Starting phenix.real_space_refine on Thu Jun 12 22:17:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0f_32241/06_2025/7w0f_32241.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0f_32241/06_2025/7w0f_32241.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0f_32241/06_2025/7w0f_32241.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0f_32241/06_2025/7w0f_32241.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0f_32241/06_2025/7w0f_32241.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0f_32241/06_2025/7w0f_32241.cif" } resolution = 4.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.79, per 1000 atoms: 0.55 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: 3.39 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 5.92 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: 8.32 Time building geometry restraints manager: 4.08 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 40.680 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.520 ------------------------------------------------------------------------------- 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 : 21.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.001 TRP A1634 HIS 0.005 0.001 HIS A 18 PHE 0.017 0.001 PHE A 938 TYR 0.017 0.001 TYR A 740 ARG 0.004 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.20010 ( 593) hydrogen bonds : angle 7.80371 ( 1654) covalent geometry : bond 0.00273 (14587) covalent geometry : angle 0.63607 (20180) *********************** 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 : 1.831 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: 0.3482 time to fit residues: 93.8546 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 : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 40.0000 chunk 118 optimal weight: 30.0000 chunk 65 optimal weight: 30.0000 chunk 40 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 47 optimal weight: 0.3980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 overall best weight: 1.0944 ------------------------------------------------------------------------------- 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 A1013 ASN A1385 HIS ** A1552 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 = 0.4589 r_free = 0.4589 target = 0.094004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.073548 restraints weight = 147626.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.072531 restraints weight = 154808.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.072919 restraints weight = 159194.703| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6417 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 14587 Z= 0.147 Angle : 0.679 18.554 20180 Z= 0.340 Chirality : 0.042 0.237 2344 Planarity : 0.005 0.078 2238 Dihedral : 16.077 81.314 3078 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.04 % Favored : 95.89 % Rotamer: Outliers : 0.30 % Allowed : 4.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.22), residues: 1484 helix: 0.06 (0.20), residues: 676 sheet: -0.55 (0.37), residues: 161 loop : -1.13 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 986 HIS 0.007 0.001 HIS A 335 PHE 0.023 0.001 PHE A1387 TYR 0.021 0.001 TYR A1232 ARG 0.016 0.001 ARG A1503 Details of bonding type rmsd hydrogen bonds : bond 0.05314 ( 593) hydrogen bonds : angle 5.13827 ( 1654) covalent geometry : bond 0.00313 (14587) covalent geometry : angle 0.67862 (20180) *********************** 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 121 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 117 time to evaluate : 1.688 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: 0.9251 (m-30) cc_final: 0.9011 (m-30) REVERT: A 186 THR cc_start: 0.7916 (p) cc_final: 0.7283 (p) REVERT: A 208 MET cc_start: 0.6980 (tmm) cc_final: 0.6482 (tmm) REVERT: A 238 ILE cc_start: 0.4425 (pt) cc_final: 0.4016 (pt) REVERT: A 625 MET cc_start: 0.4818 (ptt) cc_final: 0.4188 (ptt) REVERT: A 805 MET cc_start: 0.7129 (tmm) cc_final: 0.6458 (tmm) REVERT: A 908 MET cc_start: 0.8597 (mmp) cc_final: 0.8242 (mmp) REVERT: A 939 MET cc_start: 0.9003 (mpp) cc_final: 0.8682 (mpp) REVERT: A 990 ILE cc_start: 0.8956 (mm) cc_final: 0.8701 (mm) REVERT: A 1479 LEU cc_start: 0.7039 (mm) cc_final: 0.6834 (mm) outliers start: 4 outliers final: 0 residues processed: 119 average time/residue: 0.3527 time to fit residues: 59.5758 Evaluate side-chains 83 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 4 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 32 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 60 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 111 optimal weight: 9.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 GLN ** A 475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS A 815 HIS A 841 GLN ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 HIS A1452 GLN A1548 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.079126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.058732 restraints weight = 159958.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.058873 restraints weight = 155955.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.058873 restraints weight = 152801.368| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.119 14587 Z= 0.294 Angle : 0.923 13.892 20180 Z= 0.477 Chirality : 0.049 0.204 2344 Planarity : 0.008 0.222 2238 Dihedral : 16.978 89.734 3078 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 31.01 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.20 % Favored : 93.73 % Rotamer: Outliers : 0.60 % Allowed : 7.37 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1484 helix: -0.75 (0.18), residues: 672 sheet: -1.29 (0.39), residues: 151 loop : -1.10 (0.26), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP A 986 HIS 0.015 0.003 HIS A 576 PHE 0.025 0.003 PHE A 663 TYR 0.031 0.004 TYR A1232 ARG 0.015 0.001 ARG A1503 Details of bonding type rmsd hydrogen bonds : bond 0.07246 ( 593) hydrogen bonds : angle 5.76859 ( 1654) covalent geometry : bond 0.00605 (14587) covalent geometry : angle 0.92316 (20180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2968 Ramachandran restraints generated. 1484 Oldfield, 0 Emsley, 1484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.810 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: A 104 ASP cc_start: 0.9529 (m-30) cc_final: 0.9233 (p0) REVERT: A 204 ASP cc_start: 0.9485 (OUTLIER) cc_final: 0.9257 (p0) REVERT: A 238 ILE cc_start: 0.5085 (pt) cc_final: 0.4183 (pt) REVERT: A 372 MET cc_start: 0.8630 (mmp) cc_final: 0.8348 (mmm) REVERT: A 625 MET cc_start: 0.8658 (ptt) cc_final: 0.7991 (ptt) REVERT: A 634 PRO cc_start: 0.7977 (Cg_exo) cc_final: 0.7449 (Cg_endo) REVERT: A 939 MET cc_start: 0.9527 (mpp) cc_final: 0.9124 (mpp) REVERT: A 1503 ARG cc_start: 0.9530 (OUTLIER) cc_final: 0.9294 (ttp80) outliers start: 8 outliers final: 2 residues processed: 95 average time/residue: 0.3975 time to fit residues: 55.6022 Evaluate side-chains 79 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 118 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 15 optimal weight: 8.9990 chunk 72 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- 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 287 GLN A 475 HIS ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 912 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1178 GLN A1380 ASN ** A1385 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 = 0.4377 r_free = 0.4377 target = 0.081216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.060997 restraints weight = 156328.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.061239 restraints weight = 151094.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.061345 restraints weight = 147011.822| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.5183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14587 Z= 0.166 Angle : 0.677 8.833 20180 Z= 0.350 Chirality : 0.043 0.194 2344 Planarity : 0.005 0.072 2238 Dihedral : 16.955 90.734 3078 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 19.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.25 % Favored : 95.69 % Rotamer: Outliers : 0.07 % Allowed : 3.28 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.22), residues: 1484 helix: -0.26 (0.19), residues: 683 sheet: -1.43 (0.37), residues: 166 loop : -0.95 (0.27), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP A 986 HIS 0.009 0.001 HIS A1004 PHE 0.029 0.002 PHE A1387 TYR 0.049 0.002 TYR A1232 ARG 0.005 0.001 ARG A 602 Details of bonding type rmsd hydrogen bonds : bond 0.04871 ( 593) hydrogen bonds : angle 5.26002 ( 1654) covalent geometry : bond 0.00343 (14587) covalent geometry : angle 0.67716 (20180) *********************** 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 86 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9513 (m-30) cc_final: 0.9225 (p0) REVERT: A 344 MET cc_start: 0.6157 (ttp) cc_final: 0.5602 (ttp) REVERT: A 545 TYR cc_start: 0.9531 (m-10) cc_final: 0.9140 (p90) REVERT: A 556 ASP cc_start: 0.8526 (m-30) cc_final: 0.8211 (t70) REVERT: A 625 MET cc_start: 0.8501 (ptt) cc_final: 0.7961 (ptt) REVERT: A 634 PRO cc_start: 0.7722 (Cg_exo) cc_final: 0.7282 (Cg_endo) REVERT: A 939 MET cc_start: 0.9576 (mpp) cc_final: 0.9209 (mpp) REVERT: A 967 MET cc_start: 0.5036 (pmm) cc_final: 0.4746 (pmm) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.3899 time to fit residues: 48.4392 Evaluate side-chains 75 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 145 optimal weight: 20.0000 chunk 61 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 chunk 30 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 67 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 520 GLN ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 679 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** A 978 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.078165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.058033 restraints weight = 158788.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.058118 restraints weight = 154671.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.058133 restraints weight = 152426.508| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7210 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14587 Z= 0.189 Angle : 0.699 8.568 20180 Z= 0.362 Chirality : 0.043 0.227 2344 Planarity : 0.005 0.069 2238 Dihedral : 17.026 86.406 3078 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.74 % Favored : 93.19 % Rotamer: Outliers : 0.07 % Allowed : 4.54 % Favored : 95.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.22), residues: 1484 helix: -0.21 (0.19), residues: 676 sheet: -1.53 (0.38), residues: 151 loop : -0.98 (0.27), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A1634 HIS 0.015 0.002 HIS A 335 PHE 0.025 0.002 PHE A1387 TYR 0.040 0.003 TYR A 917 ARG 0.007 0.001 ARG A 369 Details of bonding type rmsd hydrogen bonds : bond 0.05085 ( 593) hydrogen bonds : angle 5.29470 ( 1654) covalent geometry : bond 0.00394 (14587) covalent geometry : angle 0.69867 (20180) *********************** 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 79 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 78 time to evaluate : 1.466 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: 0.9514 (m-30) cc_final: 0.9248 (p0) REVERT: A 222 MET cc_start: 0.7645 (tmm) cc_final: 0.7113 (tmm) REVERT: A 344 MET cc_start: 0.6967 (ttp) cc_final: 0.6501 (ttp) REVERT: A 556 ASP cc_start: 0.8346 (m-30) cc_final: 0.7952 (t70) REVERT: A 620 MET cc_start: -0.3537 (tpt) cc_final: -0.3881 (tpt) REVERT: A 908 MET cc_start: 0.9136 (mmp) cc_final: 0.8798 (mmp) REVERT: A 939 MET cc_start: 0.9613 (mpp) cc_final: 0.9210 (mpp) REVERT: A 967 MET cc_start: 0.5438 (pmm) cc_final: 0.5060 (pmm) outliers start: 1 outliers final: 1 residues processed: 79 average time/residue: 0.3302 time to fit residues: 38.5515 Evaluate side-chains 69 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 82 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 142 HIS ** 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 598 GLN A 619 ASN ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.072650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.053451 restraints weight = 166031.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.053451 restraints weight = 161992.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.053451 restraints weight = 161992.042| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.7441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 14587 Z= 0.264 Angle : 0.808 7.991 20180 Z= 0.425 Chirality : 0.048 0.322 2344 Planarity : 0.006 0.067 2238 Dihedral : 17.542 85.831 3078 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 32.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.94 % Favored : 92.99 % Rotamer: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.21), residues: 1484 helix: -0.63 (0.18), residues: 686 sheet: -1.87 (0.39), residues: 149 loop : -1.32 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP A1634 HIS 0.021 0.003 HIS A 335 PHE 0.029 0.003 PHE A 119 TYR 0.036 0.003 TYR A1232 ARG 0.019 0.001 ARG A 334 Details of bonding type rmsd hydrogen bonds : bond 0.06255 ( 593) hydrogen bonds : angle 5.83552 ( 1654) covalent geometry : bond 0.00549 (14587) covalent geometry : angle 0.80785 (20180) *********************** 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 77 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9513 (m-30) cc_final: 0.9249 (p0) REVERT: A 488 TYR cc_start: 0.8597 (t80) cc_final: 0.8381 (t80) REVERT: A 556 ASP cc_start: 0.8327 (m-30) cc_final: 0.7875 (t70) REVERT: A 620 MET cc_start: -0.2704 (tpp) cc_final: -0.2918 (mmt) REVERT: A 908 MET cc_start: 0.9171 (mmp) cc_final: 0.8881 (mmp) REVERT: A 939 MET cc_start: 0.9573 (mpp) cc_final: 0.9253 (mpp) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.3053 time to fit residues: 35.2784 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 : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 50 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 30.0000 chunk 4 optimal weight: 0.0030 chunk 82 optimal weight: 5.9990 chunk 144 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 overall best weight: 2.7998 ------------------------------------------------------------------------------- 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 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 760 ASN A 868 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.075374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.056945 restraints weight = 156889.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.056818 restraints weight = 167656.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.056987 restraints weight = 160401.825| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14587 Z= 0.147 Angle : 0.669 8.821 20180 Z= 0.345 Chirality : 0.043 0.191 2344 Planarity : 0.004 0.064 2238 Dihedral : 17.372 87.486 3078 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 22.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.39 % Favored : 94.54 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.22), residues: 1484 helix: -0.27 (0.19), residues: 693 sheet: -1.93 (0.40), residues: 144 loop : -1.18 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1634 HIS 0.011 0.001 HIS A1004 PHE 0.023 0.002 PHE A1387 TYR 0.035 0.002 TYR A 521 ARG 0.007 0.001 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 593) hydrogen bonds : angle 5.33581 ( 1654) covalent geometry : bond 0.00311 (14587) covalent geometry : angle 0.66881 (20180) *********************** 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 72 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 1.421 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: 0.9261 (m-30) cc_final: 0.8835 (p0) REVERT: A 222 MET cc_start: 0.6340 (tmm) cc_final: 0.5414 (tmm) REVERT: A 372 MET cc_start: 0.8444 (mmp) cc_final: 0.8181 (mmp) REVERT: A 424 MET cc_start: 0.8226 (pmm) cc_final: 0.7756 (pmm) REVERT: A 556 ASP cc_start: 0.7542 (m-30) cc_final: 0.6933 (t70) REVERT: A 620 MET cc_start: -0.5476 (tpp) cc_final: -0.6046 (mmt) REVERT: A 908 MET cc_start: 0.8243 (mmp) cc_final: 0.7894 (mmp) REVERT: A 939 MET cc_start: 0.9330 (mpp) cc_final: 0.8943 (mpp) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2852 time to fit residues: 30.9673 Evaluate side-chains 57 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 9.9990 chunk 121 optimal weight: 30.0000 chunk 123 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 119 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 39 optimal weight: 50.0000 chunk 132 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 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** ** A1019 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.072611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.054439 restraints weight = 161843.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.054040 restraints weight = 183591.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.054184 restraints weight = 173257.837| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.7941 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= 0.197 Angle : 0.720 10.046 20180 Z= 0.375 Chirality : 0.044 0.193 2344 Planarity : 0.005 0.064 2238 Dihedral : 17.420 84.736 3078 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 27.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.87 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.22), residues: 1484 helix: -0.32 (0.19), residues: 690 sheet: -1.85 (0.40), residues: 149 loop : -1.15 (0.27), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1634 HIS 0.008 0.002 HIS A1004 PHE 0.020 0.002 PHE A1387 TYR 0.032 0.002 TYR A1232 ARG 0.007 0.001 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 593) hydrogen bonds : angle 5.52020 ( 1654) covalent geometry : bond 0.00410 (14587) covalent geometry : angle 0.71988 (20180) *********************** 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 68 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 ASP cc_start: 0.9482 (m-30) cc_final: 0.9193 (p0) REVERT: A 344 MET cc_start: 0.6699 (tmm) cc_final: 0.6449 (tmm) REVERT: A 556 ASP cc_start: 0.8162 (m-30) cc_final: 0.7658 (t70) REVERT: A 908 MET cc_start: 0.9179 (mmp) cc_final: 0.8963 (mmp) REVERT: A 939 MET cc_start: 0.9603 (mpp) cc_final: 0.9235 (mpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2957 time to fit residues: 30.9961 Evaluate side-chains 57 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 28 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 86 optimal weight: 0.0870 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 126 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 68 optimal weight: 7.9990 chunk 90 optimal weight: 0.0570 overall best weight: 2.1880 ------------------------------------------------------------------------------- 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 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** A1019 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.075045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.056126 restraints weight = 158220.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.056439 restraints weight = 152131.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.056681 restraints weight = 146847.586| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.7873 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= 0.137 Angle : 0.658 9.374 20180 Z= 0.338 Chirality : 0.042 0.187 2344 Planarity : 0.004 0.065 2238 Dihedral : 17.214 86.312 3078 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 20.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.46 % Favored : 94.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.22), residues: 1484 helix: -0.10 (0.19), residues: 681 sheet: -1.80 (0.41), residues: 141 loop : -0.94 (0.27), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A1634 HIS 0.006 0.001 HIS A1004 PHE 0.016 0.002 PHE A1387 TYR 0.031 0.002 TYR A 521 ARG 0.008 0.000 ARG A 196 Details of bonding type rmsd hydrogen bonds : bond 0.04087 ( 593) hydrogen bonds : angle 5.26371 ( 1654) covalent geometry : bond 0.00292 (14587) covalent geometry : angle 0.65773 (20180) *********************** 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 68 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 2.090 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: 0.9222 (m-30) cc_final: 0.8824 (p0) REVERT: A 222 MET cc_start: 0.6121 (tmm) cc_final: 0.5285 (tmm) REVERT: A 424 MET cc_start: 0.8274 (pmm) cc_final: 0.7977 (pmm) REVERT: A 556 ASP cc_start: 0.7586 (m-30) cc_final: 0.7007 (t70) REVERT: A 908 MET cc_start: 0.8177 (mmp) cc_final: 0.7897 (mmp) REVERT: A 939 MET cc_start: 0.9240 (mpp) cc_final: 0.8870 (mpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3203 time to fit residues: 33.5108 Evaluate side-chains 55 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 20.0000 chunk 107 optimal weight: 8.9990 chunk 140 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 126 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 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 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.071488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.053706 restraints weight = 164615.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.053367 restraints weight = 164219.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.053409 restraints weight = 169442.670| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.8536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 14587 Z= 0.197 Angle : 0.727 9.598 20180 Z= 0.378 Chirality : 0.044 0.173 2344 Planarity : 0.005 0.065 2238 Dihedral : 17.367 82.583 3078 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 28.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.81 % Favored : 93.13 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.22), residues: 1484 helix: -0.25 (0.19), residues: 692 sheet: -1.94 (0.40), residues: 151 loop : -0.96 (0.27), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A1634 HIS 0.009 0.002 HIS A1004 PHE 0.017 0.002 PHE A1387 TYR 0.031 0.002 TYR A1232 ARG 0.013 0.001 ARG A 494 Details of bonding type rmsd hydrogen bonds : bond 0.05081 ( 593) hydrogen bonds : angle 5.46870 ( 1654) covalent geometry : bond 0.00414 (14587) covalent geometry : angle 0.72727 (20180) ********************** 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 68 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.646 Fit side-chains 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: 0.9227 (p0) REVERT: A 222 MET cc_start: 0.7661 (tmm) cc_final: 0.6758 (tmm) REVERT: A 344 MET cc_start: 0.7081 (tmm) cc_final: 0.6848 (tmm) REVERT: A 556 ASP cc_start: 0.8187 (m-30) cc_final: 0.7740 (t70) REVERT: A 625 MET cc_start: 0.7252 (ptp) cc_final: 0.6936 (pmm) REVERT: A 908 MET cc_start: 0.9237 (mmp) cc_final: 0.9008 (mmp) REVERT: A 939 MET cc_start: 0.9549 (mpp) cc_final: 0.9186 (mpp) REVERT: A 1029 MET cc_start: 0.9271 (mmp) cc_final: 0.9018 (mpp) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2980 time to fit residues: 31.3725 Evaluate side-chains 56 residues out of total 1343 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 0.2980 chunk 7 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 96 optimal weight: 0.0570 overall best weight: 2.4704 ------------------------------------------------------------------------------- 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 598 GLN ** A 679 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.073777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.055083 restraints weight = 162499.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.055345 restraints weight = 154237.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.055486 restraints weight = 149312.131| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.8501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14587 Z= 0.139 Angle : 0.658 9.914 20180 Z= 0.339 Chirality : 0.042 0.174 2344 Planarity : 0.004 0.065 2238 Dihedral : 17.253 84.739 3078 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 20.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.22), residues: 1484 helix: -0.08 (0.19), residues: 681 sheet: -1.88 (0.40), residues: 152 loop : -0.94 (0.27), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1634 HIS 0.008 0.001 HIS A1305 PHE 0.015 0.002 PHE A 49 TYR 0.032 0.002 TYR A 521 ARG 0.005 0.001 ARG A 496 Details of bonding type rmsd hydrogen bonds : bond 0.04060 ( 593) hydrogen bonds : angle 5.25416 ( 1654) covalent geometry : bond 0.00298 (14587) covalent geometry : angle 0.65799 (20180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5194.93 seconds wall clock time: 93 minutes 40.24 seconds (5620.24 seconds total)