Starting phenix.real_space_refine on Sat Sep 12 06:57:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0f_32241/09_2026/7w0f_32241.cif" } resolution = 4.55 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= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 93 5.49 5 S 63 5.16 5 C 8659 2.51 5 N 2406 2.21 5 O 2876 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14097 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1476, 11963 Classifications: {'peptide': 1476} Link IDs: {'PTRANS': 61, 'TRANS': 1414} Chain breaks: 2 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 451 Classifications: {'RNAv2': 21} Modifications used: {'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 437 Classifications: {'RNAv2': 21} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 14} Link IDs: {'rna3p': 20} Chain: "E" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 544 Classifications: {'RNAv2': 26} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 16} Link IDs: {'rna3p': 25} Chain: "F" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 559 Classifications: {'RNAv2': 26} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna3p': 25} Time building chain proxies: 3.24, per 1000 atoms: 0.23 Number of scatterers: 14097 At special positions: 0 Unit cell: (92.88, 97.2, 179.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 93 15.00 O 2876 8.00 N 2406 7.00 C 8659 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: 1.23 Conformation dependent library (CDL) restraints added in 538.1 milliseconds 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2852 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 9 sheets defined 54.8% alpha, 9.7% beta 27 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 2.07 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.785A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 66 through 80 removed outlier: 4.065A pdb=" N CYS A 80 " --> pdb=" O ALA A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.745A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.508A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 213 removed outlier: 4.661A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 232 through 251 removed outlier: 4.059A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 5.243A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 313 removed outlier: 3.746A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 309 " --> pdb=" O VAL A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.799A pdb=" N LYS A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 382 through 386 Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.602A pdb=" N ASN A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.575A pdb=" N ASN A 417 " --> pdb=" O PRO A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 462 through 465 Processing helix chain 'A' and resid 484 through 494 Processing helix chain 'A' and resid 510 through 529 removed outlier: 4.372A pdb=" N ALA A 529 " --> pdb=" O HIS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 535 Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.997A pdb=" N ILE A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 553 " --> pdb=" O GLY A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 580 removed outlier: 3.553A pdb=" N ILE A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 602 removed outlier: 3.699A pdb=" N ARG A 602 " --> pdb=" O GLU A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 668 through 681 removed outlier: 3.672A pdb=" N VAL A 672 " --> pdb=" O LEU A 668 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE A 675 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 681 " --> pdb=" O ASP A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 687 removed outlier: 3.786A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 741 through 750 removed outlier: 4.167A pdb=" N LEU A 748 " --> pdb=" O MET A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.699A pdb=" N MET A 849 " --> pdb=" O ASP A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 873 through 877 removed outlier: 3.525A pdb=" N PHE A 877 " --> pdb=" O PRO A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 927 through 929 No H-bonds generated for 'chain 'A' and resid 927 through 929' Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.995A pdb=" N GLY A 957 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 983 through 990 removed outlier: 3.807A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 removed outlier: 4.132A pdb=" N ARG A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.622A pdb=" N SER A1038 " --> pdb=" O ILE A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 4.158A pdb=" N LYS A1179 " --> pdb=" O LEU A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.690A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1249 removed outlier: 4.210A pdb=" N LYS A1246 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1260 Processing helix chain 'A' and resid 1261 through 1266 removed outlier: 4.179A pdb=" N LYS A1264 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1285 through 1294 Processing helix chain 'A' and resid 1295 through 1299 Processing helix chain 'A' and resid 1303 through 1308 Processing helix chain 'A' and resid 1313 through 1319 removed outlier: 3.588A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 4.609A pdb=" N CYS A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N ARG A1336 " --> pdb=" O VAL A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1353 through 1356 removed outlier: 3.646A pdb=" N VAL A1356 " --> pdb=" O ASN A1353 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1353 through 1356' Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 7.262A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.440A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A1392 " --> pdb=" O LYS A1388 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A1393 " --> pdb=" O MET A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.580A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ASP A1427 " --> pdb=" O THR A1423 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1441 removed outlier: 4.343A pdb=" N ASN A1439 " --> pdb=" O TYR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1447 through 1454 Processing helix chain 'A' and resid 1461 through 1466 Processing helix chain 'A' and resid 1468 through 1490 removed outlier: 3.583A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1524 removed outlier: 3.873A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 3.929A pdb=" N GLU A1534 " --> pdb=" O ALA A1530 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE A1536 " --> pdb=" O LEU A1532 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N SER A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1606 removed outlier: 3.990A pdb=" N ASN A1605 " --> pdb=" O MET A1602 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N VAL A1606 " --> pdb=" O SER A1603 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1602 through 1606' Processing helix chain 'A' and resid 1609 through 1628 removed outlier: 4.210A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N CYS A1627 " --> pdb=" O VAL A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1648 removed outlier: 3.762A pdb=" N THR A1633 " --> pdb=" O ASP A1629 " (cutoff:3.500A) Proline residue: A1643 - end of helix removed outlier: 3.599A pdb=" N GLN A1646 " --> pdb=" O GLU A1642 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 3.504A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY A 24 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR A 172 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ILE A 25 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 424 removed outlier: 5.986A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 8.005A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 357 " --> pdb=" O MET A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.529A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 593 through 596 Processing sheet with id=AA5, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA6, first strand: chain 'A' and resid 768 through 771 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 771 removed outlier: 3.772A pdb=" N ILE A 729 " --> pdb=" O TYR A 754 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 830 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AA9, first strand: chain 'A' and resid 969 through 971 removed outlier: 4.512A pdb=" N VAL A 969 " --> pdb=" O VAL A 942 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 939 " --> pdb=" O HIS A 899 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 895 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1530 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 124 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 4.33 Time building geometry restraints manager: 1.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3075 1.33 - 1.45: 3639 1.45 - 1.57: 7591 1.57 - 1.70: 183 1.70 - 1.82: 99 Bond restraints: 14587 Sorted by residual: bond pdb=" CA PHE A 663 " pdb=" C PHE A 663 " ideal model delta sigma weight residual 1.531 1.494 0.037 1.08e-02 8.57e+03 1.18e+01 bond pdb=" N LYS A1531 " pdb=" CA LYS A1531 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.23e-02 6.61e+03 9.03e+00 bond pdb=" N ASN A1495 " pdb=" CA ASN A1495 " ideal model delta sigma weight residual 1.454 1.484 -0.031 1.14e-02 7.69e+03 7.18e+00 bond pdb=" N LEU A1499 " pdb=" CA LEU A1499 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.29e-02 6.01e+03 5.71e+00 bond pdb=" CA VAL A 678 " pdb=" C VAL A 678 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.27e-02 6.20e+03 5.31e+00 ... (remaining 14582 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.31: 20072 3.31 - 6.61: 93 6.61 - 9.92: 11 9.92 - 13.23: 2 13.23 - 16.53: 2 Bond angle restraints: 20180 Sorted by residual: angle pdb=" C LYS A1531 " pdb=" CA LYS A1531 " pdb=" CB LYS A1531 " ideal model delta sigma weight residual 110.85 94.32 16.53 1.70e+00 3.46e-01 9.46e+01 angle pdb=" N GLY A 657 " pdb=" CA GLY A 657 " pdb=" C GLY A 657 " ideal model delta sigma weight residual 114.92 103.84 11.08 1.30e+00 5.92e-01 7.27e+01 angle pdb=" CB LYS A1531 " pdb=" CG LYS A1531 " pdb=" CD LYS A1531 " ideal model delta sigma weight residual 111.30 126.04 -14.74 2.30e+00 1.89e-01 4.10e+01 angle pdb=" N ARG A 671 " pdb=" CA ARG A 671 " pdb=" C ARG A 671 " ideal model delta sigma weight residual 111.11 103.59 7.52 1.20e+00 6.94e-01 3.93e+01 angle pdb=" N LYS A1531 " pdb=" CA LYS A1531 " pdb=" CB LYS A1531 " ideal model delta sigma weight residual 110.16 118.30 -8.14 1.48e+00 4.57e-01 3.02e+01 ... (remaining 20175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7644 17.89 - 35.78: 714 35.78 - 53.67: 205 53.67 - 71.56: 26 71.56 - 89.45: 19 Dihedral angle restraints: 8608 sinusoidal: 4210 harmonic: 4398 Sorted by residual: dihedral pdb=" C LYS A1531 " pdb=" N LYS A1531 " pdb=" CA LYS A1531 " pdb=" CB LYS A1531 " ideal model delta harmonic sigma weight residual -122.60 -105.44 -17.16 0 2.50e+00 1.60e-01 4.71e+01 dihedral pdb=" O5' C F 22 " pdb=" C5' C F 22 " pdb=" C4' C F 22 " pdb=" C3' C F 22 " ideal model delta sinusoidal sigma weight residual -180.00 -132.83 -47.17 3 6.40e+00 2.44e-02 4.64e+01 dihedral pdb=" O5' A C 13 " pdb=" C5' A C 13 " pdb=" C4' A C 13 " pdb=" C3' A C 13 " ideal model delta sinusoidal sigma weight residual 180.00 138.66 41.34 3 6.40e+00 2.44e-02 4.06e+01 ... (remaining 8605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2021 0.066 - 0.131: 204 0.131 - 0.197: 21 0.197 - 0.262: 95 0.262 - 0.328: 3 Chirality restraints: 2344 Sorted by residual: chirality pdb=" CB ILE A 813 " pdb=" CA ILE A 813 " pdb=" CG1 ILE A 813 " pdb=" CG2 ILE A 813 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA LYS A1531 " pdb=" N LYS A1531 " pdb=" C LYS A1531 " pdb=" CB LYS A1531 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" P C F 22 " pdb=" OP1 C F 22 " pdb=" OP2 C F 22 " pdb=" O5' C F 22 " both_signs ideal model delta sigma weight residual True 2.17 -2.45 -0.28 2.00e-01 2.50e+01 1.89e+00 ... (remaining 2341 not shown) Planarity restraints: 2238 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 656 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.13e+00 pdb=" C LEU A 656 " -0.046 2.00e-02 2.50e+03 pdb=" O LEU A 656 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY A 657 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 591 " 0.036 5.00e-02 4.00e+02 5.56e-02 4.94e+00 pdb=" N PRO A 592 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 592 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 592 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA A1367 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.64e+00 pdb=" C ALA A1367 " -0.028 2.00e-02 2.50e+03 pdb=" O ALA A1367 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A1368 " 0.009 2.00e-02 2.50e+03 ... (remaining 2235 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.06: 15 2.06 - 2.77: 2847 2.77 - 3.48: 20708 3.48 - 4.19: 35220 4.19 - 4.90: 57724 Nonbonded interactions: 116514 Sorted by model distance: nonbonded pdb=" O THR A 584 " pdb=" CD LYS A1415 " model vdw 1.356 3.440 nonbonded pdb=" NZ LYS A 966 " pdb=" O6 G C 1 " model vdw 1.361 3.120 nonbonded pdb=" OD1 ASN A1508 " pdb=" O3' U C 20 " model vdw 1.405 3.040 nonbonded pdb=" CG ASN A1508 " pdb=" O3' U C 20 " model vdw 1.495 3.270 nonbonded pdb=" OG SER A1038 " pdb=" C5' C C 11 " model vdw 1.651 3.440 ... (remaining 116509 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 17.400 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3753 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 0.053 14587 Z= 0.163 Angle : 0.696 16.535 20180 Z= 0.361 Chirality : 0.063 0.328 2344 Planarity : 0.004 0.056 2238 Dihedral : 15.053 89.451 5756 Min Nonbonded Distance : 1.356 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.81 % Allowed : 4.45 % Favored : 94.74 % Rotamer: Outliers : 1.19 % Allowed : 0.74 % Favored : 98.06 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.22), residues: 1484 helix: -0.01 (0.21), residues: 660 sheet: -0.60 (0.39), residues: 159 loop : -1.18 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.017 0.001 TYR A 740 PHE 0.017 0.001 PHE A 938 TRP 0.019 0.001 TRP A1634 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.16 (14587) covalent geometry : angle 0.69586 / 0.36 (20180) hydrogen bonds : bond 0.20010 / 13.07 ( 593) hydrogen bonds : angle 7.80371 / 5.39 ( 1654) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: -0.4959 (tpt) cc_final: -0.5546 (tpt) REVERT: A 675 ILE cc_start: 0.5073 (OUTLIER) cc_final: 0.4866 (mm) REVERT: A 1241 THR cc_start: 0.7890 (m) cc_final: 0.7202 (p) outliers start: 16 outliers final: 6 residues processed: 190 average time/residue: 0.1429 time to fit residues: 38.5745 Evaluate side-chains 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0770 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 10.0000 overall best weight: 2.9744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 679 HIS A 851 ASN A1004 HIS A1013 ASN A1185 HIS A1385 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.091408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.069943 restraints weight = 151637.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.070170 restraints weight = 146016.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.070316 restraints weight = 141833.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.070320 restraints weight = 139394.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.070320 restraints weight = 139340.139| |-----------------------------------------------------------------------------| r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 14587 Z= 0.168 Angle : 0.793 17.741 20180 Z= 0.369 Chirality : 0.050 0.282 2344 Planarity : 0.005 0.068 2238 Dihedral : 10.632 74.077 2740 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.82 % Rotamer: Outliers : 0.37 % Allowed : 5.14 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.22), residues: 1484 helix: 0.10 (0.20), residues: 677 sheet: -0.53 (0.38), residues: 155 loop : -1.11 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A1503 TYR 0.024 0.001 TYR A1232 PHE 0.024 0.001 PHE A1387 TRP 0.026 0.002 TRP A 986 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (14587) covalent geometry : angle 0.79334 / 0.37 (20180) hydrogen bonds : bond 0.05294 / 3.43 ( 593) hydrogen bonds : angle 5.13464 / 3.58 ( 1654) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 115 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9330 (m-30) cc_final: 0.9120 (m-30) REVERT: A 186 THR cc_start: 0.7795 (p) cc_final: 0.7068 (p) REVERT: A 208 MET cc_start: 0.6956 (tmm) cc_final: 0.6389 (tmm) REVERT: A 238 ILE cc_start: 0.4418 (pt) cc_final: 0.3929 (pt) REVERT: A 620 MET cc_start: -0.5659 (tpp) cc_final: -0.6768 (tpt) REVERT: A 627 ARG cc_start: 0.8827 (tpp80) cc_final: 0.8376 (mmm160) REVERT: A 631 TYR cc_start: 0.8097 (p90) cc_final: 0.7886 (p90) REVERT: A 805 MET cc_start: 0.6973 (tmm) cc_final: 0.6127 (tmm) REVERT: A 908 MET cc_start: 0.8460 (mmp) cc_final: 0.8153 (mmp) REVERT: A 939 MET cc_start: 0.9063 (mpp) cc_final: 0.8647 (mpp) REVERT: A 990 ILE cc_start: 0.9012 (mm) cc_final: 0.8772 (mm) REVERT: A 1004 HIS cc_start: 0.5578 (OUTLIER) cc_final: 0.4640 (m90) REVERT: A 1389 MET cc_start: 0.8505 (tpt) cc_final: 0.8060 (tpt) REVERT: A 1459 TYR cc_start: 0.8411 (t80) cc_final: 0.8166 (t80) REVERT: A 1479 LEU cc_start: 0.7288 (mm) cc_final: 0.7052 (mm) outliers start: 5 outliers final: 0 residues processed: 118 average time/residue: 0.1511 time to fit residues: 25.4143 Evaluate side-chains 87 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 1.9990 chunk 57 optimal weight: 20.0000 chunk 108 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 77 optimal weight: 30.0000 chunk 143 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 148 optimal weight: 10.0000 chunk 92 optimal weight: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 490 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.086713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.065777 restraints weight = 153156.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.065921 restraints weight = 146903.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.066053 restraints weight = 143775.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.066053 restraints weight = 141681.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.066053 restraints weight = 141681.291| |-----------------------------------------------------------------------------| r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14587 Z= 0.172 Angle : 0.746 10.092 20180 Z= 0.351 Chirality : 0.049 0.301 2344 Planarity : 0.005 0.066 2238 Dihedral : 10.623 71.631 2740 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.22), residues: 1484 helix: 0.02 (0.19), residues: 683 sheet: -0.87 (0.38), residues: 157 loop : -0.90 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 416 TYR 0.021 0.002 TYR A1232 PHE 0.025 0.002 PHE A1387 TRP 0.030 0.002 TRP A 986 HIS 0.009 0.002 HIS A 323 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (14587) covalent geometry : angle 0.74602 / 0.35 (20180) hydrogen bonds : bond 0.04943 / 3.39 ( 593) hydrogen bonds : angle 5.01708 / 3.51 ( 1654) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9357 (m-30) cc_final: 0.8962 (p0) REVERT: A 238 ILE cc_start: 0.4914 (pt) cc_final: 0.4328 (pt) REVERT: A 631 TYR cc_start: 0.8383 (p90) cc_final: 0.8174 (p90) REVERT: A 634 PRO cc_start: 0.8190 (Cg_exo) cc_final: 0.7851 (Cg_endo) REVERT: A 939 MET cc_start: 0.9103 (mpp) cc_final: 0.8673 (mpp) REVERT: A 967 MET cc_start: 0.4932 (pmm) cc_final: 0.4696 (pmm) REVERT: A 990 ILE cc_start: 0.9038 (mm) cc_final: 0.8795 (mm) REVERT: A 1389 MET cc_start: 0.8711 (tpt) cc_final: 0.8299 (tpt) REVERT: B 357 ILE cc_start: 0.6762 (tp) cc_final: 0.6562 (tp) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1300 time to fit residues: 18.5691 Evaluate side-chains 76 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 134 optimal weight: 9.9990 chunk 45 optimal weight: 30.0000 chunk 69 optimal weight: 0.0010 chunk 22 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 131 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 129 optimal weight: 20.0000 chunk 72 optimal weight: 7.9990 overall best weight: 4.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 339 GLN A 475 HIS ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.083462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.062730 restraints weight = 156529.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.063023 restraints weight = 150108.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.063205 restraints weight = 145954.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.063457 restraints weight = 142690.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.063555 restraints weight = 139942.750| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6811 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 14587 Z= 0.175 Angle : 0.764 12.146 20180 Z= 0.357 Chirality : 0.049 0.273 2344 Planarity : 0.005 0.066 2238 Dihedral : 10.657 70.976 2740 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 0.07 % Allowed : 3.65 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.72 (0.22), residues: 1484 helix: 0.10 (0.19), residues: 672 sheet: -1.05 (0.39), residues: 160 loop : -0.82 (0.27), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 602 TYR 0.017 0.002 TYR A1232 PHE 0.032 0.002 PHE A1001 TRP 0.026 0.002 TRP A 986 HIS 0.006 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (14587) covalent geometry : angle 0.76412 / 0.36 (20180) hydrogen bonds : bond 0.04634 / 3.15 ( 593) hydrogen bonds : angle 4.99476 / 3.52 ( 1654) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9315 (m-30) cc_final: 0.8885 (p0) REVERT: A 238 ILE cc_start: 0.4882 (pt) cc_final: 0.4337 (pt) REVERT: A 620 MET cc_start: -0.5859 (tpp) cc_final: -0.6445 (mmt) REVERT: A 631 TYR cc_start: 0.8580 (p90) cc_final: 0.8336 (p90) REVERT: A 634 PRO cc_start: 0.8261 (Cg_exo) cc_final: 0.7943 (Cg_endo) REVERT: A 939 MET cc_start: 0.9037 (mpp) cc_final: 0.8615 (mpp) REVERT: A 967 MET cc_start: 0.4858 (pmm) cc_final: 0.4595 (pmm) REVERT: A 990 ILE cc_start: 0.9064 (mm) cc_final: 0.8850 (mm) REVERT: B 357 ILE cc_start: 0.6725 (tp) cc_final: 0.6511 (tp) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1429 time to fit residues: 19.1585 Evaluate side-chains 76 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 56 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 120 optimal weight: 40.0000 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.082625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.062506 restraints weight = 154432.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.062764 restraints weight = 147586.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.062803 restraints weight = 143223.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.062805 restraints weight = 142364.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.062805 restraints weight = 142324.961| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14587 Z= 0.152 Angle : 0.729 10.014 20180 Z= 0.341 Chirality : 0.049 0.303 2344 Planarity : 0.004 0.065 2238 Dihedral : 10.763 73.406 2740 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 18.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.99 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.71 (0.22), residues: 1484 helix: 0.08 (0.19), residues: 677 sheet: -0.99 (0.39), residues: 153 loop : -0.80 (0.27), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1503 TYR 0.014 0.002 TYR A1232 PHE 0.019 0.001 PHE A1387 TRP 0.033 0.002 TRP A 986 HIS 0.008 0.001 HIS A 335 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (14587) covalent geometry : angle 0.72889 / 0.34 (20180) hydrogen bonds : bond 0.04348 / 3.03 ( 593) hydrogen bonds : angle 4.97161 / 3.50 ( 1654) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9483 (m-30) cc_final: 0.9215 (p0) REVERT: A 222 MET cc_start: 0.7402 (tmm) cc_final: 0.6917 (tmm) REVERT: A 238 ILE cc_start: 0.5213 (pt) cc_final: 0.4264 (pt) REVERT: A 344 MET cc_start: 0.6387 (tmm) cc_final: 0.6073 (tmm) REVERT: A 545 TYR cc_start: 0.9518 (m-10) cc_final: 0.9139 (p90) REVERT: A 620 MET cc_start: -0.4009 (tpp) cc_final: -0.4790 (mmt) REVERT: A 625 MET cc_start: 0.8438 (ptt) cc_final: 0.8222 (ptt) REVERT: A 634 PRO cc_start: 0.7740 (Cg_exo) cc_final: 0.7231 (Cg_endo) REVERT: A 939 MET cc_start: 0.9471 (mpp) cc_final: 0.9065 (mpp) REVERT: A 967 MET cc_start: 0.5404 (pmm) cc_final: 0.4969 (pmm) REVERT: A 990 ILE cc_start: 0.9327 (mm) cc_final: 0.9079 (mm) REVERT: A 1389 MET cc_start: 0.9500 (tpt) cc_final: 0.9289 (tpp) outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.1413 time to fit residues: 18.7371 Evaluate side-chains 76 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 96 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 119 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 14 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 121 optimal weight: 0.0870 chunk 142 optimal weight: 20.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 520 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN A1270 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.079699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.059486 restraints weight = 157985.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.059691 restraints weight = 152760.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.059751 restraints weight = 148059.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.059777 restraints weight = 147270.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.059777 restraints weight = 146646.329| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14587 Z= 0.181 Angle : 0.773 8.620 20180 Z= 0.364 Chirality : 0.050 0.327 2344 Planarity : 0.005 0.065 2238 Dihedral : 10.883 77.221 2740 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.05 % Favored : 94.81 % Rotamer: Outliers : 0.15 % Allowed : 2.98 % Favored : 96.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.79 (0.22), residues: 1484 helix: 0.03 (0.19), residues: 679 sheet: -1.19 (0.40), residues: 151 loop : -0.82 (0.27), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1503 TYR 0.019 0.002 TYR A 246 PHE 0.019 0.002 PHE A 245 TRP 0.030 0.003 TRP A 986 HIS 0.012 0.002 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.18 (14587) covalent geometry : angle 0.77286 / 0.36 (20180) hydrogen bonds : bond 0.04676 / 3.20 ( 593) hydrogen bonds : angle 5.05199 / 3.55 ( 1654) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 85 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9503 (m-30) cc_final: 0.9259 (p0) REVERT: A 545 TYR cc_start: 0.9524 (m-10) cc_final: 0.9146 (p90) REVERT: A 556 ASP cc_start: 0.8377 (m-30) cc_final: 0.8017 (t70) REVERT: A 620 MET cc_start: -0.3922 (tpp) cc_final: -0.4171 (mmt) REVERT: A 634 PRO cc_start: 0.7793 (Cg_exo) cc_final: 0.7248 (Cg_endo) REVERT: A 908 MET cc_start: 0.9101 (mmp) cc_final: 0.8792 (mmp) REVERT: A 939 MET cc_start: 0.9530 (mpp) cc_final: 0.9076 (mpp) REVERT: A 967 MET cc_start: 0.5492 (pmm) cc_final: 0.5016 (pmm) REVERT: A 990 ILE cc_start: 0.9295 (mm) cc_final: 0.9063 (mm) outliers start: 2 outliers final: 0 residues processed: 87 average time/residue: 0.1319 time to fit residues: 16.8905 Evaluate side-chains 73 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 73 optimal weight: 8.9990 chunk 117 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 chunk 11 optimal weight: 8.9990 chunk 8 optimal weight: 20.0000 chunk 92 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 42 optimal weight: 40.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 ASN A 454 ASN ** A 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 619 ASN ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.071840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052752 restraints weight = 166485.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052752 restraints weight = 162424.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052752 restraints weight = 162417.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052752 restraints weight = 162417.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.052752 restraints weight = 162417.726| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.7737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 14587 Z= 0.290 Angle : 0.998 11.046 20180 Z= 0.478 Chirality : 0.059 0.391 2344 Planarity : 0.006 0.070 2238 Dihedral : 11.552 83.259 2740 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 35.74 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.55 % Favored : 92.32 % Rotamer: Outliers : 0.07 % Allowed : 3.35 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.21), residues: 1484 helix: -0.71 (0.18), residues: 682 sheet: -1.69 (0.41), residues: 150 loop : -1.26 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1274 TYR 0.024 0.003 TYR A 88 PHE 0.028 0.003 PHE A 119 TRP 0.030 0.004 TRP A1634 HIS 0.019 0.003 HIS A 800 Details of bonding type rmsd/Z covalent geometry : bond 0.00613 / 0.29 (14587) covalent geometry : angle 0.99770 / 0.48 (20180) hydrogen bonds : bond 0.06729 / 4.62 ( 593) hydrogen bonds : angle 5.93553 / 4.17 ( 1654) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9505 (m-30) cc_final: 0.9243 (p0) REVERT: A 208 MET cc_start: 0.7946 (tmm) cc_final: 0.7690 (tmm) REVERT: A 222 MET cc_start: 0.7650 (tmm) cc_final: 0.6979 (tmm) REVERT: A 344 MET cc_start: 0.7154 (tmm) cc_final: 0.6838 (tmm) REVERT: A 556 ASP cc_start: 0.8264 (m-30) cc_final: 0.7796 (t70) REVERT: A 620 MET cc_start: -0.2852 (tpp) cc_final: -0.3054 (mmt) REVERT: A 908 MET cc_start: 0.9271 (mmp) cc_final: 0.8955 (mmp) REVERT: A 939 MET cc_start: 0.9450 (mpp) cc_final: 0.9036 (mpp) REVERT: A 1494 MET cc_start: 0.8667 (ptt) cc_final: 0.8260 (ppp) REVERT: B 344 ILE cc_start: 0.7424 (mt) cc_final: 0.6921 (mt) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.1291 time to fit residues: 15.7490 Evaluate side-chains 61 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 58 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 131 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 18 optimal weight: 0.1980 chunk 27 optimal weight: 7.9990 chunk 145 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 86 optimal weight: 0.0060 chunk 151 optimal weight: 30.0000 overall best weight: 1.8400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A 868 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1380 ASN A1385 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.076856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.057598 restraints weight = 158490.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.057922 restraints weight = 150481.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.058175 restraints weight = 144538.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.058175 restraints weight = 139320.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.058175 restraints weight = 139320.171| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.7505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14587 Z= 0.146 Angle : 0.787 9.336 20180 Z= 0.371 Chirality : 0.053 0.368 2344 Planarity : 0.005 0.063 2238 Dihedral : 11.594 87.467 2740 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.88 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.24 (0.22), residues: 1484 helix: -0.30 (0.19), residues: 685 sheet: -1.74 (0.40), residues: 148 loop : -1.02 (0.26), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1503 TYR 0.015 0.002 TYR A1232 PHE 0.022 0.002 PHE A1001 TRP 0.037 0.003 TRP A1634 HIS 0.004 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (14587) covalent geometry : angle 0.78681 / 0.37 (20180) hydrogen bonds : bond 0.04228 / 2.88 ( 593) hydrogen bonds : angle 5.26952 / 3.71 ( 1654) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9486 (m-30) cc_final: 0.9224 (p0) REVERT: A 222 MET cc_start: 0.7077 (tmm) cc_final: 0.6330 (tmm) REVERT: A 344 MET cc_start: 0.6648 (tmm) cc_final: 0.6358 (tmm) REVERT: A 372 MET cc_start: 0.8756 (mmp) cc_final: 0.8365 (mmp) REVERT: A 556 ASP cc_start: 0.8222 (m-30) cc_final: 0.7792 (t70) REVERT: A 625 MET cc_start: 0.6951 (ptp) cc_final: 0.6614 (pmm) REVERT: A 908 MET cc_start: 0.9132 (mmp) cc_final: 0.8844 (mmp) REVERT: A 939 MET cc_start: 0.9604 (mpp) cc_final: 0.9082 (mpp) REVERT: A 1494 MET cc_start: 0.8659 (ptt) cc_final: 0.7986 (ppp) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.1215 time to fit residues: 14.6325 Evaluate side-chains 62 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 66 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 154 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 40.0000 chunk 119 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 130 optimal weight: 0.0060 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A 865 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.075337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.056179 restraints weight = 161516.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.056376 restraints weight = 153856.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.056693 restraints weight = 148704.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.056693 restraints weight = 144175.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.056693 restraints weight = 144175.454| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.7756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14587 Z= 0.158 Angle : 0.781 10.317 20180 Z= 0.364 Chirality : 0.051 0.375 2344 Planarity : 0.004 0.065 2238 Dihedral : 11.370 82.722 2740 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.19 (0.22), residues: 1484 helix: -0.20 (0.19), residues: 695 sheet: -1.72 (0.40), residues: 148 loop : -1.07 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1503 TYR 0.029 0.002 TYR A 402 PHE 0.020 0.002 PHE A1331 TRP 0.041 0.003 TRP A 986 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.16 (14587) covalent geometry : angle 0.78053 / 0.36 (20180) hydrogen bonds : bond 0.04395 / 2.99 ( 593) hydrogen bonds : angle 5.20555 / 3.67 ( 1654) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9497 (m-30) cc_final: 0.9258 (p0) REVERT: A 222 MET cc_start: 0.7425 (tmm) cc_final: 0.6657 (tmm) REVERT: A 344 MET cc_start: 0.7176 (tmm) cc_final: 0.6873 (tmm) REVERT: A 556 ASP cc_start: 0.8263 (m-30) cc_final: 0.7856 (t70) REVERT: A 908 MET cc_start: 0.9200 (mmp) cc_final: 0.8959 (mmp) REVERT: A 939 MET cc_start: 0.9614 (mpp) cc_final: 0.9233 (mpp) REVERT: A 1029 MET cc_start: 0.9402 (mmp) cc_final: 0.9163 (mpp) REVERT: A 1494 MET cc_start: 0.8630 (ptt) cc_final: 0.8024 (ppp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1203 time to fit residues: 13.4692 Evaluate side-chains 59 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 16 optimal weight: 8.9990 chunk 132 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 89 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.076901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.057634 restraints weight = 159376.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.057728 restraints weight = 151498.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.058025 restraints weight = 148271.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.058025 restraints weight = 144146.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.058025 restraints weight = 144146.473| |-----------------------------------------------------------------------------| r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.7826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14587 Z= 0.134 Angle : 0.743 9.780 20180 Z= 0.349 Chirality : 0.050 0.360 2344 Planarity : 0.004 0.067 2238 Dihedral : 11.300 83.585 2740 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.85 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.00 (0.22), residues: 1484 helix: -0.03 (0.19), residues: 692 sheet: -1.74 (0.39), residues: 154 loop : -0.97 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A1503 TYR 0.016 0.002 TYR A 402 PHE 0.027 0.002 PHE A 818 TRP 0.042 0.002 TRP A 986 HIS 0.007 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (14587) covalent geometry : angle 0.74299 / 0.35 (20180) hydrogen bonds : bond 0.03952 / 2.68 ( 593) hydrogen bonds : angle 5.06128 / 3.55 ( 1654) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9492 (m-30) cc_final: 0.9267 (p0) REVERT: A 222 MET cc_start: 0.7302 (tmm) cc_final: 0.6598 (tmm) REVERT: A 344 MET cc_start: 0.7171 (tmm) cc_final: 0.6862 (tmm) REVERT: A 556 ASP cc_start: 0.8246 (m-30) cc_final: 0.7845 (t70) REVERT: A 620 MET cc_start: -0.4161 (tpp) cc_final: -0.4743 (mmt) REVERT: A 908 MET cc_start: 0.9183 (mmp) cc_final: 0.8941 (mmp) REVERT: A 939 MET cc_start: 0.9678 (mpp) cc_final: 0.9324 (mpp) REVERT: A 1029 MET cc_start: 0.9459 (mmp) cc_final: 0.9228 (mpp) REVERT: A 1494 MET cc_start: 0.8718 (ptt) cc_final: 0.8062 (ppp) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1202 time to fit residues: 13.9892 Evaluate side-chains 60 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 5 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 800 HIS A 868 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS ** A1286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.072939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.054779 restraints weight = 164231.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.054555 restraints weight = 171786.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.054638 restraints weight = 167466.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.054667 restraints weight = 170891.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.054727 restraints weight = 160892.833| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.8424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14587 Z= 0.194 Angle : 0.825 11.138 20180 Z= 0.388 Chirality : 0.052 0.376 2344 Planarity : 0.005 0.068 2238 Dihedral : 11.326 83.464 2740 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 25.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.67 % Favored : 93.26 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.16 (0.22), residues: 1484 helix: -0.20 (0.19), residues: 699 sheet: -1.84 (0.41), residues: 148 loop : -1.00 (0.27), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1503 TYR 0.017 0.002 TYR A1232 PHE 0.036 0.002 PHE A 818 TRP 0.043 0.003 TRP A 986 HIS 0.007 0.002 HIS A 815 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.19 (14587) covalent geometry : angle 0.82486 / 0.39 (20180) hydrogen bonds : bond 0.04804 / 3.27 ( 593) hydrogen bonds : angle 5.27259 / 3.71 ( 1654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2942.75 seconds wall clock time: 51 minutes 48.92 seconds (3108.92 seconds total)