Starting phenix.real_space_refine on Wed Mar 4 14:50:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0f_32241/03_2026/7w0f_32241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0f_32241/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7w0f_32241/03_2026/7w0f_32241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0f_32241/03_2026/7w0f_32241.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0f_32241/03_2026/7w0f_32241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0f_32241/03_2026/7w0f_32241.map" } 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-dev-5986/lib/python3.9/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: {'RNA': 21} Modifications used: {'5*END': 1, 'rna3p_pur': 13, 'rna3p_pyr': 8} Link IDs: {'rna3p': 20} Chain: "D" Number of atoms: 437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 437 Classifications: {'RNA': 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: {'RNA': 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: {'RNA': 26} Modifications used: {'rna3p_pur': 15, 'rna3p_pyr': 11} Link IDs: {'rna3p': 25} Time building chain proxies: 3.02, per 1000 atoms: 0.21 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: 1.31 Conformation dependent library (CDL) restraints added in 566.2 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: 2.14 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: 3.82 Time building geometry restraints manager: 1.73 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: 20075 3.31 - 6.61: 90 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=" C4' C F 22 " pdb=" C3' C F 22 " pdb=" O3' C F 22 " ideal model delta sigma weight residual 113.00 104.49 8.51 1.50e+00 4.44e-01 3.22e+01 ... (remaining 20175 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 7841 17.89 - 35.78: 728 35.78 - 53.67: 213 53.67 - 71.56: 122 71.56 - 89.45: 42 Dihedral angle restraints: 8946 sinusoidal: 4548 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=" CA PHE A 938 " pdb=" C PHE A 938 " pdb=" N MET A 939 " pdb=" CA MET A 939 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASP A 936 " pdb=" C ASP A 936 " pdb=" N LYS A 937 " pdb=" CA LYS A 937 " ideal model delta harmonic sigma weight residual 180.00 156.07 23.93 0 5.00e+00 4.00e-02 2.29e+01 ... (remaining 8943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 2113 0.066 - 0.131: 205 0.131 - 0.197: 21 0.197 - 0.262: 3 0.262 - 0.328: 2 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=" CA VAL A 678 " pdb=" N VAL A 678 " pdb=" C VAL A 678 " pdb=" CB VAL A 678 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+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: 0.870 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.640 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3794 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= 0.160 Angle : 0.636 16.535 20180 Z= 0.355 Chirality : 0.041 0.328 2344 Planarity : 0.004 0.056 2238 Dihedral : 17.272 89.451 6094 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 covalent geometry : bond 0.00273 (14587) covalent geometry : angle 0.63607 (20180) hydrogen bonds : bond 0.20010 ( 593) hydrogen bonds : angle 7.80371 ( 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 : 0.526 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: 0.1468 time to fit residues: 38.9839 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 : 0.498 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 679 HIS A 851 ASN A1004 HIS A1013 ASN A1185 HIS A1385 HIS ** A1552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.091511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.071032 restraints weight = 150761.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.070041 restraints weight = 155185.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.070378 restraints weight = 160505.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.070460 restraints weight = 156555.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.070514 restraints weight = 147431.441| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14587 Z= 0.165 Angle : 0.692 18.000 20180 Z= 0.350 Chirality : 0.043 0.197 2344 Planarity : 0.005 0.070 2238 Dihedral : 16.173 83.943 3078 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 0.30 % Allowed : 5.29 % Favored : 94.42 % 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: -0.80 (0.22), residues: 1484 helix: 0.09 (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 0.021 0.001 ARG A1503 TYR 0.024 0.001 TYR A1232 PHE 0.025 0.001 PHE A1387 TRP 0.025 0.002 TRP A 986 HIS 0.005 0.001 HIS A 682 Details of bonding type rmsd covalent geometry : bond 0.00337 (14587) covalent geometry : angle 0.69226 (20180) hydrogen bonds : bond 0.05493 ( 593) hydrogen bonds : angle 5.14065 ( 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 119 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 115 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: 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: 0.9311 (m-30) cc_final: 0.9091 (m-30) REVERT: A 186 THR cc_start: 0.7912 (p) cc_final: 0.7215 (p) REVERT: A 208 MET cc_start: 0.7028 (tmm) cc_final: 0.6481 (tmm) REVERT: A 238 ILE cc_start: 0.4412 (pt) cc_final: 0.3932 (pt) REVERT: A 620 MET cc_start: -0.5930 (tpp) cc_final: -0.6155 (tpt) REVERT: A 631 TYR cc_start: 0.8154 (p90) cc_final: 0.7939 (p90) REVERT: A 805 MET cc_start: 0.7060 (tmm) cc_final: 0.6208 (tmm) REVERT: A 908 MET cc_start: 0.8461 (mmp) cc_final: 0.8097 (mmp) REVERT: A 939 MET cc_start: 0.9131 (mpp) cc_final: 0.8676 (mpp) REVERT: A 990 ILE cc_start: 0.9009 (mm) cc_final: 0.8754 (mm) REVERT: A 1004 HIS cc_start: 0.5639 (OUTLIER) cc_final: 0.4694 (m90) REVERT: A 1389 MET cc_start: 0.8497 (tpt) cc_final: 0.8021 (tpt) REVERT: A 1479 LEU cc_start: 0.7224 (mm) cc_final: 0.7000 (mm) outliers start: 4 outliers final: 0 residues processed: 118 average time/residue: 0.1501 time to fit residues: 24.9870 Evaluate side-chains 89 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 5.9990 chunk 57 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 143 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 0.9990 chunk 101 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 HIS A 490 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 815 HIS ** A 912 GLN ** 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 = 0.4376 r_free = 0.4376 target = 0.081808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.061263 restraints weight = 156457.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.061451 restraints weight = 152061.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.061451 restraints weight = 148528.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.061451 restraints weight = 148528.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.061451 restraints weight = 148528.405| |-----------------------------------------------------------------------------| r_work (final): 0.3871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14587 Z= 0.233 Angle : 0.778 9.562 20180 Z= 0.403 Chirality : 0.045 0.201 2344 Planarity : 0.006 0.073 2238 Dihedral : 16.724 89.084 3078 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 24.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.47 % Rotamer: Outliers : 0.15 % Allowed : 5.73 % Favored : 94.12 % 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: -1.22 (0.21), residues: 1484 helix: -0.38 (0.19), residues: 681 sheet: -1.12 (0.38), residues: 149 loop : -1.06 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1503 TYR 0.025 0.003 TYR A1232 PHE 0.031 0.003 PHE A1387 TRP 0.039 0.003 TRP A 986 HIS 0.012 0.003 HIS A 323 Details of bonding type rmsd covalent geometry : bond 0.00483 (14587) covalent geometry : angle 0.77816 (20180) hydrogen bonds : bond 0.06168 ( 593) hydrogen bonds : angle 5.40930 ( 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 92 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 90 time to evaluate : 0.496 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: 0.9385 (m-30) cc_final: 0.8936 (p0) REVERT: A 238 ILE cc_start: 0.4457 (pt) cc_final: 0.3885 (pt) REVERT: A 458 MET cc_start: -0.6591 (mmm) cc_final: -0.7031 (mmm) REVERT: A 625 MET cc_start: 0.5720 (ptt) cc_final: 0.5457 (ptt) REVERT: A 631 TYR cc_start: 0.8648 (p90) cc_final: 0.8394 (p90) REVERT: A 634 PRO cc_start: 0.8452 (Cg_exo) cc_final: 0.8124 (Cg_endo) REVERT: A 939 MET cc_start: 0.9186 (mpp) cc_final: 0.8710 (mpp) REVERT: A 967 MET cc_start: 0.4883 (pmm) cc_final: 0.4596 (pmm) REVERT: A 990 ILE cc_start: 0.8980 (mm) cc_final: 0.8751 (mm) REVERT: B 357 ILE cc_start: 0.6991 (tp) cc_final: 0.6781 (tp) outliers start: 2 outliers final: 0 residues processed: 92 average time/residue: 0.1383 time to fit residues: 18.6760 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 : 0.530 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 22 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 155 optimal weight: 20.0000 chunk 71 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 82 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 overall best weight: 5.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A 520 GLN ** A 576 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** A1178 GLN A1380 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.080198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.060048 restraints weight = 160012.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.060337 restraints weight = 153731.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.060337 restraints weight = 148244.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.060337 restraints weight = 148239.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.060337 restraints weight = 148239.978| |-----------------------------------------------------------------------------| r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.5356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14587 Z= 0.191 Angle : 0.700 12.736 20180 Z= 0.359 Chirality : 0.043 0.196 2344 Planarity : 0.005 0.067 2238 Dihedral : 16.923 90.370 3078 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 20.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 0.07 % Allowed : 4.62 % Favored : 95.31 % 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: -1.08 (0.22), residues: 1484 helix: -0.19 (0.19), residues: 684 sheet: -1.29 (0.38), residues: 166 loop : -1.00 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1009 TYR 0.023 0.002 TYR A 740 PHE 0.025 0.002 PHE A1387 TRP 0.027 0.003 TRP A 986 HIS 0.006 0.002 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00396 (14587) covalent geometry : angle 0.69953 (20180) hydrogen bonds : bond 0.04922 ( 593) hydrogen bonds : angle 5.23282 ( 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 89 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 0.507 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: A 104 ASP cc_start: 0.9516 (m-30) cc_final: 0.9238 (p0) REVERT: A 222 MET cc_start: 0.7655 (tmm) cc_final: 0.7066 (tmm) REVERT: A 238 ILE cc_start: 0.4974 (pt) cc_final: 0.3922 (pt) REVERT: A 545 TYR cc_start: 0.9501 (m-10) cc_final: 0.9076 (p90) REVERT: A 556 ASP cc_start: 0.8348 (m-30) cc_final: 0.8001 (t70) REVERT: A 625 MET cc_start: 0.8481 (ptt) cc_final: 0.8267 (ptt) REVERT: A 634 PRO cc_start: 0.7643 (Cg_exo) cc_final: 0.7138 (Cg_endo) REVERT: A 939 MET cc_start: 0.9563 (mpp) cc_final: 0.9119 (mpp) REVERT: A 967 MET cc_start: 0.5580 (pmm) cc_final: 0.5150 (pmm) REVERT: A 990 ILE cc_start: 0.9252 (mm) cc_final: 0.9013 (mm) REVERT: A 1389 MET cc_start: 0.9529 (tpt) cc_final: 0.9281 (tpp) REVERT: A 1503 ARG cc_start: 0.9262 (ppt170) cc_final: 0.9041 (ttp80) outliers start: 1 outliers final: 0 residues processed: 89 average time/residue: 0.1371 time to fit residues: 17.7747 Evaluate side-chains 77 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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: 1.9990 chunk 27 optimal weight: 7.9990 chunk 56 optimal weight: 50.0000 chunk 34 optimal weight: 10.0000 chunk 120 optimal weight: 20.0000 chunk 95 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 135 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 978 ASN ** A1267 ASN ** 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 = 0.4312 r_free = 0.4312 target = 0.077314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.057298 restraints weight = 161679.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 16)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.057365 restraints weight = 157229.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.057499 restraints weight = 155305.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.057499 restraints weight = 153950.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.057499 restraints weight = 153950.486| |-----------------------------------------------------------------------------| r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.6148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14587 Z= 0.215 Angle : 0.719 9.607 20180 Z= 0.372 Chirality : 0.044 0.192 2344 Planarity : 0.005 0.066 2238 Dihedral : 17.089 86.539 3078 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 26.54 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.00 % Favored : 93.94 % Rotamer: Outliers : 0.15 % Allowed : 3.72 % Favored : 96.13 % 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: -1.27 (0.22), residues: 1484 helix: -0.32 (0.19), residues: 685 sheet: -1.64 (0.36), residues: 167 loop : -1.04 (0.27), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 866 TYR 0.021 0.002 TYR A1232 PHE 0.019 0.002 PHE A1387 TRP 0.028 0.003 TRP A1634 HIS 0.015 0.002 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00451 (14587) covalent geometry : angle 0.71871 (20180) hydrogen bonds : bond 0.05442 ( 593) hydrogen bonds : angle 5.41368 ( 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 85 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9502 (m-30) cc_final: 0.9238 (p0) REVERT: A 372 MET cc_start: 0.8487 (mmp) cc_final: 0.8281 (mmp) REVERT: A 545 TYR cc_start: 0.9471 (m-10) cc_final: 0.9031 (p90) REVERT: A 556 ASP cc_start: 0.8330 (m-30) cc_final: 0.7912 (t70) REVERT: A 620 MET cc_start: -0.3813 (tpp) cc_final: -0.4138 (mmt) REVERT: A 634 PRO cc_start: 0.7817 (Cg_exo) cc_final: 0.7377 (Cg_endo) REVERT: A 908 MET cc_start: 0.9194 (mmp) cc_final: 0.8854 (mmp) REVERT: A 939 MET cc_start: 0.9624 (mpp) cc_final: 0.9254 (mpp) REVERT: A 990 ILE cc_start: 0.9293 (mm) cc_final: 0.9048 (mm) REVERT: A 1494 MET cc_start: 0.8328 (ptt) cc_final: 0.7595 (ppp) REVERT: A 1503 ARG cc_start: 0.9320 (ppt170) cc_final: 0.9119 (ttp80) outliers start: 2 outliers final: 0 residues processed: 85 average time/residue: 0.1355 time to fit residues: 16.8776 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 : 0.506 ------------------------------------------------------------------------------- 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: 0.0470 chunk 118 optimal weight: 7.9990 chunk 119 optimal weight: 30.0000 chunk 77 optimal weight: 5.9990 chunk 73 optimal weight: 20.0000 chunk 145 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 142 optimal weight: 10.0000 overall best weight: 5.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 HIS ** 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 ** 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.076051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056159 restraints weight = 164226.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 14)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056161 restraints weight = 158949.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056161 restraints weight = 158874.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056161 restraints weight = 158874.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056161 restraints weight = 158874.762| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.6782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14587 Z= 0.199 Angle : 0.704 8.415 20180 Z= 0.368 Chirality : 0.044 0.203 2344 Planarity : 0.005 0.062 2238 Dihedral : 17.281 86.183 3078 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 26.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.93 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % 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: -1.33 (0.22), residues: 1484 helix: -0.32 (0.19), residues: 686 sheet: -1.69 (0.38), residues: 161 loop : -1.16 (0.26), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1274 TYR 0.026 0.002 TYR A 917 PHE 0.021 0.002 PHE A1393 TRP 0.030 0.003 TRP A1634 HIS 0.009 0.002 HIS A 934 Details of bonding type rmsd covalent geometry : bond 0.00415 (14587) covalent geometry : angle 0.70363 (20180) hydrogen bonds : bond 0.05187 ( 593) hydrogen bonds : angle 5.38074 ( 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 79 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9510 (m-30) cc_final: 0.9251 (p0) REVERT: A 222 MET cc_start: 0.7348 (tmm) cc_final: 0.6631 (tmm) REVERT: A 344 MET cc_start: 0.7502 (ppp) cc_final: 0.7292 (ppp) REVERT: A 372 MET cc_start: 0.8485 (mmp) cc_final: 0.8249 (mmp) REVERT: A 545 TYR cc_start: 0.9451 (m-10) cc_final: 0.8974 (p90) REVERT: A 556 ASP cc_start: 0.8279 (m-30) cc_final: 0.7816 (t70) REVERT: A 620 MET cc_start: -0.3706 (tpp) cc_final: -0.4026 (mmt) REVERT: A 908 MET cc_start: 0.9130 (mmp) cc_final: 0.8853 (mmp) REVERT: A 939 MET cc_start: 0.9627 (mpp) cc_final: 0.9235 (mpp) REVERT: A 990 ILE cc_start: 0.9310 (mm) cc_final: 0.9080 (mm) REVERT: A 1494 MET cc_start: 0.8461 (ptt) cc_final: 0.7731 (ppp) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.1294 time to fit residues: 15.4907 Evaluate side-chains 64 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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: 0.0770 chunk 117 optimal weight: 6.9990 chunk 138 optimal weight: 20.0000 chunk 11 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 109 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 2.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 598 GLN ** A 800 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** ** A1267 ASN ** 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 = 0.4325 r_free = 0.4325 target = 0.077383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.057784 restraints weight = 158147.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.057844 restraints weight = 152074.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.057844 restraints weight = 150107.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.057844 restraints weight = 150107.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.057844 restraints weight = 150107.428| |-----------------------------------------------------------------------------| r_work (final): 0.3808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14587 Z= 0.138 Angle : 0.635 8.429 20180 Z= 0.327 Chirality : 0.042 0.188 2344 Planarity : 0.004 0.061 2238 Dihedral : 17.120 86.622 3078 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.74 % Rotamer: Outliers : 0.07 % Allowed : 1.71 % Favored : 98.21 % 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: -1.12 (0.22), residues: 1484 helix: -0.12 (0.19), residues: 692 sheet: -1.66 (0.38), residues: 165 loop : -1.04 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 334 TYR 0.024 0.002 TYR A 402 PHE 0.018 0.001 PHE A 423 TRP 0.032 0.002 TRP A 986 HIS 0.010 0.001 HIS A 800 Details of bonding type rmsd covalent geometry : bond 0.00290 (14587) covalent geometry : angle 0.63469 (20180) hydrogen bonds : bond 0.04321 ( 593) hydrogen bonds : angle 5.13649 ( 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 78 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 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: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9272 (m-30) cc_final: 0.8875 (p0) REVERT: A 222 MET cc_start: 0.6163 (tmm) cc_final: 0.5370 (tmm) REVERT: A 344 MET cc_start: 0.3657 (ppp) cc_final: 0.3305 (ppp) REVERT: A 372 MET cc_start: 0.8394 (mmp) cc_final: 0.8111 (mmp) REVERT: A 545 TYR cc_start: 0.9247 (m-10) cc_final: 0.8811 (p90) REVERT: A 556 ASP cc_start: 0.7728 (m-30) cc_final: 0.7201 (t70) REVERT: A 620 MET cc_start: -0.5865 (tpp) cc_final: -0.6414 (mmt) REVERT: A 908 MET cc_start: 0.8001 (mmp) cc_final: 0.7763 (mmp) REVERT: A 939 MET cc_start: 0.9318 (mpp) cc_final: 0.8943 (mpp) REVERT: A 990 ILE cc_start: 0.9014 (mm) cc_final: 0.8752 (mm) REVERT: A 1494 MET cc_start: 0.8634 (ptt) cc_final: 0.7673 (ppp) outliers start: 1 outliers final: 1 residues processed: 78 average time/residue: 0.1164 time to fit residues: 14.0655 Evaluate side-chains 64 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 40.0000 chunk 125 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 38 optimal weight: 2.9990 chunk 86 optimal weight: 0.0570 chunk 151 optimal weight: 40.0000 overall best weight: 1.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** 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** A1019 HIS ** A1267 ASN ** 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 = 0.4343 r_free = 0.4343 target = 0.078393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.059502 restraints weight = 155365.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.058782 restraints weight = 163083.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.058890 restraints weight = 165106.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.058984 restraints weight = 163660.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.059024 restraints weight = 154644.095| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.6927 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= 0.126 Angle : 0.614 9.880 20180 Z= 0.319 Chirality : 0.041 0.181 2344 Planarity : 0.004 0.064 2238 Dihedral : 16.912 85.558 3078 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.78 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.89 (0.22), residues: 1484 helix: 0.06 (0.19), residues: 689 sheet: -1.52 (0.40), residues: 146 loop : -0.96 (0.27), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 334 TYR 0.017 0.002 TYR A1000 PHE 0.018 0.001 PHE A1331 TRP 0.035 0.002 TRP A 986 HIS 0.004 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00268 (14587) covalent geometry : angle 0.61431 (20180) hydrogen bonds : bond 0.03944 ( 593) hydrogen bonds : angle 4.96357 ( 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 84 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.491 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: 0.9462 (m-30) cc_final: 0.9212 (p0) REVERT: A 222 MET cc_start: 0.7358 (tmm) cc_final: 0.6681 (tmm) REVERT: A 344 MET cc_start: 0.6898 (ppp) cc_final: 0.6602 (ppp) REVERT: A 372 MET cc_start: 0.8721 (mmp) cc_final: 0.8451 (mmp) REVERT: A 545 TYR cc_start: 0.9449 (m-10) cc_final: 0.8986 (p90) REVERT: A 556 ASP cc_start: 0.8190 (m-30) cc_final: 0.7777 (t70) REVERT: A 620 MET cc_start: -0.4272 (tpp) cc_final: -0.4617 (mmt) REVERT: A 908 MET cc_start: 0.9032 (mmp) cc_final: 0.8782 (mmp) REVERT: A 939 MET cc_start: 0.9657 (mpp) cc_final: 0.9286 (mpp) REVERT: A 1494 MET cc_start: 0.8697 (ptt) cc_final: 0.7852 (ppp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.1390 time to fit residues: 17.2158 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 : 0.489 ------------------------------------------------------------------------------- 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: 6.9990 chunk 48 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 154 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 119 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS ** A 335 HIS ** 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 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN A 868 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 HIS ** 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 = 0.4226 r_free = 0.4226 target = 0.072230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.053222 restraints weight = 164672.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.053328 restraints weight = 159528.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.053560 restraints weight = 156549.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.053598 restraints weight = 152905.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.053598 restraints weight = 151365.989| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.8005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 14587 Z= 0.229 Angle : 0.755 8.899 20180 Z= 0.397 Chirality : 0.045 0.206 2344 Planarity : 0.005 0.068 2238 Dihedral : 17.273 81.641 3078 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 30.13 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.33 % Rotamer: Outliers : 0.07 % Allowed : 0.67 % Favored : 99.26 % 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: -1.28 (0.22), residues: 1484 helix: -0.34 (0.19), residues: 682 sheet: -1.72 (0.41), residues: 146 loop : -1.05 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 752 TYR 0.026 0.002 TYR A 917 PHE 0.024 0.003 PHE A1393 TRP 0.036 0.003 TRP A 986 HIS 0.008 0.002 HIS A 576 Details of bonding type rmsd covalent geometry : bond 0.00481 (14587) covalent geometry : angle 0.75490 (20180) hydrogen bonds : bond 0.05526 ( 593) hydrogen bonds : angle 5.45430 ( 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 73 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.561 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: 0.9440 (m-30) cc_final: 0.9174 (p0) REVERT: A 372 MET cc_start: 0.8694 (mmp) cc_final: 0.8409 (mmp) REVERT: A 556 ASP cc_start: 0.8250 (m-30) cc_final: 0.7801 (t70) REVERT: A 620 MET cc_start: -0.4155 (tpp) cc_final: -0.4433 (mmt) REVERT: A 939 MET cc_start: 0.9557 (mpp) cc_final: 0.9272 (mpp) REVERT: A 1494 MET cc_start: 0.8683 (ptt) cc_final: 0.7902 (ppp) outliers start: 1 outliers final: 0 residues processed: 73 average time/residue: 0.1275 time to fit residues: 14.0976 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 : 0.474 ------------------------------------------------------------------------------- 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: 5.9990 chunk 125 optimal weight: 30.0000 chunk 70 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 18 optimal weight: 0.5980 chunk 110 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 153 optimal weight: 30.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** 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 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.073539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.054524 restraints weight = 163525.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.054728 restraints weight = 157438.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.054803 restraints weight = 153424.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.054870 restraints weight = 151250.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.054870 restraints weight = 149694.306| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.8197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 14587 Z= 0.166 Angle : 0.681 8.736 20180 Z= 0.353 Chirality : 0.043 0.223 2344 Planarity : 0.004 0.067 2238 Dihedral : 17.294 84.144 3078 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.13 % Favored : 93.80 % 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: -1.27 (0.22), residues: 1484 helix: -0.28 (0.19), residues: 691 sheet: -1.90 (0.39), residues: 154 loop : -1.05 (0.27), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 494 TYR 0.018 0.002 TYR A 917 PHE 0.024 0.002 PHE A 119 TRP 0.036 0.003 TRP A 986 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00357 (14587) covalent geometry : angle 0.68059 (20180) hydrogen bonds : bond 0.04541 ( 593) hydrogen bonds : angle 5.28779 ( 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 71 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9479 (m-30) cc_final: 0.9212 (p0) REVERT: A 222 MET cc_start: 0.7329 (tmm) cc_final: 0.6540 (tmm) REVERT: A 372 MET cc_start: 0.8599 (mmp) cc_final: 0.8346 (mmp) REVERT: A 458 MET cc_start: -0.4041 (mmt) cc_final: -0.4403 (mtt) REVERT: A 556 ASP cc_start: 0.8152 (m-30) cc_final: 0.7727 (t70) REVERT: A 908 MET cc_start: 0.8883 (mmp) cc_final: 0.8667 (mmp) REVERT: A 939 MET cc_start: 0.9622 (mpp) cc_final: 0.9287 (mpp) REVERT: A 967 MET cc_start: 0.5310 (pmm) cc_final: 0.5048 (pmm) REVERT: A 1029 MET cc_start: 0.9329 (mmp) cc_final: 0.9077 (mpp) REVERT: A 1494 MET cc_start: 0.8584 (ptt) cc_final: 0.7767 (ppp) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.1243 time to fit residues: 13.4286 Evaluate side-chains 58 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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: 7.9990 chunk 124 optimal weight: 7.9990 chunk 84 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 131 optimal weight: 8.9990 chunk 144 optimal weight: 8.9990 chunk 47 optimal weight: 50.0000 chunk 114 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 868 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 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 = 0.4199 r_free = 0.4199 target = 0.070817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.053132 restraints weight = 166857.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.052752 restraints weight = 172659.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.052834 restraints weight = 168732.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.052944 restraints weight = 167795.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.052998 restraints weight = 160676.980| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.8830 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= 0.215 Angle : 0.743 8.996 20180 Z= 0.388 Chirality : 0.045 0.232 2344 Planarity : 0.005 0.065 2238 Dihedral : 17.462 81.464 3078 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 29.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.82 % Favored : 92.12 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % 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: -1.42 (0.22), residues: 1484 helix: -0.40 (0.19), residues: 688 sheet: -2.03 (0.39), residues: 154 loop : -1.12 (0.27), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 155 TYR 0.022 0.002 TYR A 917 PHE 0.018 0.002 PHE A1387 TRP 0.039 0.003 TRP A 986 HIS 0.007 0.002 HIS A 803 Details of bonding type rmsd covalent geometry : bond 0.00445 (14587) covalent geometry : angle 0.74339 (20180) hydrogen bonds : bond 0.05194 ( 593) hydrogen bonds : angle 5.50712 ( 1654) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2897.49 seconds wall clock time: 50 minutes 59.10 seconds (3059.10 seconds total)