Starting phenix.real_space_refine on Fri Jul 3 17:32:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0e_32240/07_2026/7w0e_32240.map" } resolution = 4.03 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= 0.005 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 106 5.49 5 Mg 3 5.21 5 S 67 5.16 5 C 9084 2.51 5 N 2542 2.21 5 O 3048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14850 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1104 Classifications: {'DNA': 1, 'RNA': 52} Modifications used: {'5*END': 1, 'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna3p': 52} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' A%5*END:plan': 1, ' A%5*END:plan2': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1103 Classifications: {'RNA': 52} Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 27} Link IDs: {'rna3p': 51} Chain: "A" Number of atoms: 12470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 12470 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 63, 'TRANS': 1477} 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: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 30 Unusual residues: {' MG': 3, 'ADP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.32, per 1000 atoms: 0.16 Number of scatterers: 14850 At special positions: 0 Unit cell: (95.26, 97.425, 188.355, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 106 15.00 Mg 3 11.99 O 3048 8.00 N 2542 7.00 C 9084 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: 0.87 Conformation dependent library (CDL) restraints added in 444.6 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 10 sheets defined 52.3% alpha, 8.8% beta 38 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.648A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 3.500A 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: 4.050A 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: 3.725A pdb=" N LEU A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 157 " --> pdb=" O PHE A 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ILE A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 196 removed outlier: 3.588A pdb=" N LYS A 189 " --> pdb=" O ALA A 185 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLU A 190 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 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: 3.874A pdb=" N ARG A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 292 removed outlier: 5.270A pdb=" N VAL A 277 " --> pdb=" O LYS A 273 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS A 278 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 313 removed outlier: 3.719A pdb=" N ILE A 298 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 344 removed outlier: 3.792A pdb=" N LYS A 320 " --> pdb=" O THR A 316 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 321 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.628A 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: 3.777A pdb=" N ASN A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.535A 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 466 removed outlier: 4.252A pdb=" N GLU A 466 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 493 Processing helix chain 'A' and resid 510 through 534 removed outlier: 4.697A pdb=" N ALA A 529 " --> pdb=" O HIS A 525 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N TYR A 531 " --> pdb=" O ASP A 527 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU A 532 " --> pdb=" O ILE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.931A pdb=" N ILE A 547 " --> pdb=" O GLU A 543 " (cutoff:3.500A) removed outlier: 3.646A 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: 3.584A pdb=" N ILE A 574 " --> pdb=" O ASN A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 600 No H-bonds generated for 'chain 'A' and resid 598 through 600' Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 671 through 675 Processing helix chain 'A' and resid 683 through 687 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 747 Processing helix chain 'A' and resid 792 through 810 Processing helix chain 'A' and resid 845 through 852 removed outlier: 3.710A 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: 3.512A 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: 4.214A pdb=" N GLY A 957 " --> pdb=" O HIS A 954 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 991 removed outlier: 3.794A pdb=" N LYS A 988 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1015 removed outlier: 3.660A pdb=" N ARG A 998 " --> pdb=" O SER A 994 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N PHE A1001 " --> pdb=" O ASN A 997 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.562A pdb=" N ASN A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1034 through 1038 removed outlier: 3.506A pdb=" N SER A1038 " --> pdb=" O ILE A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1179 removed outlier: 4.219A 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 removed outlier: 3.566A pdb=" N ALA A1203 " --> pdb=" O ALA A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.954A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1249 removed outlier: 4.378A 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: 4.104A pdb=" N LYS A1264 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 3.686A 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: 3.629A pdb=" N VAL A1319 " --> pdb=" O GLU A1315 " (cutoff:3.500A) Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 4.666A pdb=" N CYS A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ARG A1336 " --> pdb=" O VAL A1332 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1393 removed outlier: 7.294A pdb=" N LEU A1383 " --> pdb=" O LYS A1379 " (cutoff:3.500A) removed outlier: 9.443A pdb=" N GLN A1384 " --> pdb=" O ASN A1380 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N HIS A1385 " --> pdb=" O TYR A1381 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR A1392 " --> pdb=" O LYS A1388 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N PHE A1393 " --> pdb=" O MET A1389 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1430 removed outlier: 3.576A pdb=" N PHE A1429 " --> pdb=" O GLU A1425 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1441 removed outlier: 4.006A pdb=" N ASN A1439 " --> pdb=" O TYR A1435 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1455 removed outlier: 4.531A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1459 through 1464 removed outlier: 3.671A pdb=" N ARG A1463 " --> pdb=" O PRO A1460 " (cutoff:3.500A) Processing helix chain 'A' and resid 1468 through 1491 removed outlier: 3.702A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A1477 " --> pdb=" O PHE A1473 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN A1491 " --> pdb=" O ILE A1487 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1508 removed outlier: 4.087A pdb=" N ASP A1501 " --> pdb=" O GLY A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1529 through 1546 removed outlier: 4.134A pdb=" N GLU A1534 " --> pdb=" O ALA A1530 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE A1536 " --> pdb=" O LEU A1532 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N SER A1537 " --> pdb=" O SER A1533 " (cutoff:3.500A) Processing helix chain 'A' and resid 1602 through 1606 removed outlier: 3.755A pdb=" N ASN A1605 " --> pdb=" O MET A1602 " (cutoff:3.500A) removed outlier: 3.948A 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 1626 removed outlier: 4.300A pdb=" N GLY A1613 " --> pdb=" O PRO A1609 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A1621 " --> pdb=" O GLU A1617 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1648 removed outlier: 3.980A pdb=" N THR A1633 " --> pdb=" O ASP A1629 " (cutoff:3.500A) Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1655 through 1662 Processing helix chain 'A' and resid 1701 through 1717 removed outlier: 4.121A pdb=" N LEU A1707 " --> pdb=" O ASP A1703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 88 removed outlier: 5.640A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 112 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 114 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ARG A 59 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL A 136 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU A 61 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ILE A 138 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N MET A 63 " --> pdb=" O ILE A 138 " (cutoff:3.500A) removed outlier: 5.708A 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: 5.900A pdb=" N GLN A 422 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU A 389 " --> pdb=" O PHE A 477 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.547A 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 786 through 789 removed outlier: 4.024A pdb=" N ASN A 753 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 830 " --> pdb=" O LEU A 757 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 729 through 733 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 970 through 971 removed outlier: 5.846A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL A 895 " --> pdb=" O LYS A 880 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1669 through 1670 542 hydrogen bonds defined for protein. 1527 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 1.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4376 1.34 - 1.46: 3249 1.46 - 1.58: 7436 1.58 - 1.70: 210 1.70 - 1.82: 105 Bond restraints: 15376 Sorted by residual: bond pdb=" C ILE A1262 " pdb=" N PRO A1263 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.86e+00 bond pdb=" N9 G C 1 " pdb=" C4 G C 1 " ideal model delta sigma weight residual 1.375 1.401 -0.026 2.00e-02 2.50e+03 1.66e+00 bond pdb=" CA ILE A1262 " pdb=" C ILE A1262 " ideal model delta sigma weight residual 1.520 1.531 -0.011 8.80e-03 1.29e+04 1.61e+00 bond pdb=" C1' G C 1 " pdb=" N9 G C 1 " ideal model delta sigma weight residual 1.475 1.457 0.018 1.50e-02 4.44e+03 1.42e+00 bond pdb=" SD MET A 893 " pdb=" CE MET A 893 " ideal model delta sigma weight residual 1.791 1.765 0.026 2.50e-02 1.60e+03 1.08e+00 ... (remaining 15371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 20827 1.63 - 3.27: 379 3.27 - 4.90: 69 4.90 - 6.54: 22 6.54 - 8.17: 6 Bond angle restraints: 21303 Sorted by residual: angle pdb=" N ILE A 298 " pdb=" CA ILE A 298 " pdb=" C ILE A 298 " ideal model delta sigma weight residual 112.96 108.62 4.34 1.00e+00 1.00e+00 1.88e+01 angle pdb=" C LEU A1370 " pdb=" N GLU A1371 " pdb=" CA GLU A1371 " ideal model delta sigma weight residual 121.94 114.06 7.88 2.00e+00 2.50e-01 1.55e+01 angle pdb=" C ASP A 936 " pdb=" N LYS A 937 " pdb=" CA LYS A 937 " ideal model delta sigma weight residual 121.54 127.51 -5.97 1.91e+00 2.74e-01 9.76e+00 angle pdb=" N VAL A1356 " pdb=" CA VAL A1356 " pdb=" C VAL A1356 " ideal model delta sigma weight residual 113.07 108.92 4.15 1.37e+00 5.33e-01 9.16e+00 angle pdb=" CA MET A 344 " pdb=" CB MET A 344 " pdb=" CG MET A 344 " ideal model delta sigma weight residual 114.10 119.78 -5.68 2.00e+00 2.50e-01 8.06e+00 ... (remaining 21298 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.58: 8604 25.58 - 51.16: 413 51.16 - 76.75: 35 76.75 - 102.33: 12 102.33 - 127.91: 2 Dihedral angle restraints: 9066 sinusoidal: 4478 harmonic: 4588 Sorted by residual: dihedral pdb=" O2A ADP A1804 " pdb=" O3A ADP A1804 " pdb=" PA ADP A1804 " pdb=" PB ADP A1804 " ideal model delta sinusoidal sigma weight residual -60.00 67.91 -127.91 1 2.00e+01 2.50e-03 3.87e+01 dihedral pdb=" O1B ADP A1804 " pdb=" O3A ADP A1804 " pdb=" PB ADP A1804 " pdb=" PA ADP A1804 " ideal model delta sinusoidal sigma weight residual -60.00 -169.02 109.01 1 2.00e+01 2.50e-03 3.18e+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 180.00 152.45 27.55 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 9063 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1928 0.044 - 0.089: 419 0.089 - 0.133: 119 0.133 - 0.177: 9 0.177 - 0.222: 2 Chirality restraints: 2477 Sorted by residual: chirality pdb=" CA GLU A1371 " pdb=" N GLU A1371 " pdb=" C GLU A1371 " pdb=" CB GLU A1371 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CB VAL A1507 " pdb=" CA VAL A1507 " pdb=" CG1 VAL A1507 " pdb=" CG2 VAL A1507 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU A 406 " pdb=" CB LEU A 406 " pdb=" CD1 LEU A 406 " pdb=" CD2 LEU A 406 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.49e-01 ... (remaining 2474 not shown) Planarity restraints: 2337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1456 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.52e+00 pdb=" N PRO A1457 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A1457 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A1457 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 591 " 0.025 5.00e-02 4.00e+02 3.80e-02 2.31e+00 pdb=" N PRO A 592 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 592 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 592 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1371 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.04e+00 pdb=" C GLU A1371 " -0.025 2.00e-02 2.50e+03 pdb=" O GLU A1371 " 0.009 2.00e-02 2.50e+03 pdb=" N ALA A1372 " 0.008 2.00e-02 2.50e+03 ... (remaining 2334 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 310 2.65 - 3.22: 14600 3.22 - 3.78: 24900 3.78 - 4.34: 32927 4.34 - 4.90: 49808 Nonbonded interactions: 122545 Sorted by model distance: nonbonded pdb=" OP1 G D 32 " pdb="MG MG A1801 " model vdw 2.094 2.170 nonbonded pdb=" OD1 ASP A1368 " pdb="MG MG A1801 " model vdw 2.105 2.170 nonbonded pdb="MG MG A1803 " pdb=" O1A ADP A1804 " model vdw 2.141 2.170 nonbonded pdb=" O VAL A 77 " pdb=" OG1 THR A 81 " model vdw 2.147 3.040 nonbonded pdb=" NH2 ARG A1009 " pdb=" OH TYR A1028 " model vdw 2.163 3.120 ... (remaining 122540 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 Found NCS groups: ncs_group { reference = (chain 'C' and resid 1 through 52) selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.030 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 0.040 15376 Z= 0.126 Angle : 0.595 8.174 21303 Z= 0.304 Chirality : 0.040 0.222 2477 Planarity : 0.003 0.040 2337 Dihedral : 13.973 127.910 6090 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % 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: -0.82 (0.21), residues: 1549 helix: 0.09 (0.20), residues: 685 sheet: -0.47 (0.40), residues: 162 loop : -1.12 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 808 TYR 0.014 0.001 TYR A 402 PHE 0.019 0.001 PHE A 959 TRP 0.018 0.001 TRP A1634 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (15376) covalent geometry : angle 0.59482 / 0.30 (21303) hydrogen bonds : bond 0.16966 / 9.95 ( 635) hydrogen bonds : angle 6.56039 / 3.87 ( 1713) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.352 Fit side-chains REVERT: A 75 MET cc_start: 0.8013 (ttt) cc_final: 0.7658 (tmm) REVERT: A 268 LEU cc_start: 0.7956 (mt) cc_final: 0.7753 (mt) REVERT: A 336 LEU cc_start: 0.8065 (pp) cc_final: 0.7826 (pp) REVERT: A 579 CYS cc_start: 0.7818 (t) cc_final: 0.7592 (t) REVERT: A 768 MET cc_start: 0.7524 (pmm) cc_final: 0.6614 (ptt) REVERT: A 893 MET cc_start: 0.7255 (mmm) cc_final: 0.6615 (tpp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0876 time to fit residues: 18.5959 Evaluate side-chains 101 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN A1217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.088564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072349 restraints weight = 62647.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.074111 restraints weight = 37911.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.075280 restraints weight = 26823.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.076070 restraints weight = 21218.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076595 restraints weight = 18140.253| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.0867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15376 Z= 0.159 Angle : 0.605 7.316 21303 Z= 0.308 Chirality : 0.041 0.165 2477 Planarity : 0.004 0.042 2337 Dihedral : 7.994 112.764 2946 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % 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: -0.84 (0.22), residues: 1549 helix: 0.14 (0.20), residues: 689 sheet: -0.88 (0.38), residues: 166 loop : -1.11 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 998 TYR 0.026 0.001 TYR A 402 PHE 0.015 0.002 PHE A1001 TRP 0.016 0.001 TRP A1634 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (15376) covalent geometry : angle 0.60450 / 0.31 (21303) hydrogen bonds : bond 0.04714 / 2.76 ( 635) hydrogen bonds : angle 5.02459 / 2.94 ( 1713) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.493 Fit side-chains REVERT: A 75 MET cc_start: 0.7956 (ttt) cc_final: 0.7642 (tmm) REVERT: A 893 MET cc_start: 0.7182 (mmm) cc_final: 0.6547 (tpp) REVERT: A 1371 GLU cc_start: 0.8031 (pm20) cc_final: 0.7643 (pm20) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0803 time to fit residues: 16.2860 Evaluate side-chains 92 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 121 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.085582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069585 restraints weight = 63535.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.071231 restraints weight = 38884.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.072356 restraints weight = 27720.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.073079 restraints weight = 22008.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073594 restraints weight = 18906.624| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15376 Z= 0.285 Angle : 0.747 7.595 21303 Z= 0.382 Chirality : 0.046 0.183 2477 Planarity : 0.005 0.044 2337 Dihedral : 8.745 114.576 2946 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.58 % Favored : 93.35 % Rotamer: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % 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: -1.35 (0.21), residues: 1549 helix: -0.36 (0.19), residues: 674 sheet: -1.05 (0.38), residues: 173 loop : -1.29 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 719 TYR 0.025 0.002 TYR A1028 PHE 0.032 0.002 PHE A1001 TRP 0.015 0.002 TRP A1634 HIS 0.010 0.002 HIS A1656 Details of bonding type rmsd/Z covalent geometry : bond 0.00626 / 0.29 (15376) covalent geometry : angle 0.74704 / 0.38 (21303) hydrogen bonds : bond 0.05347 / 3.12 ( 635) hydrogen bonds : angle 5.23589 / 3.05 ( 1713) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.408 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8091 (tpp) cc_final: 0.7365 (tpp) REVERT: A 487 MET cc_start: 0.7889 (tmm) cc_final: 0.7634 (tmm) REVERT: A 939 MET cc_start: 0.5733 (mpp) cc_final: 0.5292 (mpp) REVERT: A 985 LEU cc_start: 0.8951 (tp) cc_final: 0.8731 (tt) REVERT: A 1257 LEU cc_start: 0.8923 (tp) cc_final: 0.8646 (tt) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.0895 time to fit residues: 16.7167 Evaluate side-chains 91 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.9990 chunk 155 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 90 optimal weight: 0.4980 chunk 136 optimal weight: 0.3980 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 9.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN A1217 ASN A1656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.089386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.073425 restraints weight = 61608.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.075201 restraints weight = 36914.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076427 restraints weight = 25857.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077213 restraints weight = 20157.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077733 restraints weight = 17159.990| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15376 Z= 0.115 Angle : 0.579 6.353 21303 Z= 0.294 Chirality : 0.040 0.183 2477 Planarity : 0.004 0.042 2337 Dihedral : 8.104 101.493 2946 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.21), residues: 1549 helix: 0.02 (0.20), residues: 679 sheet: -1.12 (0.39), residues: 157 loop : -1.05 (0.24), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1251 TYR 0.011 0.001 TYR A1000 PHE 0.021 0.001 PHE A1648 TRP 0.017 0.001 TRP A1634 HIS 0.005 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (15376) covalent geometry : angle 0.57859 / 0.29 (21303) hydrogen bonds : bond 0.03862 / 2.26 ( 635) hydrogen bonds : angle 4.68339 / 2.69 ( 1713) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 146 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 198 ASN cc_start: 0.7245 (m-40) cc_final: 0.7027 (m-40) REVERT: A 360 MET cc_start: 0.8042 (tpp) cc_final: 0.7536 (tpp) REVERT: A 487 MET cc_start: 0.7845 (tmm) cc_final: 0.7534 (tmm) REVERT: A 579 CYS cc_start: 0.7768 (t) cc_final: 0.7536 (t) REVERT: A 602 ARG cc_start: 0.7038 (mpt-90) cc_final: 0.6385 (mmt-90) REVERT: A 939 MET cc_start: 0.5587 (mpp) cc_final: 0.5378 (mpp) REVERT: A 1257 LEU cc_start: 0.8879 (tp) cc_final: 0.8613 (tt) REVERT: A 1371 GLU cc_start: 0.8065 (pm20) cc_final: 0.7552 (pm20) outliers start: 0 outliers final: 0 residues processed: 146 average time/residue: 0.1010 time to fit residues: 23.0231 Evaluate side-chains 106 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 85 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 141 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 73 optimal weight: 9.9990 chunk 86 optimal weight: 5.9990 chunk 161 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 12 GLN ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 GLN A1252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.085494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.069408 restraints weight = 63843.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.071042 restraints weight = 39503.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072154 restraints weight = 28518.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.072894 restraints weight = 22719.434| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073381 restraints weight = 19517.933| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 15376 Z= 0.298 Angle : 0.783 9.058 21303 Z= 0.398 Chirality : 0.046 0.180 2477 Planarity : 0.005 0.046 2337 Dihedral : 8.976 107.482 2946 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.62 % Favored : 92.32 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % 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: -1.52 (0.21), residues: 1549 helix: -0.46 (0.19), residues: 667 sheet: -1.35 (0.37), residues: 175 loop : -1.35 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1251 TYR 0.025 0.002 TYR A1028 PHE 0.047 0.003 PHE A1648 TRP 0.015 0.002 TRP A1634 HIS 0.009 0.002 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.30 (15376) covalent geometry : angle 0.78278 / 0.40 (21303) hydrogen bonds : bond 0.05354 / 3.12 ( 635) hydrogen bonds : angle 5.20706 / 3.03 ( 1713) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.526 Fit side-chains REVERT: A 208 MET cc_start: 0.6734 (tpp) cc_final: 0.6412 (tpp) REVERT: A 360 MET cc_start: 0.8212 (tpp) cc_final: 0.7426 (tpp) REVERT: A 372 MET cc_start: 0.7530 (pmm) cc_final: 0.7288 (pmm) REVERT: A 487 MET cc_start: 0.8053 (tmm) cc_final: 0.7655 (tmm) REVERT: A 602 ARG cc_start: 0.7094 (mpt-90) cc_final: 0.6891 (mtt180) REVERT: A 939 MET cc_start: 0.5753 (mpp) cc_final: 0.5489 (mpp) REVERT: A 985 LEU cc_start: 0.8973 (tp) cc_final: 0.8743 (tt) REVERT: A 1371 GLU cc_start: 0.7828 (pm20) cc_final: 0.7558 (pm20) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.0995 time to fit residues: 19.0321 Evaluate side-chains 95 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 71 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 114 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 107 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 614 HIS A 954 HIS A1217 ASN A1491 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.088575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.072592 restraints weight = 61896.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074355 restraints weight = 37491.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075512 restraints weight = 26362.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076187 restraints weight = 20871.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076799 restraints weight = 17948.265| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15376 Z= 0.129 Angle : 0.601 7.352 21303 Z= 0.306 Chirality : 0.041 0.260 2477 Planarity : 0.004 0.043 2337 Dihedral : 8.409 98.068 2946 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.23 % Favored : 94.71 % Rotamer: Outliers : 0.07 % Allowed : 2.36 % Favored : 97.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.21), residues: 1549 helix: -0.16 (0.20), residues: 677 sheet: -1.34 (0.37), residues: 170 loop : -1.15 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1031 TYR 0.013 0.001 TYR A 754 PHE 0.025 0.002 PHE A 938 TRP 0.019 0.001 TRP A1634 HIS 0.005 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (15376) covalent geometry : angle 0.60099 / 0.31 (21303) hydrogen bonds : bond 0.03976 / 2.32 ( 635) hydrogen bonds : angle 4.74266 / 2.71 ( 1713) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 372 MET cc_start: 0.7597 (pmm) cc_final: 0.7339 (pmm) REVERT: A 487 MET cc_start: 0.7984 (tmm) cc_final: 0.7630 (tmm) REVERT: A 579 CYS cc_start: 0.7683 (t) cc_final: 0.7453 (t) REVERT: A 602 ARG cc_start: 0.7101 (mpt-90) cc_final: 0.6427 (mmt-90) REVERT: A 893 MET cc_start: 0.6950 (mmm) cc_final: 0.6355 (tmm) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.0988 time to fit residues: 21.6413 Evaluate side-chains 101 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 8.9990 chunk 133 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 144 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS A1217 ASN ** A1327 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 = 0.3772 r_free = 0.3772 target = 0.089660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.073625 restraints weight = 61821.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075403 restraints weight = 37558.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.076580 restraints weight = 26484.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.077380 restraints weight = 20911.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077823 restraints weight = 17787.875| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 15376 Z= 0.111 Angle : 0.572 6.963 21303 Z= 0.289 Chirality : 0.040 0.218 2477 Planarity : 0.004 0.042 2337 Dihedral : 8.011 86.078 2946 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % 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: -0.93 (0.21), residues: 1549 helix: 0.08 (0.20), residues: 687 sheet: -1.20 (0.36), residues: 167 loop : -1.08 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1518 TYR 0.014 0.001 TYR A 402 PHE 0.014 0.001 PHE A 807 TRP 0.017 0.001 TRP A1634 HIS 0.004 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15376) covalent geometry : angle 0.57165 / 0.29 (21303) hydrogen bonds : bond 0.03563 / 2.09 ( 635) hydrogen bonds : angle 4.55821 / 2.63 ( 1713) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 0.504 Fit side-chains REVERT: A 122 MET cc_start: 0.9011 (tmm) cc_final: 0.8673 (tmm) REVERT: A 288 MET cc_start: 0.8188 (tmm) cc_final: 0.7959 (tmm) REVERT: A 487 MET cc_start: 0.7892 (tmm) cc_final: 0.7569 (tmm) REVERT: A 579 CYS cc_start: 0.7746 (t) cc_final: 0.7497 (t) REVERT: A 602 ARG cc_start: 0.7027 (mpt-90) cc_final: 0.6380 (mmt-90) REVERT: A 849 MET cc_start: 0.7480 (mpp) cc_final: 0.6791 (mpp) REVERT: A 893 MET cc_start: 0.6866 (mmm) cc_final: 0.6195 (tmm) REVERT: A 1371 GLU cc_start: 0.8167 (pm20) cc_final: 0.7858 (pm20) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1028 time to fit residues: 22.5069 Evaluate side-chains 102 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 35 optimal weight: 7.9990 chunk 122 optimal weight: 0.7980 chunk 128 optimal weight: 5.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 428 ASN A 576 HIS A1217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.088548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072663 restraints weight = 62748.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.074412 restraints weight = 38133.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075617 restraints weight = 26899.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.076289 restraints weight = 21147.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076869 restraints weight = 18186.618| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15376 Z= 0.152 Angle : 0.615 7.880 21303 Z= 0.310 Chirality : 0.041 0.227 2477 Planarity : 0.004 0.047 2337 Dihedral : 8.091 81.872 2946 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.29 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % 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: -0.96 (0.21), residues: 1549 helix: 0.03 (0.20), residues: 688 sheet: -1.29 (0.37), residues: 170 loop : -1.05 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1031 TYR 0.014 0.002 TYR A1000 PHE 0.024 0.002 PHE A1648 TRP 0.016 0.001 TRP A1634 HIS 0.008 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.15 (15376) covalent geometry : angle 0.61527 / 0.31 (21303) hydrogen bonds : bond 0.03933 / 2.29 ( 635) hydrogen bonds : angle 4.64888 / 2.68 ( 1713) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.458 Fit side-chains REVERT: A 360 MET cc_start: 0.8233 (tpp) cc_final: 0.7537 (tpp) REVERT: A 487 MET cc_start: 0.8013 (tmm) cc_final: 0.7625 (tmm) REVERT: A 602 ARG cc_start: 0.7022 (mpt-90) cc_final: 0.6404 (mmt-90) REVERT: A 893 MET cc_start: 0.7037 (mmm) cc_final: 0.6320 (tmm) REVERT: A 1371 GLU cc_start: 0.8004 (pm20) cc_final: 0.7642 (pm20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0960 time to fit residues: 20.4930 Evaluate side-chains 93 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 149 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 53 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.089406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.073564 restraints weight = 62328.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075340 restraints weight = 37623.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.076526 restraints weight = 26412.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077314 restraints weight = 20797.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.077766 restraints weight = 17685.252| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15376 Z= 0.121 Angle : 0.590 7.923 21303 Z= 0.296 Chirality : 0.040 0.270 2477 Planarity : 0.004 0.042 2337 Dihedral : 7.954 82.181 2946 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -0.88 (0.21), residues: 1549 helix: 0.12 (0.20), residues: 687 sheet: -1.21 (0.37), residues: 168 loop : -1.05 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 808 TYR 0.012 0.001 TYR A1000 PHE 0.025 0.001 PHE A1648 TRP 0.016 0.001 TRP A1634 HIS 0.005 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (15376) covalent geometry : angle 0.58963 / 0.30 (21303) hydrogen bonds : bond 0.03645 / 2.13 ( 635) hydrogen bonds : angle 4.55417 / 2.62 ( 1713) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.541 Fit side-chains REVERT: A 122 MET cc_start: 0.9031 (tmm) cc_final: 0.8712 (tmm) REVERT: A 153 PHE cc_start: 0.8385 (t80) cc_final: 0.8003 (t80) REVERT: A 288 MET cc_start: 0.8226 (tmm) cc_final: 0.8023 (tmm) REVERT: A 360 MET cc_start: 0.8241 (tpp) cc_final: 0.7545 (tpp) REVERT: A 487 MET cc_start: 0.7982 (tmm) cc_final: 0.7601 (tmm) REVERT: A 579 CYS cc_start: 0.7652 (t) cc_final: 0.7421 (t) REVERT: A 602 ARG cc_start: 0.6976 (mpt-90) cc_final: 0.6373 (mmt-90) REVERT: A 849 MET cc_start: 0.7434 (mpp) cc_final: 0.6909 (mpp) REVERT: A 893 MET cc_start: 0.6940 (mmm) cc_final: 0.6234 (tmm) REVERT: A 1371 GLU cc_start: 0.8066 (pm20) cc_final: 0.7603 (pm20) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0978 time to fit residues: 21.1011 Evaluate side-chains 105 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 147 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A 517 GLN A1217 ASN ** A1327 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 = 0.3785 r_free = 0.3785 target = 0.090197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074348 restraints weight = 61492.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076097 restraints weight = 37113.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077309 restraints weight = 26170.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.078129 restraints weight = 20537.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.078609 restraints weight = 17381.482| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15376 Z= 0.111 Angle : 0.586 8.439 21303 Z= 0.293 Chirality : 0.040 0.199 2477 Planarity : 0.004 0.042 2337 Dihedral : 7.811 82.575 2946 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: -0.82 (0.21), residues: 1549 helix: 0.15 (0.20), residues: 690 sheet: -1.06 (0.37), residues: 165 loop : -1.03 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 808 TYR 0.014 0.001 TYR A 402 PHE 0.039 0.001 PHE A1648 TRP 0.025 0.002 TRP A 102 HIS 0.005 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (15376) covalent geometry : angle 0.58573 / 0.29 (21303) hydrogen bonds : bond 0.03582 / 2.09 ( 635) hydrogen bonds : angle 4.52029 / 2.60 ( 1713) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.570 Fit side-chains REVERT: A 122 MET cc_start: 0.9018 (tmm) cc_final: 0.8698 (tmm) REVERT: A 288 MET cc_start: 0.8305 (tmm) cc_final: 0.8089 (tmm) REVERT: A 360 MET cc_start: 0.8220 (tpp) cc_final: 0.7529 (tpp) REVERT: A 487 MET cc_start: 0.8020 (tmm) cc_final: 0.7623 (tmm) REVERT: A 579 CYS cc_start: 0.7639 (t) cc_final: 0.7419 (t) REVERT: A 849 MET cc_start: 0.7382 (mpp) cc_final: 0.6823 (mpp) REVERT: A 893 MET cc_start: 0.6870 (mmm) cc_final: 0.6210 (tmm) REVERT: A 1371 GLU cc_start: 0.8126 (pm20) cc_final: 0.7617 (pm20) REVERT: A 1644 GLU cc_start: 0.7789 (tp30) cc_final: 0.7579 (tp30) REVERT: A 1648 PHE cc_start: 0.7379 (m-80) cc_final: 0.7010 (m-80) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.1000 time to fit residues: 21.9687 Evaluate side-chains 104 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 133 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 149 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 66 optimal weight: 0.0010 chunk 13 optimal weight: 8.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A1217 ASN A1380 ASN ** A1509 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 = 0.3779 r_free = 0.3779 target = 0.089932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074043 restraints weight = 60984.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.075834 restraints weight = 36766.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.077043 restraints weight = 25768.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.077846 restraints weight = 20217.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078375 restraints weight = 17164.909| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 15376 Z= 0.114 Angle : 0.584 8.382 21303 Z= 0.291 Chirality : 0.040 0.195 2477 Planarity : 0.004 0.042 2337 Dihedral : 7.744 81.669 2946 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.52 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.22), residues: 1549 helix: 0.16 (0.20), residues: 698 sheet: -1.11 (0.37), residues: 168 loop : -0.99 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1031 TYR 0.014 0.001 TYR A1000 PHE 0.035 0.001 PHE A1648 TRP 0.016 0.001 TRP A1634 HIS 0.005 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.11 (15376) covalent geometry : angle 0.58420 / 0.29 (21303) hydrogen bonds : bond 0.03526 / 2.06 ( 635) hydrogen bonds : angle 4.50465 / 2.59 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2013.63 seconds wall clock time: 35 minutes 57.78 seconds (2157.78 seconds total)