2.170 nonbonded pdb=" OE1 GLN A1425 " pdb="MG MG A1802 " model vdw 1.975 2.170 nonbonded pdb=" O SER A 516 " pdb=" ND2 ASN A 550 " model vdw 2.218 3.120 nonbonded pdb=" OG SER A1117 " pdb=" OE1 GLU A1119 " model vdw 2.219 3.040 nonbonded pdb=" O MET A 591 " pdb=" OG SER A 594 " model vdw 2.241 3.040 ... (remaining 108282 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: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 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 : 0.003 0.121 14350 Z= 0.164 Angle : 0.626 9.972 19896 Z= 0.399 Chirality : 0.047 0.225 2355 Planarity : 0.005 0.119 2144 Dihedral : 19.094 93.172 5993 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.77 % Favored : 92.89 % Rotamer: Outliers : 0.46 % Allowed : 30.75 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.43 (0.23), residues: 1448 helix: -0.85 (0.21), residues: 614 sheet: 0.27 (0.38), residues: 216 loop : -1.38 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1415 TYR 0.019 0.001 TYR A1326 PHE 0.016 0.001 PHE A 843 TRP 0.008 0.001 TRP A1693 HIS 0.006 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.16 (14350) covalent geometry : angle 0.62587 / 0.40 (19896) hydrogen bonds : bond 0.26182 / 17.71 ( 583) hydrogen bonds : angle 7.58648 / 5.29 ( 1578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 105 time to evaluate : 0.382 Fit side-chains REVERT: A 1016 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.6880 (tptm) REVERT: A 1544 ASN cc_start: 0.8028 (m-40) cc_final: 0.7779 (m110) outliers start: 6 outliers final: 1 residues processed: 107 average time/residue: 0.1033 time to fit residues: 16.3957 Evaluate side-chains 103 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 383 MET Chi-restraints excluded: chain A residue 1016 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 30.0000 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 152 HIS A 324 GLN A 348 GLN A 408 GLN A 726 HIS A 793 HIS A 831 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1190 HIS A1472 GLN A1520 GLN A1639 HIS ** A1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.190278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.145906 restraints weight = 21445.133| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.71 r_work: 0.3496 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 14350 Z= 0.137 Angle : 0.579 11.296 19896 Z= 0.304 Chirality : 0.039 0.164 2355 Planarity : 0.006 0.118 2144 Dihedral : 15.292 89.724 3133 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.04 % Favored : 92.75 % Rotamer: Outliers : 2.82 % Allowed : 29.15 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -1.14 (0.22), residues: 1448 helix: -0.25 (0.20), residues: 630 sheet: 0.13 (0.35), residues: 230 loop : -1.61 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1415 TYR 0.019 0.001 TYR A1326 PHE 0.014 0.001 PHE A1131 TRP 0.008 0.001 TRP A 214 HIS 0.007 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (14350) covalent geometry : angle 0.57866 / 0.30 (19896) hydrogen bonds : bond 0.06559 / 4.46 ( 583) hydrogen bonds : angle 5.02019 / 3.61 ( 1578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 1039 ASP cc_start: 0.7138 (t70) cc_final: 0.6896 (m-30) REVERT: A 1041 TYR cc_start: 0.6212 (t80) cc_final: 0.5771 (t80) outliers start: 37 outliers final: 19 residues processed: 142 average time/residue: 0.1005 time to fit residues: 21.8415 Evaluate side-chains 129 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1064 SER Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1541 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.0060 chunk 131 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 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 = 0.4420 r_free = 0.4420 target = 0.190317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.143713 restraints weight = 21375.507| |-----------------------------------------------------------------------------| r_work (start): 0.3860 rms_B_bonded: 2.39 r_work: 0.3520 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 14350 Z= 0.128 Angle : 0.538 11.430 19896 Z= 0.281 Chirality : 0.038 0.163 2355 Planarity : 0.005 0.118 2144 Dihedral : 15.177 86.709 3130 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.84 % Favored : 92.96 % Rotamer: Outliers : 3.42 % Allowed : 28.23 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.88 (0.23), residues: 1448 helix: 0.10 (0.21), residues: 639 sheet: 0.16 (0.35), residues: 230 loop : -1.62 (0.27), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.019 0.001 TYR A1326 PHE 0.015 0.001 PHE A1131 TRP 0.007 0.001 TRP A1693 HIS 0.006 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14350) covalent geometry : angle 0.53844 / 0.28 (19896) hydrogen bonds : bond 0.05492 / 3.67 ( 583) hydrogen bonds : angle 4.50138 / 3.23 ( 1578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 112 time to evaluate : 0.514 Fit side-chains REVERT: A 1016 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7705 (mtpt) REVERT: A 1041 TYR cc_start: 0.6148 (t80) cc_final: 0.5904 (t80) REVERT: A 1076 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8192 (tm-30) REVERT: A 1646 GLU cc_start: 0.2868 (OUTLIER) cc_final: 0.2504 (tm-30) outliers start: 45 outliers final: 26 residues processed: 148 average time/residue: 0.1143 time to fit residues: 26.0421 Evaluate side-chains 134 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 105 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 857 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1076 GLU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1566 VAL Chi-restraints excluded: chain A residue 1646 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.3980 chunk 13 optimal weight: 0.1980 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 0.0470 chunk 80 optimal weight: 20.0000 chunk 21 optimal weight: 0.0970 chunk 106 optimal weight: 0.1980 chunk 139 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 ASN A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.193505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.149041 restraints weight = 21597.633| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.71 r_work: 0.3559 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.089 14350 Z= 0.101 Angle : 0.503 11.823 19896 Z= 0.262 Chirality : 0.036 0.160 2355 Planarity : 0.005 0.117 2144 Dihedral : 15.138 85.611 3130 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.52 % Favored : 94.27 % Rotamer: Outliers : 2.82 % Allowed : 28.84 % Favored : 68.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.54 (0.23), residues: 1448 helix: 0.46 (0.21), residues: 643 sheet: 0.27 (0.35), residues: 230 loop : -1.53 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 281 TYR 0.012 0.001 TYR A 796 PHE 0.012 0.001 PHE A 971 TRP 0.012 0.001 TRP A1635 HIS 0.004 0.000 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (14350) covalent geometry : angle 0.50339 / 0.26 (19896) hydrogen bonds : bond 0.04074 / 2.74 ( 583) hydrogen bonds : angle 4.10532 / 2.95 ( 1578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 121 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 853 ASP cc_start: 0.8228 (p0) cc_final: 0.7696 (p0) REVERT: A 1016 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7589 (tttm) REVERT: A 1041 TYR cc_start: 0.6130 (t80) cc_final: 0.5880 (t80) REVERT: A 1646 GLU cc_start: 0.2953 (OUTLIER) cc_final: 0.2632 (tm-30) outliers start: 37 outliers final: 19 residues processed: 148 average time/residue: 0.0991 time to fit residues: 22.2679 Evaluate side-chains 132 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 1016 LYS Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1190 HIS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1646 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 0.0060 chunk 77 optimal weight: 0.0570 chunk 22 optimal weight: 10.0000 chunk 126 optimal weight: 20.0000 chunk 127 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.2120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 348 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1030 GLN ** A1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.191120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.145846 restraints weight = 21458.847| |-----------------------------------------------------------------------------| r_work (start): 0.3885 rms_B_bonded: 2.73 r_work: 0.3513 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 14350 Z= 0.124 Angle : 0.517 11.607 19896 Z= 0.266 Chirality : 0.038 0.159 2355 Planarity : 0.005 0.117 2144 Dihedral : 15.043 84.576 3130 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.70 % Favored : 93.09 % Rotamer: Outliers : 2.97 % Allowed : 28.61 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.60 (0.23), residues: 1448 helix: 0.44 (0.21), residues: 644 sheet: 0.13 (0.35), residues: 235 loop : -1.56 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1415 TYR 0.019 0.001 TYR A1326 PHE 0.023 0.001 PHE A 971 TRP 0.007 0.001 TRP A 517 HIS 0.006 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (14350) covalent geometry : angle 0.51678 / 0.27 (19896) hydrogen bonds : bond 0.04676 / 3.07 ( 583) hydrogen bonds : angle 4.09607 / 2.94 ( 1578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.401 Fit side-chains REVERT: A 1016 LYS cc_start: 0.7868 (ttpt) cc_final: 0.7594 (tttm) REVERT: A 1646 GLU cc_start: 0.2962 (OUTLIER) cc_final: 0.2644 (tm-30) outliers start: 39 outliers final: 31 residues processed: 140 average time/residue: 0.1027 time to fit residues: 21.5429 Evaluate side-chains 142 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1190 HIS Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1646 GLU Chi-restraints excluded: chain A residue 1658 VAL Chi-restraints excluded: chain B residue 348 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 17 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 153 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 348 GLN A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN ** A1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.192040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147001 restraints weight = 21489.185| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.79 r_work: 0.3535 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.090 14350 Z= 0.103 Angle : 0.487 11.816 19896 Z= 0.253 Chirality : 0.036 0.165 2355 Planarity : 0.005 0.119 2144 Dihedral : 15.007 83.605 3126 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.01 % Favored : 93.85 % Rotamer: Outliers : 3.50 % Allowed : 28.31 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.47 (0.23), residues: 1448 helix: 0.56 (0.21), residues: 645 sheet: 0.19 (0.35), residues: 235 loop : -1.52 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 363 TYR 0.014 0.001 TYR A1326 PHE 0.023 0.001 PHE A 971 TRP 0.008 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.10 (14350) covalent geometry : angle 0.48692 / 0.25 (19896) hydrogen bonds : bond 0.04096 / 2.70 ( 583) hydrogen bonds : angle 3.96148 / 2.84 ( 1578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 122 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8208 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 1016 LYS cc_start: 0.7791 (ttpt) cc_final: 0.7555 (tttm) REVERT: A 1018 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7216 (mp) REVERT: A 1646 GLU cc_start: 0.2835 (OUTLIER) cc_final: 0.2552 (tm-30) outliers start: 46 outliers final: 31 residues processed: 156 average time/residue: 0.1020 time to fit residues: 24.2491 Evaluate side-chains 145 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1566 VAL Chi-restraints excluded: chain A residue 1646 GLU Chi-restraints excluded: chain B residue 348 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 1.9990 chunk 38 optimal weight: 0.2980 chunk 124 optimal weight: 7.9990 chunk 49 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1170 ASN A1686 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.192192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.147674 restraints weight = 21416.867| |-----------------------------------------------------------------------------| r_work (start): 0.3898 rms_B_bonded: 2.88 r_work: 0.3530 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14350 Z= 0.102 Angle : 0.518 24.100 19896 Z= 0.256 Chirality : 0.036 0.216 2355 Planarity : 0.006 0.192 2144 Dihedral : 14.989 83.012 3126 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 3.58 % Allowed : 28.31 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % 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: -0.39 (0.23), residues: 1448 helix: 0.65 (0.21), residues: 645 sheet: 0.24 (0.35), residues: 235 loop : -1.50 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1415 TYR 0.014 0.001 TYR A1326 PHE 0.018 0.001 PHE A 971 TRP 0.007 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (14350) covalent geometry : angle 0.51832 / 0.26 (19896) hydrogen bonds : bond 0.04022 / 2.64 ( 583) hydrogen bonds : angle 3.90666 / 2.80 ( 1578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 113 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 1016 LYS cc_start: 0.7803 (ttpt) cc_final: 0.7569 (tttm) REVERT: A 1646 GLU cc_start: 0.2831 (OUTLIER) cc_final: 0.2550 (tm-30) outliers start: 47 outliers final: 38 residues processed: 149 average time/residue: 0.1105 time to fit residues: 24.7591 Evaluate side-chains 151 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 112 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1566 VAL Chi-restraints excluded: chain A residue 1646 GLU Chi-restraints excluded: chain A residue 1658 VAL Chi-restraints excluded: chain B residue 348 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 0.9990 chunk 136 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1686 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.191126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.145470 restraints weight = 21394.001| |-----------------------------------------------------------------------------| r_work (start): 0.3875 rms_B_bonded: 2.91 r_work: 0.3505 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14350 Z= 0.121 Angle : 0.521 15.219 19896 Z= 0.264 Chirality : 0.037 0.176 2355 Planarity : 0.005 0.161 2144 Dihedral : 14.962 81.955 3126 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.77 % Favored : 93.09 % Rotamer: Outliers : 4.03 % Allowed : 27.93 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -0.45 (0.23), residues: 1448 helix: 0.61 (0.21), residues: 644 sheet: 0.22 (0.35), residues: 235 loop : -1.55 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1415 TYR 0.021 0.001 TYR A1326 PHE 0.018 0.001 PHE A 971 TRP 0.008 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 (14350) covalent geometry : angle 0.52071 / 0.26 (19896) hydrogen bonds : bond 0.04400 / 2.86 ( 583) hydrogen bonds : angle 3.94195 / 2.83 ( 1578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 111 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7925 (mt-10) REVERT: A 727 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8296 (tt0) REVERT: A 1016 LYS cc_start: 0.7838 (ttpt) cc_final: 0.7628 (tttm) REVERT: A 1018 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7207 (mp) REVERT: A 1057 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7641 (tp) REVERT: A 1646 GLU cc_start: 0.2892 (OUTLIER) cc_final: 0.2593 (tm-30) outliers start: 53 outliers final: 43 residues processed: 151 average time/residue: 0.1059 time to fit residues: 24.2091 Evaluate side-chains 156 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 109 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1070 SER Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1566 VAL Chi-restraints excluded: chain A residue 1646 GLU Chi-restraints excluded: chain A residue 1658 VAL Chi-restraints excluded: chain B residue 348 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 94 optimal weight: 0.8980 chunk 149 optimal weight: 30.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN A1010 GLN A1686 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.190525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.144907 restraints weight = 21571.410| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.97 r_work: 0.3490 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14350 Z= 0.139 Angle : 0.529 11.827 19896 Z= 0.269 Chirality : 0.038 0.152 2355 Planarity : 0.005 0.147 2144 Dihedral : 14.958 81.407 3126 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.84 % Favored : 93.02 % Rotamer: Outliers : 3.88 % Allowed : 27.93 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -0.51 (0.23), residues: 1448 helix: 0.54 (0.21), residues: 644 sheet: 0.21 (0.35), residues: 235 loop : -1.58 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.023 0.001 TYR A1326 PHE 0.017 0.001 PHE A 971 TRP 0.008 0.001 TRP A 517 HIS 0.006 0.001 HIS A1315 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (14350) covalent geometry : angle 0.52878 / 0.27 (19896) hydrogen bonds : bond 0.04584 / 2.98 ( 583) hydrogen bonds : angle 3.98349 / 2.86 ( 1578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7912 (mt-10) REVERT: A 727 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8309 (tt0) REVERT: A 1016 LYS cc_start: 0.7819 (ttpt) cc_final: 0.7594 (tttm) REVERT: A 1018 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7177 (mp) REVERT: A 1057 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7637 (tp) REVERT: A 1646 GLU cc_start: 0.2894 (OUTLIER) cc_final: 0.2616 (tm-30) outliers start: 51 outliers final: 42 residues processed: 150 average time/residue: 0.1139 time to fit residues: 25.7746 Evaluate side-chains 156 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1566 VAL Chi-restraints excluded: chain A residue 1646 GLU Chi-restraints excluded: chain A residue 1658 VAL Chi-restraints excluded: chain B residue 348 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 97 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 105 optimal weight: 0.0270 chunk 52 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1051 HIS A1686 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.191708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.146147 restraints weight = 21351.201| |-----------------------------------------------------------------------------| r_work (start): 0.3877 rms_B_bonded: 2.96 r_work: 0.3522 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14350 Z= 0.104 Angle : 0.510 11.897 19896 Z= 0.261 Chirality : 0.037 0.147 2355 Planarity : 0.005 0.140 2144 Dihedral : 14.965 80.812 3126 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.42 % Favored : 93.44 % Rotamer: Outliers : 3.65 % Allowed : 28.16 % Favored : 68.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -0.40 (0.23), residues: 1448 helix: 0.68 (0.21), residues: 644 sheet: 0.24 (0.35), residues: 235 loop : -1.57 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 363 TYR 0.016 0.001 TYR A1326 PHE 0.016 0.001 PHE A 971 TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.10 (14350) covalent geometry : angle 0.50951 / 0.26 (19896) hydrogen bonds : bond 0.04110 / 2.68 ( 583) hydrogen bonds : angle 3.89034 / 2.79 ( 1578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2896 Ramachandran restraints generated. 1448 Oldfield, 0 Emsley, 1448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 110 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: A 354 GLU cc_start: 0.8193 (mt-10) cc_final: 0.7907 (mt-10) REVERT: A 727 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: A 1016 LYS cc_start: 0.7780 (ttpt) cc_final: 0.7565 (tttm) REVERT: A 1018 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7289 (mp) REVERT: A 1057 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 1646 GLU cc_start: 0.2875 (OUTLIER) cc_final: 0.2575 (tm-30) outliers start: 48 outliers final: 39 residues processed: 147 average time/residue: 0.0996 time to fit residues: 22.0942 Evaluate side-chains 152 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 253 CYS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 347 SER Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 559 GLU Chi-restraints excluded: chain A residue 591 MET Chi-restraints excluded: chain A residue 634 CYS Chi-restraints excluded: chain A residue 665 SER Chi-restraints excluded: chain A residue 670 ASP Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain A residue 727 GLU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1018 LEU Chi-restraints excluded: chain A residue 1019 CYS Chi-restraints excluded: chain A residue 1050 SER Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1160 SER Chi-restraints excluded: chain A residue 1165 LEU Chi-restraints excluded: chain A residue 1171 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP Chi-restraints excluded: chain A residue 1278 ILE Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1325 CYS Chi-restraints excluded: chain A residue 1326 TYR Chi-restraints excluded: chain A residue 1385 CYS Chi-restraints excluded: chain A residue 1502 LEU Chi-restraints excluded: chain A residue 1541 VAL Chi-restraints excluded: chain A residue 1566 VAL Chi-restraints excluded: chain A residue 1646 GLU Chi-restraints excluded: chain A residue 1658 VAL Chi-restraints excluded: chain B residue 348 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 52 optimal weight: 0.9990 chunk 53 optimal weight: 4.9990 chunk 138 optimal weight: 20.0000 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 0.1980 chunk 93 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1686 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.192573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.147305 restraints weight = 21307.385| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.91 r_work: 0.3523 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 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 : 0.002 0.048 14350 Z= 0.101 Angle : 0.497 11.992 19896 Z= 0.253 Chirality : 0.036 0.150 2355 Planarity : 0.005 0.136 2144 Dihedral : 14.929 79.415 3126 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.15 % Favored : 93.72 % Rotamer: Outliers : 3.65 % Allowed : 28.23 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 1.64 % 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: -0.27 (0.23), residues: 1448 helix: 0.85 (0.21), residues: 644 sheet: 0.25 (0.35), residues: 234 loop : -1.56 (0.27), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.014 0.001 TYR A 796 PHE 0.015 0.001 PHE A 971 TRP 0.008 0.001 TRP A 517 HIS 0.006 0.001 HIS A1536 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (14350) covalent geometry : angle 0.49692 / 0.25 (19896) hydrogen bonds : bond 0.03808 / 2.48 ( 583) hydrogen bonds : angle 3.78464 / 2.71 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.03 seconds wall clock time: 59 minutes 18.09 seconds (3558.09 seconds total)