Starting phenix.real_space_refine on Wed Mar 4 14:39:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kbz_62235/03_2026/9kbz_62235.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kbz_62235/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/9kbz_62235/03_2026/9kbz_62235.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kbz_62235/03_2026/9kbz_62235.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kbz_62235/03_2026/9kbz_62235.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kbz_62235/03_2026/9kbz_62235.map" } 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-dev-5986/lib/python3.9/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: 3.24, per 1000 atoms: 0.23 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: 1.25 Conformation dependent library (CDL) restraints added in 450.7 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: 2.09 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: 3.98 Time building geometry restraints manager: 1.67 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=" CB PRO A 803 " pdb=" CG PRO A 803 " ideal model delta sigma weight residual 1.492 1.578 -0.086 5.00e-02 4.00e+02 2.97e+00 bond pdb=" N ASP A1039 " pdb=" CA ASP A1039 " ideal model delta sigma weight residual 1.457 1.478 -0.021 1.29e-02 6.01e+03 2.58e+00 ... (remaining 14345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 19615 1.99 - 3.99: 246 3.99 - 5.98: 23 5.98 - 7.98: 6 7.98 - 9.97: 6 Bond angle restraints: 19896 Sorted by residual: 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 angle pdb=" C4' C D 2 " pdb=" C3' C D 2 " pdb=" O3' C D 2 " ideal model delta sigma weight residual 113.00 107.88 5.12 1.50e+00 4.44e-01 1.17e+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: 1924 0.045 - 0.090: 324 0.090 - 0.135: 94 0.135 - 0.180: 11 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: 4.380 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: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.490 Find NCS groups from input model: 0.080 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: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 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= 0.141 Angle : 0.556 9.972 19896 Z= 0.294 Chirality : 0.038 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 covalent geometry : bond 0.00288 (14350) covalent geometry : angle 0.55620 (19896) hydrogen bonds : bond 0.26182 ( 583) hydrogen bonds : angle 7.58648 ( 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 : 0.464 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: 0.1148 time to fit residues: 17.9600 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 : 0.369 ------------------------------------------------------------------------------- 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: 10.0000 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 324 GLN A 408 GLN A 726 HIS A 793 HIS A1010 GLN A1190 HIS A1472 GLN A1639 HIS ** A1686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.190763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.146029 restraints weight = 21541.236| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.75 r_work: 0.3518 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1118 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= 0.126 Angle : 0.550 11.741 19896 Z= 0.282 Chirality : 0.038 0.167 2355 Planarity : 0.005 0.118 2144 Dihedral : 15.216 88.483 3133 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.77 % Favored : 93.02 % Rotamer: Outliers : 2.74 % Allowed : 29.22 % 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: -1.01 (0.22), residues: 1448 helix: -0.10 (0.20), residues: 635 sheet: 0.13 (0.35), residues: 240 loop : -1.60 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1415 TYR 0.017 0.001 TYR A1326 PHE 0.016 0.001 PHE A1131 TRP 0.009 0.001 TRP A1693 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00281 (14350) covalent geometry : angle 0.54984 (19896) hydrogen bonds : bond 0.05149 ( 583) hydrogen bonds : angle 4.60366 ( 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 156 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 120 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 1016 LYS cc_start: 0.8057 (OUTLIER) cc_final: 0.7559 (mtpt) REVERT: A 1039 ASP cc_start: 0.6893 (t70) cc_final: 0.6588 (m-30) REVERT: A 1041 TYR cc_start: 0.6134 (t80) cc_final: 0.5496 (t80) REVERT: A 1445 MET cc_start: 0.7628 (mtt) cc_final: 0.7400 (mtt) REVERT: A 1646 GLU cc_start: 0.3048 (OUTLIER) cc_final: 0.2729 (tm-30) outliers start: 36 outliers final: 17 residues processed: 146 average time/residue: 0.1101 time to fit residues: 24.1620 Evaluate side-chains 130 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 491 CYS Chi-restraints excluded: chain A residue 519 SER 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 1016 LYS Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER 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 1541 VAL Chi-restraints excluded: chain A residue 1646 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 144 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 133 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN A 355 ASN A 408 GLN ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1686 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.192189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.146836 restraints weight = 21356.233| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.87 r_work: 0.3534 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.087 14350 Z= 0.107 Angle : 0.504 11.712 19896 Z= 0.257 Chirality : 0.037 0.164 2355 Planarity : 0.005 0.117 2144 Dihedral : 15.036 84.815 3130 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.08 % Favored : 93.72 % Rotamer: Outliers : 2.97 % Allowed : 28.77 % Favored : 68.26 % 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: -0.57 (0.23), residues: 1448 helix: 0.44 (0.21), residues: 637 sheet: 0.27 (0.35), residues: 235 loop : -1.56 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1415 TYR 0.014 0.001 TYR A1326 PHE 0.018 0.001 PHE A1186 TRP 0.007 0.001 TRP A 517 HIS 0.005 0.000 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00244 (14350) covalent geometry : angle 0.50411 (19896) hydrogen bonds : bond 0.04027 ( 583) hydrogen bonds : angle 4.02064 ( 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 160 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 121 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: A 1016 LYS cc_start: 0.8108 (ttpt) cc_final: 0.7643 (tttm) REVERT: A 1646 GLU cc_start: 0.2958 (OUTLIER) cc_final: 0.2656 (tm-30) outliers start: 39 outliers final: 20 residues processed: 152 average time/residue: 0.1112 time to fit residues: 24.9533 Evaluate side-chains 124 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 103 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 317 TYR Chi-restraints excluded: chain A residue 365 LEU 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 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 955 ASP Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1247 LEU Chi-restraints excluded: chain A residue 1249 ASP 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 B residue 348 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 54 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 0.0170 chunk 139 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN A1051 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.191773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.146696 restraints weight = 21442.121| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.91 r_work: 0.3509 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 14350 Z= 0.113 Angle : 0.511 11.838 19896 Z= 0.258 Chirality : 0.037 0.162 2355 Planarity : 0.005 0.117 2144 Dihedral : 14.950 83.157 3126 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 3.50 % Allowed : 27.93 % Favored : 68.57 % 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: -0.50 (0.23), residues: 1448 helix: 0.54 (0.21), residues: 644 sheet: 0.29 (0.36), residues: 235 loop : -1.59 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1415 TYR 0.016 0.001 TYR A1326 PHE 0.014 0.001 PHE A1131 TRP 0.009 0.001 TRP A1635 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00259 (14350) covalent geometry : angle 0.51104 (19896) hydrogen bonds : bond 0.03987 ( 583) hydrogen bonds : angle 3.94832 ( 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 155 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 1016 LYS cc_start: 0.7875 (ttpt) cc_final: 0.7513 (mttt) REVERT: A 1646 GLU cc_start: 0.3004 (OUTLIER) cc_final: 0.2728 (tm-30) outliers start: 46 outliers final: 34 residues processed: 144 average time/residue: 0.1020 time to fit residues: 22.5078 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 317 TYR Chi-restraints excluded: chain A residue 365 LEU 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 551 LEU 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 866 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1165 LEU 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 1.9990 chunk 61 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 831 HIS ** A 835 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1170 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.188867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.142965 restraints weight = 21524.511| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 3.03 r_work: 0.3455 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 14350 Z= 0.171 Angle : 0.570 11.960 19896 Z= 0.290 Chirality : 0.039 0.160 2355 Planarity : 0.005 0.118 2144 Dihedral : 14.980 80.713 3126 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.32 % Favored : 92.54 % Rotamer: Outliers : 4.26 % Allowed : 27.55 % 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: -0.74 (0.23), residues: 1448 helix: 0.32 (0.21), residues: 643 sheet: 0.37 (0.36), residues: 220 loop : -1.74 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1415 TYR 0.029 0.002 TYR A1326 PHE 0.017 0.001 PHE A1131 TRP 0.011 0.001 TRP A 517 HIS 0.007 0.001 HIS A1315 Details of bonding type rmsd covalent geometry : bond 0.00402 (14350) covalent geometry : angle 0.56989 (19896) hydrogen bonds : bond 0.05205 ( 583) hydrogen bonds : angle 4.19094 ( 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 159 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 103 time to evaluate : 0.449 Fit side-chains revert: symmetry clash REVERT: A 727 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: A 1016 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7595 (mttt) REVERT: A 1646 GLU cc_start: 0.2956 (OUTLIER) cc_final: 0.2695 (tm-30) outliers start: 56 outliers final: 38 residues processed: 150 average time/residue: 0.0993 time to fit residues: 22.6470 Evaluate side-chains 141 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 THR 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 388 LYS 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 551 LEU 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 727 GLU Chi-restraints excluded: chain A residue 794 SER Chi-restraints excluded: chain A residue 864 ILE Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 916 THR Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1057 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1089 SER Chi-restraints excluded: chain A residue 1095 ILE 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 92 optimal weight: 0.0470 chunk 117 optimal weight: 0.0570 chunk 120 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 17 optimal weight: 0.0970 chunk 53 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 8.9990 chunk 153 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** 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 = 0.4457 r_free = 0.4457 target = 0.193494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.149286 restraints weight = 21546.348| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 2.96 r_work: 0.3540 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.093 14350 Z= 0.094 Angle : 0.489 12.005 19896 Z= 0.246 Chirality : 0.036 0.156 2355 Planarity : 0.005 0.116 2144 Dihedral : 14.913 78.410 3126 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.32 % Favored : 94.61 % Rotamer: Outliers : 3.20 % Allowed : 28.39 % 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: -0.34 (0.23), residues: 1448 helix: 0.73 (0.21), residues: 647 sheet: 0.28 (0.35), residues: 234 loop : -1.55 (0.27), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1415 TYR 0.020 0.001 TYR A1041 PHE 0.011 0.001 PHE A1131 TRP 0.009 0.001 TRP A 517 HIS 0.004 0.000 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00212 (14350) covalent geometry : angle 0.48944 (19896) hydrogen bonds : bond 0.03320 ( 583) hydrogen bonds : angle 3.74445 ( 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 159 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 117 time to evaluate : 0.378 Fit side-chains revert: symmetry clash REVERT: A 542 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8066 (tppt) REVERT: A 548 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6055 (tm-30) REVERT: A 859 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 1016 LYS cc_start: 0.7832 (ttpt) cc_final: 0.7521 (mttt) REVERT: A 1522 MET cc_start: 0.6739 (tpt) cc_final: 0.6469 (mtt) REVERT: A 1544 ASN cc_start: 0.7962 (m-40) cc_final: 0.7653 (m110) REVERT: A 1646 GLU cc_start: 0.3103 (OUTLIER) cc_final: 0.2862 (tm-30) outliers start: 42 outliers final: 29 residues processed: 151 average time/residue: 0.0976 time to fit residues: 22.6075 Evaluate side-chains 140 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 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 492 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 551 LEU 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 713 THR 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 1057 LEU Chi-restraints excluded: chain A residue 1087 VAL Chi-restraints excluded: chain A residue 1165 LEU 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 1296 GLU Chi-restraints excluded: chain A residue 1298 GLN Chi-restraints excluded: chain A residue 1376 SER Chi-restraints excluded: chain A residue 1385 CYS 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: 3.9990 chunk 38 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 49 optimal weight: 20.0000 chunk 117 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** 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 = 0.4436 r_free = 0.4436 target = 0.191643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.146606 restraints weight = 21341.490| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.81 r_work: 0.3518 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14350 Z= 0.116 Angle : 0.533 22.231 19896 Z= 0.259 Chirality : 0.037 0.248 2355 Planarity : 0.006 0.185 2144 Dihedral : 14.876 77.290 3126 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.49 % Favored : 93.44 % Rotamer: Outliers : 3.42 % Allowed : 28.01 % Favored : 68.57 % 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: -0.34 (0.23), residues: 1448 helix: 0.77 (0.21), residues: 640 sheet: 0.28 (0.35), residues: 234 loop : -1.58 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1415 TYR 0.019 0.001 TYR A1041 PHE 0.014 0.001 PHE A1131 TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00263 (14350) covalent geometry : angle 0.53335 (19896) hydrogen bonds : bond 0.03981 ( 583) hydrogen bonds : angle 3.80595 ( 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 153 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 859 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7842 (tm-30) REVERT: A 1016 LYS cc_start: 0.7825 (ttpt) cc_final: 0.7481 (mttt) REVERT: A 1028 ARG cc_start: 0.8813 (OUTLIER) cc_final: 0.8519 (mtp180) REVERT: A 1190 HIS cc_start: 0.7124 (OUTLIER) cc_final: 0.6847 (p90) REVERT: A 1522 MET cc_start: 0.6784 (tpt) cc_final: 0.6505 (mtt) REVERT: A 1544 ASN cc_start: 0.7992 (m-40) cc_final: 0.7711 (m110) REVERT: A 1646 GLU cc_start: 0.3062 (OUTLIER) cc_final: 0.2821 (tm-30) outliers start: 45 outliers final: 37 residues processed: 146 average time/residue: 0.1023 time to fit residues: 22.6437 Evaluate side-chains 146 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 106 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 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 492 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 551 LEU 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 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1028 ARG Chi-restraints excluded: chain A residue 1057 LEU 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 1190 HIS 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 69 optimal weight: 0.9990 chunk 136 optimal weight: 10.0000 chunk 92 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** 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 = 0.4448 r_free = 0.4448 target = 0.192757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.148597 restraints weight = 21392.585| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.85 r_work: 0.3541 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.2119 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= 0.099 Angle : 0.506 15.151 19896 Z= 0.248 Chirality : 0.036 0.185 2355 Planarity : 0.005 0.159 2144 Dihedral : 14.862 75.894 3126 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 3.88 % Allowed : 27.55 % Favored : 68.57 % 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: -0.24 (0.23), residues: 1448 helix: 0.84 (0.21), residues: 646 sheet: 0.31 (0.35), residues: 239 loop : -1.53 (0.27), residues: 563 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1415 TYR 0.018 0.001 TYR A1041 PHE 0.016 0.001 PHE A 843 TRP 0.009 0.001 TRP A 517 HIS 0.005 0.000 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00219 (14350) covalent geometry : angle 0.50553 (19896) hydrogen bonds : bond 0.03560 ( 583) hydrogen bonds : angle 3.70301 ( 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 163 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 542 LYS cc_start: 0.8303 (ttmm) cc_final: 0.8040 (tppt) REVERT: A 548 GLU cc_start: 0.7219 (OUTLIER) cc_final: 0.5992 (tm-30) REVERT: A 859 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7828 (tm-30) REVERT: A 1016 LYS cc_start: 0.7800 (ttpt) cc_final: 0.7471 (mttt) REVERT: A 1028 ARG cc_start: 0.8763 (OUTLIER) cc_final: 0.8498 (mtp180) REVERT: A 1522 MET cc_start: 0.6699 (tpt) cc_final: 0.6432 (mtt) REVERT: A 1544 ASN cc_start: 0.7961 (m-40) cc_final: 0.7670 (m110) REVERT: A 1646 GLU cc_start: 0.3052 (OUTLIER) cc_final: 0.2838 (tm-30) outliers start: 51 outliers final: 39 residues processed: 156 average time/residue: 0.1048 time to fit residues: 24.6519 Evaluate side-chains 153 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 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 492 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 551 LEU 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 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1028 ARG 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 1165 LEU 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 1296 GLU 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 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: 0.6980 chunk 149 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 105 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 278 GLN ** A 835 GLN ** 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 = 0.4429 r_free = 0.4429 target = 0.191120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.146289 restraints weight = 21609.767| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 3.15 r_work: 0.3469 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14350 Z= 0.126 Angle : 0.531 11.840 19896 Z= 0.263 Chirality : 0.037 0.171 2355 Planarity : 0.005 0.144 2144 Dihedral : 14.852 74.521 3126 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.63 % Favored : 93.30 % Rotamer: Outliers : 3.58 % Allowed : 28.01 % Favored : 68.42 % 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: -0.34 (0.23), residues: 1448 helix: 0.77 (0.21), residues: 640 sheet: 0.23 (0.35), residues: 234 loop : -1.57 (0.27), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1415 TYR 0.020 0.001 TYR A1041 PHE 0.017 0.001 PHE A 843 TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00287 (14350) covalent geometry : angle 0.53057 (19896) hydrogen bonds : bond 0.04198 ( 583) hydrogen bonds : angle 3.82173 ( 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 153 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 106 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 207 ILE cc_start: 0.6694 (pt) cc_final: 0.6468 (mt) REVERT: A 548 GLU cc_start: 0.7319 (OUTLIER) cc_final: 0.6061 (tm-30) REVERT: A 859 GLU cc_start: 0.8092 (tm-30) cc_final: 0.7797 (tm-30) REVERT: A 1016 LYS cc_start: 0.7811 (ttpt) cc_final: 0.7469 (mttt) REVERT: A 1028 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8561 (mtp180) REVERT: A 1522 MET cc_start: 0.6748 (tpt) cc_final: 0.6421 (mtt) REVERT: A 1544 ASN cc_start: 0.8025 (m-40) cc_final: 0.7681 (m-40) REVERT: A 1646 GLU cc_start: 0.3039 (OUTLIER) cc_final: 0.2812 (tm-30) outliers start: 47 outliers final: 41 residues processed: 146 average time/residue: 0.1097 time to fit residues: 24.3025 Evaluate side-chains 148 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 104 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 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 492 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 551 LEU 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 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1028 ARG 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 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 1296 GLU 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 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: 0.9990 chunk 36 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** 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 = 0.4439 r_free = 0.4439 target = 0.192007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.147721 restraints weight = 21405.635| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.98 r_work: 0.3511 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14350 Z= 0.109 Angle : 0.520 11.900 19896 Z= 0.257 Chirality : 0.037 0.158 2355 Planarity : 0.005 0.137 2144 Dihedral : 14.850 73.604 3126 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.22 % Favored : 93.72 % Rotamer: Outliers : 3.50 % Allowed : 28.08 % Favored : 68.42 % 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: 0.84 (0.21), residues: 640 sheet: 0.26 (0.35), residues: 239 loop : -1.55 (0.27), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1415 TYR 0.020 0.001 TYR A1041 PHE 0.026 0.001 PHE A 843 TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00245 (14350) covalent geometry : angle 0.52026 (19896) hydrogen bonds : bond 0.03844 ( 583) hydrogen bonds : angle 3.76129 ( 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 156 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 548 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.5995 (tm-30) REVERT: A 859 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7790 (tm-30) REVERT: A 1016 LYS cc_start: 0.7765 (ttpt) cc_final: 0.7445 (mttt) REVERT: A 1028 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8510 (mtp180) REVERT: A 1522 MET cc_start: 0.6795 (tpt) cc_final: 0.6449 (mtt) REVERT: A 1544 ASN cc_start: 0.8028 (m-40) cc_final: 0.7694 (m-40) REVERT: A 1646 GLU cc_start: 0.3048 (OUTLIER) cc_final: 0.2835 (tm-30) outliers start: 46 outliers final: 42 residues processed: 149 average time/residue: 0.1023 time to fit residues: 23.0778 Evaluate side-chains 152 residues out of total 1314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 107 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 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 492 ILE Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 551 LEU 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 794 SER Chi-restraints excluded: chain A residue 862 GLN Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 901 LEU Chi-restraints excluded: chain A residue 955 ASP Chi-restraints excluded: chain A residue 964 THR Chi-restraints excluded: chain A residue 1028 ARG 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 1089 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 1296 GLU 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 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: 0.6980 chunk 138 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 835 GLN ** 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 = 0.4440 r_free = 0.4440 target = 0.192134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.147493 restraints weight = 21326.421| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 3.11 r_work: 0.3498 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14350 Z= 0.109 Angle : 0.518 11.986 19896 Z= 0.255 Chirality : 0.037 0.159 2355 Planarity : 0.005 0.130 2144 Dihedral : 14.832 73.619 3126 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.42 % Favored : 93.44 % Rotamer: Outliers : 3.65 % Allowed : 27.93 % Favored : 68.42 % 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: -0.24 (0.23), residues: 1448 helix: 0.88 (0.21), residues: 640 sheet: 0.25 (0.35), residues: 235 loop : -1.53 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1415 TYR 0.020 0.001 TYR A1041 PHE 0.014 0.001 PHE A1131 TRP 0.009 0.001 TRP A 517 HIS 0.005 0.001 HIS A1536 Details of bonding type rmsd covalent geometry : bond 0.00246 (14350) covalent geometry : angle 0.51818 (19896) hydrogen bonds : bond 0.03787 ( 583) hydrogen bonds : angle 3.73030 ( 1578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3498.03 seconds wall clock time: 60 minutes 33.89 seconds (3633.89 seconds total)