Starting phenix.real_space_refine on Sat Sep 12 10:36:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7w0e_32240/09_2026/7w0e_32240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0e_32240/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7w0e_32240/09_2026/7w0e_32240.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7w0e_32240/09_2026/7w0e_32240.cif" model { file = "/net/cci-nas-00/data/ceres_data/7w0e_32240/09_2026/7w0e_32240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0e_32240/09_2026/7w0e_32240.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7w0e_32240/09_2026/7w0e_32240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0e_32240/09_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): 0.20s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 'RNAv2': 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: 1 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: {'RNAv2': 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: 3.15, per 1000 atoms: 0.21 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: 1.26 Conformation dependent library (CDL) restraints added in 601.8 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: 2.25 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: 4.46 Time building geometry restraints manager: 1.69 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 1.478 1.457 0.021 2.00e-02 2.50e+03 1.09e+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: 20611 1.63 - 3.27: 588 3.27 - 4.90: 73 4.90 - 6.54: 22 6.54 - 8.17: 6 Bond angle restraints: 21300 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 21295 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.58: 8498 25.58 - 51.16: 497 51.16 - 76.75: 56 76.75 - 102.33: 12 102.33 - 127.91: 2 Dihedral angle restraints: 9065 sinusoidal: 4477 harmonic: 4588 Sorted by residual: dihedral pdb=" O5' U D 39 " pdb=" C5' U D 39 " pdb=" C4' U D 39 " pdb=" C3' U D 39 " ideal model delta sinusoidal sigma weight residual 180.00 126.07 53.93 3 6.40e+00 2.44e-02 5.08e+01 dihedral pdb=" O5' A D 37 " pdb=" C5' A D 37 " pdb=" C4' A D 37 " pdb=" C3' A D 37 " ideal model delta sinusoidal sigma weight residual 180.00 131.63 48.37 3 6.40e+00 2.44e-02 4.74e+01 dihedral pdb=" O5' A C 13 " pdb=" C5' A C 13 " pdb=" C4' A C 13 " pdb=" C3' A C 13 " ideal model delta sinusoidal sigma weight residual 180.00 133.66 46.34 3 6.40e+00 2.44e-02 4.57e+01 ... (remaining 9062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1938 0.051 - 0.103: 377 0.103 - 0.154: 54 0.154 - 0.205: 4 0.205 - 0.257: 104 Chirality restraints: 2477 Sorted by residual: chirality pdb=" P G C 15 " pdb=" OP1 G C 15 " pdb=" OP2 G C 15 " pdb=" O5' G C 15 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" P A C 37 " pdb=" OP1 A C 37 " pdb=" OP2 A C 37 " pdb=" O5' A C 37 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" P U C 16 " pdb=" OP1 U C 16 " pdb=" OP2 U C 16 " pdb=" O5' U C 16 " both_signs ideal model delta sigma weight residual True 2.17 -2.42 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (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: 1.460 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: 0.020 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.730 Find NCS groups from input model: 0.090 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: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.090 ------------------------------------------------------------------------------- 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= 0.130 Angle : 0.661 8.174 21300 Z= 0.314 Chirality : 0.062 0.257 2477 Planarity : 0.003 0.040 2337 Dihedral : 15.174 127.910 6089 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 0.00275 / 0.13 (15376) covalent geometry : angle 0.66079 / 0.31 (21300) hydrogen bonds : bond 0.16966 / 8.88 ( 635) hydrogen bonds : angle 6.56039 / 2.64 ( 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 : 0.590 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: 0.0987 time to fit residues: 21.1898 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 : 0.506 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.088428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.072104 restraints weight = 62582.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.073877 restraints weight = 37936.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075071 restraints weight = 26831.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075857 restraints weight = 21157.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.076299 restraints weight = 18069.900| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15376 Z= 0.169 Angle : 0.706 7.933 21300 Z= 0.329 Chirality : 0.048 0.237 2477 Planarity : 0.004 0.047 2337 Dihedral : 10.763 111.245 2945 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.97 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % 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 (0.21), residues: 1549 helix: 0.14 (0.20), residues: 689 sheet: -0.87 (0.38), residues: 166 loop : -1.10 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 998 TYR 0.025 0.001 TYR A 402 PHE 0.016 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 0.00368 / 0.17 (15376) covalent geometry : angle 0.70556 / 0.33 (21300) hydrogen bonds : bond 0.04635 / 2.40 ( 635) hydrogen bonds : angle 4.97345 / 1.95 ( 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 : 0.449 Fit side-chains REVERT: A 75 MET cc_start: 0.7945 (ttt) cc_final: 0.7631 (tmm) REVERT: A 579 CYS cc_start: 0.7681 (t) cc_final: 0.7426 (t) REVERT: A 893 MET cc_start: 0.7141 (mmm) cc_final: 0.6743 (mmm) REVERT: A 1371 GLU cc_start: 0.8015 (pm20) cc_final: 0.7618 (pm20) outliers start: 0 outliers final: 0 residues processed: 125 average time/residue: 0.0924 time to fit residues: 18.9264 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 : 0.396 ------------------------------------------------------------------------------- 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: 7.9990 chunk 149 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 125 optimal weight: 0.8980 chunk 59 optimal weight: 0.3980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN A1519 HIS A1656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.072808 restraints weight = 62281.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074531 restraints weight = 37897.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075681 restraints weight = 26904.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.076500 restraints weight = 21220.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.076914 restraints weight = 18012.667| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15376 Z= 0.149 Angle : 0.677 8.185 21300 Z= 0.315 Chirality : 0.048 0.258 2477 Planarity : 0.004 0.040 2337 Dihedral : 10.529 101.894 2945 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 0.07 % Allowed : 3.71 % Favored : 96.21 % 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: -0.81 (0.21), residues: 1549 helix: 0.13 (0.20), residues: 687 sheet: -0.90 (0.39), residues: 155 loop : -1.04 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1251 TYR 0.019 0.001 TYR A 402 PHE 0.016 0.002 PHE A1001 TRP 0.015 0.001 TRP A1634 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (15376) covalent geometry : angle 0.67747 / 0.32 (21300) hydrogen bonds : bond 0.04228 / 2.19 ( 635) hydrogen bonds : angle 4.75802 / 1.85 ( 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 130 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 0.369 Fit side-chains REVERT: A 198 ASN cc_start: 0.7442 (m-40) cc_final: 0.6970 (m-40) REVERT: A 360 MET cc_start: 0.7957 (tpp) cc_final: 0.7616 (tpp) REVERT: A 487 MET cc_start: 0.7809 (tmm) cc_final: 0.7537 (tmm) REVERT: A 579 CYS cc_start: 0.7715 (t) cc_final: 0.7490 (t) REVERT: A 1371 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7888 (pm20) outliers start: 1 outliers final: 0 residues processed: 129 average time/residue: 0.0942 time to fit residues: 19.3571 Evaluate side-chains 96 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 2.9990 chunk 155 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 59 optimal weight: 10.0000 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3762 r_free = 0.3762 target = 0.089229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073146 restraints weight = 61739.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074934 restraints weight = 37189.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.076139 restraints weight = 26081.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076967 restraints weight = 20427.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.077482 restraints weight = 17247.228| |-----------------------------------------------------------------------------| r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1470 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= 0.132 Angle : 0.660 8.091 21300 Z= 0.307 Chirality : 0.047 0.263 2477 Planarity : 0.004 0.040 2337 Dihedral : 10.364 92.876 2945 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % 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: -0.75 (0.22), residues: 1549 helix: 0.19 (0.20), residues: 685 sheet: -0.94 (0.39), residues: 156 loop : -0.99 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1251 TYR 0.014 0.001 TYR A 402 PHE 0.022 0.001 PHE A1648 TRP 0.014 0.001 TRP A1634 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (15376) covalent geometry : angle 0.66026 / 0.31 (21300) hydrogen bonds : bond 0.03930 / 2.03 ( 635) hydrogen bonds : angle 4.57966 / 1.77 ( 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 132 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.342 Fit side-chains REVERT: A 198 ASN cc_start: 0.7366 (m-40) cc_final: 0.7089 (m-40) REVERT: A 360 MET cc_start: 0.8016 (tpp) cc_final: 0.7509 (tpp) REVERT: A 487 MET cc_start: 0.7887 (tmm) cc_final: 0.7553 (tmm) REVERT: A 579 CYS cc_start: 0.7778 (t) cc_final: 0.7500 (t) REVERT: A 602 ARG cc_start: 0.6994 (mpt-90) cc_final: 0.6173 (mmt-90) REVERT: A 1371 GLU cc_start: 0.8122 (pm20) cc_final: 0.7592 (pm20) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.0906 time to fit residues: 19.4024 Evaluate side-chains 100 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 9.9990 chunk 37 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 161 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 29 optimal weight: 7.9990 chunk 60 optimal weight: 4.9990 chunk 139 optimal weight: 4.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1217 ASN A1491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.088413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.072328 restraints weight = 62243.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074059 restraints weight = 37696.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.075236 restraints weight = 26702.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076020 restraints weight = 21023.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076565 restraints weight = 17900.066| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15376 Z= 0.168 Angle : 0.707 7.865 21300 Z= 0.329 Chirality : 0.049 0.263 2477 Planarity : 0.004 0.042 2337 Dihedral : 10.346 87.621 2945 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % 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: -0.89 (0.21), residues: 1549 helix: 0.07 (0.20), residues: 684 sheet: -1.07 (0.39), residues: 157 loop : -1.05 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1251 TYR 0.018 0.002 TYR A 402 PHE 0.019 0.002 PHE A1001 TRP 0.014 0.002 TRP A1634 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (15376) covalent geometry : angle 0.70705 / 0.33 (21300) hydrogen bonds : bond 0.04222 / 2.17 ( 635) hydrogen bonds : angle 4.67518 / 1.81 ( 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 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.500 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8010 (tpp) cc_final: 0.7340 (tpp) REVERT: A 487 MET cc_start: 0.8011 (tmm) cc_final: 0.7667 (tmm) REVERT: A 579 CYS cc_start: 0.7764 (t) cc_final: 0.7490 (t) REVERT: A 602 ARG cc_start: 0.7108 (mpt-90) cc_final: 0.6409 (mmt-90) REVERT: A 939 MET cc_start: 0.5488 (mpp) cc_final: 0.5264 (mpp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.0989 time to fit residues: 21.2544 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 : 0.508 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 152 optimal weight: 0.0980 chunk 131 optimal weight: 10.0000 chunk 114 optimal weight: 0.0570 chunk 122 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 56 optimal weight: 0.4980 overall best weight: 1.1100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 954 HIS A1217 ASN ** A1491 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 = 0.3779 r_free = 0.3779 target = 0.089585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073456 restraints weight = 62345.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075237 restraints weight = 37395.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.076458 restraints weight = 26362.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.077255 restraints weight = 20753.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077797 restraints weight = 17672.528| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15376 Z= 0.121 Angle : 0.659 7.961 21300 Z= 0.305 Chirality : 0.047 0.252 2477 Planarity : 0.003 0.041 2337 Dihedral : 10.213 81.511 2945 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % 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: 0.13 (0.20), residues: 682 sheet: -1.07 (0.39), residues: 155 loop : -0.96 (0.25), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 808 TYR 0.016 0.001 TYR A 402 PHE 0.021 0.001 PHE A1648 TRP 0.015 0.001 TRP A1634 HIS 0.006 0.001 HIS A 803 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15376) covalent geometry : angle 0.65915 / 0.30 (21300) hydrogen bonds : bond 0.03737 / 1.93 ( 635) hydrogen bonds : angle 4.50758 / 1.72 ( 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 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 0.552 Fit side-chains REVERT: A 360 MET cc_start: 0.8055 (tpp) cc_final: 0.7525 (tpp) REVERT: A 487 MET cc_start: 0.7968 (tmm) cc_final: 0.7616 (tmm) REVERT: A 579 CYS cc_start: 0.7767 (t) cc_final: 0.7467 (t) REVERT: A 602 ARG cc_start: 0.7056 (mpt-90) cc_final: 0.5955 (mmt90) REVERT: A 893 MET cc_start: 0.7449 (tpt) cc_final: 0.6948 (tmm) REVERT: A 1371 GLU cc_start: 0.8052 (pm20) cc_final: 0.7691 (pm20) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1043 time to fit residues: 25.0602 Evaluate side-chains 103 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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: 0.0670 chunk 92 optimal weight: 0.5980 chunk 135 optimal weight: 0.9980 chunk 122 optimal weight: 4.9990 chunk 130 optimal weight: 10.0000 chunk 133 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.090713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074607 restraints weight = 62453.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.076428 restraints weight = 37348.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077642 restraints weight = 26220.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078465 restraints weight = 20639.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.078987 restraints weight = 17529.573| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 15376 Z= 0.108 Angle : 0.651 7.933 21300 Z= 0.299 Chirality : 0.047 0.269 2477 Planarity : 0.003 0.041 2337 Dihedral : 10.039 79.172 2945 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.73 (0.22), residues: 1549 helix: 0.19 (0.20), residues: 698 sheet: -1.09 (0.38), residues: 155 loop : -0.93 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 808 TYR 0.010 0.001 TYR A1000 PHE 0.013 0.001 PHE A1331 TRP 0.015 0.001 TRP A1634 HIS 0.004 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15376) covalent geometry : angle 0.65094 / 0.30 (21300) hydrogen bonds : bond 0.03483 / 1.80 ( 635) hydrogen bonds : angle 4.40301 / 1.68 ( 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 155 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.515 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8043 (tpp) cc_final: 0.7380 (tpp) REVERT: A 487 MET cc_start: 0.7961 (tmm) cc_final: 0.7620 (tmm) REVERT: A 579 CYS cc_start: 0.7765 (t) cc_final: 0.7415 (t) REVERT: A 805 MET cc_start: 0.4247 (tpt) cc_final: 0.3695 (mmm) REVERT: A 893 MET cc_start: 0.7569 (tpt) cc_final: 0.7260 (tpt) REVERT: A 1371 GLU cc_start: 0.8091 (pm20) cc_final: 0.7532 (pm20) REVERT: A 1648 PHE cc_start: 0.7273 (m-80) cc_final: 0.6842 (m-80) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1043 time to fit residues: 25.6740 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 : 0.496 ------------------------------------------------------------------------------- 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: 3.9990 chunk 83 optimal weight: 0.0870 chunk 157 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 28 optimal weight: 0.3980 chunk 77 optimal weight: 0.4980 chunk 43 optimal weight: 2.9990 chunk 35 optimal weight: 0.0050 chunk 122 optimal weight: 0.8980 chunk 128 optimal weight: 7.9990 overall best weight: 0.2972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1217 ASN ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.091719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.075506 restraints weight = 61640.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.077330 restraints weight = 36681.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078603 restraints weight = 25697.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.079443 restraints weight = 20110.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.079985 restraints weight = 17096.384| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15376 Z= 0.103 Angle : 0.643 8.198 21300 Z= 0.295 Chirality : 0.046 0.274 2477 Planarity : 0.003 0.047 2337 Dihedral : 9.916 77.557 2945 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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: -0.62 (0.22), residues: 1549 helix: 0.27 (0.20), residues: 693 sheet: -1.06 (0.38), residues: 155 loop : -0.86 (0.25), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 808 TYR 0.012 0.001 TYR A 294 PHE 0.014 0.001 PHE A 276 TRP 0.014 0.001 TRP A1634 HIS 0.003 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (15376) covalent geometry : angle 0.64346 / 0.30 (21300) hydrogen bonds : bond 0.03372 / 1.74 ( 635) hydrogen bonds : angle 4.29603 / 1.64 ( 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 158 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.547 Fit side-chains REVERT: A 165 LEU cc_start: 0.6851 (tp) cc_final: 0.6649 (tt) REVERT: A 360 MET cc_start: 0.8058 (tpp) cc_final: 0.7391 (tpp) REVERT: A 487 MET cc_start: 0.7930 (tmm) cc_final: 0.7557 (tmm) REVERT: A 579 CYS cc_start: 0.7851 (t) cc_final: 0.7588 (t) REVERT: A 631 TYR cc_start: 0.7405 (m-80) cc_final: 0.7139 (m-80) REVERT: A 744 MET cc_start: 0.7921 (mmt) cc_final: 0.6924 (mmm) REVERT: A 805 MET cc_start: 0.4526 (tpt) cc_final: 0.4252 (mmm) REVERT: A 849 MET cc_start: 0.7609 (mpp) cc_final: 0.6941 (mpp) REVERT: A 893 MET cc_start: 0.7554 (tpt) cc_final: 0.7236 (tpt) REVERT: A 939 MET cc_start: 0.4862 (mpp) cc_final: 0.4483 (mpp) REVERT: A 1371 GLU cc_start: 0.8034 (pm20) cc_final: 0.7508 (pm20) REVERT: A 1494 MET cc_start: 0.7924 (ttm) cc_final: 0.7709 (ttm) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1151 time to fit residues: 28.1276 Evaluate side-chains 108 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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: 0.7980 chunk 25 optimal weight: 0.9990 chunk 111 optimal weight: 0.0060 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 6 optimal weight: 8.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A1217 ASN ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1490 ASN ** A1491 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075497 restraints weight = 62080.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.077307 restraints weight = 37116.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.078544 restraints weight = 26008.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079359 restraints weight = 20403.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079930 restraints weight = 17359.288| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15376 Z= 0.108 Angle : 0.648 8.307 21300 Z= 0.299 Chirality : 0.046 0.272 2477 Planarity : 0.003 0.040 2337 Dihedral : 9.848 77.639 2945 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % 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: -0.68 (0.22), residues: 1549 helix: 0.19 (0.20), residues: 710 sheet: -0.96 (0.39), residues: 151 loop : -0.90 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1330 TYR 0.014 0.001 TYR A1442 PHE 0.013 0.001 PHE A 807 TRP 0.011 0.001 TRP A1634 HIS 0.005 0.001 HIS A1004 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (15376) covalent geometry : angle 0.64804 / 0.30 (21300) hydrogen bonds : bond 0.03463 / 1.79 ( 635) hydrogen bonds : angle 4.24200 / 1.61 ( 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 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.523 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.8163 (ttt) cc_final: 0.7641 (mmp) REVERT: A 360 MET cc_start: 0.8082 (tpp) cc_final: 0.7380 (tpp) REVERT: A 458 MET cc_start: 0.6639 (tpt) cc_final: 0.6252 (tpp) REVERT: A 487 MET cc_start: 0.8015 (tmm) cc_final: 0.7624 (tmm) REVERT: A 579 CYS cc_start: 0.7624 (t) cc_final: 0.7302 (t) REVERT: A 744 MET cc_start: 0.7905 (mmt) cc_final: 0.6899 (mmm) REVERT: A 805 MET cc_start: 0.4241 (tpt) cc_final: 0.4013 (mmm) REVERT: A 849 MET cc_start: 0.7539 (mpp) cc_final: 0.6883 (mpp) REVERT: A 893 MET cc_start: 0.7476 (tpt) cc_final: 0.7126 (tpt) REVERT: A 1031 ARG cc_start: 0.7421 (mmm-85) cc_final: 0.6924 (mtp85) REVERT: A 1371 GLU cc_start: 0.7990 (pm20) cc_final: 0.7431 (pm20) REVERT: A 1489 GLU cc_start: 0.7244 (tt0) cc_final: 0.6988 (tm-30) REVERT: A 1494 MET cc_start: 0.7735 (ttm) cc_final: 0.7522 (ttm) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.1076 time to fit residues: 24.9976 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 : 0.528 ------------------------------------------------------------------------------- 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: 6.9990 chunk 77 optimal weight: 0.2980 chunk 147 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A1217 ASN ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1490 ASN ** A1491 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 = 0.3801 r_free = 0.3801 target = 0.090558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074439 restraints weight = 61687.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.076163 restraints weight = 37074.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.077363 restraints weight = 26257.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.078155 restraints weight = 20750.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.078715 restraints weight = 17717.538| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2432 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= 0.120 Angle : 0.667 8.360 21300 Z= 0.308 Chirality : 0.047 0.264 2477 Planarity : 0.004 0.040 2337 Dihedral : 9.853 78.249 2945 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.33 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.67 (0.22), residues: 1549 helix: 0.19 (0.20), residues: 711 sheet: -0.97 (0.38), residues: 152 loop : -0.88 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1330 TYR 0.016 0.001 TYR A 402 PHE 0.026 0.001 PHE A1648 TRP 0.010 0.001 TRP A1634 HIS 0.005 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (15376) covalent geometry : angle 0.66735 / 0.31 (21300) hydrogen bonds : bond 0.03606 / 1.86 ( 635) hydrogen bonds : angle 4.36790 / 1.66 ( 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 134 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8134 (tpp) cc_final: 0.7360 (tpp) REVERT: A 458 MET cc_start: 0.6703 (tpt) cc_final: 0.6316 (tpp) REVERT: A 487 MET cc_start: 0.7987 (tmm) cc_final: 0.7563 (tmm) REVERT: A 579 CYS cc_start: 0.7687 (t) cc_final: 0.7349 (t) REVERT: A 744 MET cc_start: 0.7868 (mmt) cc_final: 0.6883 (mmm) REVERT: A 805 MET cc_start: 0.4530 (tpt) cc_final: 0.4262 (mmm) REVERT: A 893 MET cc_start: 0.7538 (tpt) cc_final: 0.7186 (tpt) REVERT: A 939 MET cc_start: 0.5194 (mpp) cc_final: 0.4701 (mpp) REVERT: A 1031 ARG cc_start: 0.7554 (mmm-85) cc_final: 0.7052 (mtp85) REVERT: A 1209 MET cc_start: 0.8337 (ppp) cc_final: 0.8051 (ptt) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1111 time to fit residues: 23.7662 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 : 0.550 ------------------------------------------------------------------------------- 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: 0.6980 chunk 155 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 7.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN A1217 ASN ** A1327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1491 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 = 0.3811 r_free = 0.3811 target = 0.091092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.074954 restraints weight = 61487.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.076720 restraints weight = 37143.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.077910 restraints weight = 26243.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.078739 restraints weight = 20706.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.079304 restraints weight = 17686.373| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15376 Z= 0.109 Angle : 0.649 8.604 21300 Z= 0.299 Chirality : 0.046 0.266 2477 Planarity : 0.004 0.041 2337 Dihedral : 9.835 77.279 2945 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.71 (0.22), residues: 1549 helix: 0.16 (0.20), residues: 717 sheet: -1.02 (0.38), residues: 154 loop : -0.90 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1330 TYR 0.013 0.001 TYR A 402 PHE 0.024 0.001 PHE A1648 TRP 0.011 0.001 TRP A1634 HIS 0.003 0.001 HIS A1519 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 (15376) covalent geometry : angle 0.64886 / 0.30 (21300) hydrogen bonds : bond 0.03515 / 1.81 ( 635) hydrogen bonds : angle 4.31271 / 1.64 ( 1713) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.67 seconds wall clock time: 39 minutes 14.50 seconds (2354.50 seconds total)