Starting phenix.real_space_refine on Fri Jun 13 18:47:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7w0e_32240/06_2025/7w0e_32240.cif Found real_map, /net/cci-nas-00/data/ceres_data/7w0e_32240/06_2025/7w0e_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7w0e_32240/06_2025/7w0e_32240.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7w0e_32240/06_2025/7w0e_32240.map" model { file = "/net/cci-nas-00/data/ceres_data/7w0e_32240/06_2025/7w0e_32240.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7w0e_32240/06_2025/7w0e_32240.cif" } resolution = 4.03 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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:plan2': 1, ' A%5*END:plan': 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: 9.26, per 1000 atoms: 0.62 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: 4.55 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 6.15 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: 7.82 Time building geometry restraints manager: 4.64 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: 8721 25.58 - 51.16: 517 51.16 - 76.75: 186 76.75 - 102.33: 12 102.33 - 127.91: 2 Dihedral angle restraints: 9438 sinusoidal: 4850 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 9435 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: 0.990 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 43.620 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.060 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:3.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 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 : 17.350 127.910 6462 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (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 TRP 0.018 0.001 TRP A1634 HIS 0.005 0.001 HIS A 803 PHE 0.019 0.001 PHE A 959 TYR 0.014 0.001 TYR A 402 ARG 0.004 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.16966 ( 635) hydrogen bonds : angle 6.56039 ( 1713) covalent geometry : bond 0.00263 (15376) covalent geometry : angle 0.59482 (21303) *********************** 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 : 1.453 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: 0.7819 (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: 0.7254 (mmm) cc_final: 0.6615 (tpp) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.2315 time to fit residues: 48.8310 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 : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 9.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 749 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.085772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.069672 restraints weight = 63580.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071260 restraints weight = 39455.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072384 restraints weight = 28497.786| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 15376 Z= 0.286 Angle : 0.746 8.321 21303 Z= 0.382 Chirality : 0.045 0.184 2477 Planarity : 0.005 0.050 2337 Dihedral : 16.749 118.299 3318 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.33 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.21), residues: 1549 helix: -0.30 (0.19), residues: 686 sheet: -1.22 (0.38), residues: 169 loop : -1.26 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A1634 HIS 0.009 0.002 HIS A1656 PHE 0.028 0.002 PHE A1001 TYR 0.029 0.002 TYR A1028 ARG 0.005 0.001 ARG A 395 Details of bonding type rmsd hydrogen bonds : bond 0.05893 ( 635) hydrogen bonds : angle 5.41503 ( 1713) covalent geometry : bond 0.00622 (15376) covalent geometry : angle 0.74594 (21303) *********************** 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 118 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 1.512 Fit side-chains REVERT: A 893 MET cc_start: 0.7246 (mmm) cc_final: 0.6771 (mmm) REVERT: A 985 LEU cc_start: 0.8925 (tp) cc_final: 0.8707 (tt) outliers start: 0 outliers final: 0 residues processed: 118 average time/residue: 0.2338 time to fit residues: 44.4782 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 : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 11 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 GLN A1217 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.088639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072722 restraints weight = 61480.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074438 restraints weight = 37363.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.075616 restraints weight = 26460.919| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15376 Z= 0.133 Angle : 0.592 6.488 21303 Z= 0.301 Chirality : 0.040 0.163 2477 Planarity : 0.004 0.041 2337 Dihedral : 16.613 109.005 3318 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.04 % Favored : 94.90 % Rotamer: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.21), residues: 1549 helix: 0.00 (0.20), residues: 678 sheet: -0.98 (0.39), residues: 154 loop : -1.11 (0.24), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1634 HIS 0.005 0.001 HIS A 803 PHE 0.019 0.002 PHE A1648 TYR 0.016 0.001 TYR A 402 ARG 0.005 0.000 ARG A1251 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 635) hydrogen bonds : angle 4.86328 ( 1713) covalent geometry : bond 0.00289 (15376) covalent geometry : angle 0.59200 (21303) *********************** 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 136 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 2.025 Fit side-chains REVERT: A 198 ASN cc_start: 0.7431 (m-40) cc_final: 0.6938 (m-40) REVERT: A 360 MET cc_start: 0.8015 (tpp) cc_final: 0.7658 (tpp) REVERT: A 487 MET cc_start: 0.7712 (tmm) cc_final: 0.7502 (tmm) REVERT: A 602 ARG cc_start: 0.6864 (mpt-90) cc_final: 0.6223 (mmt-90) REVERT: A 985 LEU cc_start: 0.8878 (tp) cc_final: 0.8657 (tt) REVERT: A 1371 GLU cc_start: 0.8063 (pm20) cc_final: 0.7557 (pm20) outliers start: 0 outliers final: 0 residues processed: 136 average time/residue: 0.2413 time to fit residues: 51.9352 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 : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 125 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 154 optimal weight: 0.7980 chunk 151 optimal weight: 0.0010 chunk 149 optimal weight: 5.9990 chunk 134 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 800 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 HIS ** A1004 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN A1252 ASN A1656 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.090004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074033 restraints weight = 60950.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.075795 restraints weight = 36800.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.076984 restraints weight = 25978.559| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1587 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= 0.112 Angle : 0.562 6.297 21303 Z= 0.285 Chirality : 0.039 0.169 2477 Planarity : 0.004 0.040 2337 Dihedral : 16.489 96.248 3318 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1549 helix: 0.17 (0.20), residues: 679 sheet: -1.05 (0.39), residues: 155 loop : -0.99 (0.24), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1634 HIS 0.006 0.001 HIS A 803 PHE 0.030 0.001 PHE A1648 TYR 0.021 0.001 TYR A 402 ARG 0.014 0.000 ARG A1330 Details of bonding type rmsd hydrogen bonds : bond 0.03687 ( 635) hydrogen bonds : angle 4.58401 ( 1713) covalent geometry : bond 0.00235 (15376) covalent geometry : angle 0.56181 (21303) *********************** 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 138 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.7262 (m-40) cc_final: 0.6999 (m-40) REVERT: A 208 MET cc_start: 0.6517 (tpp) cc_final: 0.6259 (tpp) REVERT: A 268 LEU cc_start: 0.8107 (mt) cc_final: 0.7856 (mt) REVERT: A 360 MET cc_start: 0.7992 (tpp) cc_final: 0.7777 (tpp) REVERT: A 487 MET cc_start: 0.7825 (tmm) cc_final: 0.7548 (tmm) REVERT: A 579 CYS cc_start: 0.7823 (t) cc_final: 0.7562 (t) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2640 time to fit residues: 56.6341 Evaluate side-chains 99 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 40 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 137 optimal weight: 0.0170 chunk 110 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 112 optimal weight: 0.0040 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 7.9990 chunk 84 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.5834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1004 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.090968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.074959 restraints weight = 61813.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.076774 restraints weight = 37202.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.077971 restraints weight = 26111.167| |-----------------------------------------------------------------------------| r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15376 Z= 0.104 Angle : 0.557 7.084 21303 Z= 0.280 Chirality : 0.039 0.171 2477 Planarity : 0.003 0.041 2337 Dihedral : 16.400 85.009 3318 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.20 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.22), residues: 1549 helix: 0.15 (0.20), residues: 687 sheet: -1.01 (0.39), residues: 155 loop : -0.98 (0.25), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1634 HIS 0.005 0.001 HIS A 803 PHE 0.043 0.001 PHE A1648 TYR 0.021 0.001 TYR A 402 ARG 0.008 0.000 ARG A1330 Details of bonding type rmsd hydrogen bonds : bond 0.03504 ( 635) hydrogen bonds : angle 4.45257 ( 1713) covalent geometry : bond 0.00218 (15376) covalent geometry : angle 0.55734 (21303) *********************** 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 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 75 MET cc_start: 0.7928 (ttt) cc_final: 0.7582 (tmm) REVERT: A 198 ASN cc_start: 0.7294 (m-40) cc_final: 0.6896 (m-40) REVERT: A 208 MET cc_start: 0.6361 (tpp) cc_final: 0.6102 (tpp) REVERT: A 268 LEU cc_start: 0.8156 (mt) cc_final: 0.7905 (mt) REVERT: A 360 MET cc_start: 0.8033 (tpp) cc_final: 0.7725 (tpp) REVERT: A 372 MET cc_start: 0.7635 (pmm) cc_final: 0.7244 (pmm) REVERT: A 487 MET cc_start: 0.7820 (tmm) cc_final: 0.7502 (tmm) REVERT: A 579 CYS cc_start: 0.7756 (t) cc_final: 0.7541 (t) REVERT: A 1221 LYS cc_start: 0.8644 (tppt) cc_final: 0.8061 (tttm) REVERT: A 1371 GLU cc_start: 0.8111 (pm20) cc_final: 0.7614 (pm20) REVERT: A 1662 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6964 (mm-30) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.2635 time to fit residues: 59.5229 Evaluate side-chains 107 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 37 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 157 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 97 optimal weight: 5.9990 overall best weight: 1.7820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.089461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073491 restraints weight = 61898.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075261 restraints weight = 37538.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.076452 restraints weight = 26543.950| |-----------------------------------------------------------------------------| r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15376 Z= 0.137 Angle : 0.578 6.832 21303 Z= 0.292 Chirality : 0.040 0.153 2477 Planarity : 0.004 0.041 2337 Dihedral : 16.378 81.380 3318 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.65 % Favored : 95.29 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1549 helix: 0.19 (0.20), residues: 683 sheet: -1.02 (0.39), residues: 155 loop : -0.97 (0.25), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 97 HIS 0.003 0.001 HIS A1004 PHE 0.016 0.001 PHE A1001 TYR 0.015 0.001 TYR A1000 ARG 0.010 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.03734 ( 635) hydrogen bonds : angle 4.48543 ( 1713) covalent geometry : bond 0.00300 (15376) covalent geometry : angle 0.57786 (21303) *********************** 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 135 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 135 time to evaluate : 1.816 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8116 (tpp) cc_final: 0.7632 (tpp) REVERT: A 487 MET cc_start: 0.7995 (tmm) cc_final: 0.7630 (tmm) REVERT: A 579 CYS cc_start: 0.7762 (t) cc_final: 0.7504 (t) REVERT: A 893 MET cc_start: 0.7506 (tpt) cc_final: 0.7045 (tmm) REVERT: A 1371 GLU cc_start: 0.8031 (pm20) cc_final: 0.7593 (pm20) REVERT: A 1662 GLU cc_start: 0.7215 (mm-30) cc_final: 0.7012 (mm-30) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2696 time to fit residues: 56.9386 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 : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 70 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 1 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 18 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1491 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.088774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072693 restraints weight = 62488.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074446 restraints weight = 38051.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075501 restraints weight = 26986.856| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1913 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= 0.151 Angle : 0.601 8.029 21303 Z= 0.303 Chirality : 0.040 0.165 2477 Planarity : 0.004 0.042 2337 Dihedral : 16.411 80.698 3318 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 0.07 % Allowed : 2.79 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.22), residues: 1549 helix: 0.06 (0.20), residues: 684 sheet: -1.31 (0.38), residues: 162 loop : -0.94 (0.25), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.005 0.001 HIS A1519 PHE 0.022 0.002 PHE A1648 TYR 0.015 0.001 TYR A1000 ARG 0.008 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 635) hydrogen bonds : angle 4.55376 ( 1713) covalent geometry : bond 0.00334 (15376) covalent geometry : angle 0.60073 (21303) *********************** 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 138 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 137 time to evaluate : 2.350 Fit side-chains revert: symmetry clash REVERT: A 360 MET cc_start: 0.8120 (tpp) cc_final: 0.7346 (tpp) REVERT: A 487 MET cc_start: 0.8036 (tmm) cc_final: 0.7657 (tmm) REVERT: A 579 CYS cc_start: 0.7723 (t) cc_final: 0.7388 (t) REVERT: A 849 MET cc_start: 0.7628 (mpp) cc_final: 0.6952 (mpp) REVERT: A 893 MET cc_start: 0.7545 (tpt) cc_final: 0.7158 (tpt) outliers start: 1 outliers final: 0 residues processed: 138 average time/residue: 0.3820 time to fit residues: 84.9503 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 : 3.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 161 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 148 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 136 optimal weight: 4.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 614 HIS A1217 ASN ** A1267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.089165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.073090 restraints weight = 62146.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.074844 restraints weight = 37674.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.076035 restraints weight = 26707.932| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15376 Z= 0.139 Angle : 0.607 8.053 21303 Z= 0.306 Chirality : 0.041 0.289 2477 Planarity : 0.004 0.042 2337 Dihedral : 16.421 81.891 3318 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.78 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.21), residues: 1549 helix: -0.01 (0.20), residues: 696 sheet: -1.07 (0.39), residues: 153 loop : -1.00 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1634 HIS 0.005 0.001 HIS A1519 PHE 0.039 0.002 PHE A1648 TYR 0.014 0.001 TYR A1000 ARG 0.007 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 635) hydrogen bonds : angle 4.58445 ( 1713) covalent geometry : bond 0.00306 (15376) covalent geometry : angle 0.60659 (21303) *********************** 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 140 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 1.679 Fit side-chains REVERT: A 360 MET cc_start: 0.8177 (tpp) cc_final: 0.7381 (tpp) REVERT: A 487 MET cc_start: 0.8022 (tmm) cc_final: 0.7631 (tmm) REVERT: A 579 CYS cc_start: 0.7771 (t) cc_final: 0.7484 (t) REVERT: A 1209 MET cc_start: 0.8605 (ppp) cc_final: 0.8009 (ptt) REVERT: A 1644 GLU cc_start: 0.6729 (tp30) cc_final: 0.6452 (tp30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2515 time to fit residues: 54.6911 Evaluate side-chains 98 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 160 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 141 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 142 HIS A 143 HIS A1217 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.086587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.070430 restraints weight = 63234.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.072130 restraints weight = 38557.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.073278 restraints weight = 27457.137| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15376 Z= 0.245 Angle : 0.723 8.693 21303 Z= 0.367 Chirality : 0.044 0.214 2477 Planarity : 0.005 0.044 2337 Dihedral : 16.600 77.579 3318 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.07 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.21), residues: 1549 helix: -0.33 (0.19), residues: 692 sheet: -1.12 (0.38), residues: 165 loop : -1.14 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 102 HIS 0.008 0.001 HIS A1519 PHE 0.030 0.002 PHE A1648 TYR 0.019 0.002 TYR A1000 ARG 0.009 0.001 ARG A 9 Details of bonding type rmsd hydrogen bonds : bond 0.04681 ( 635) hydrogen bonds : angle 4.98348 ( 1713) covalent geometry : bond 0.00541 (15376) covalent geometry : angle 0.72312 (21303) *********************** 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 122 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 122 time to evaluate : 1.497 Fit side-chains REVERT: A 75 MET cc_start: 0.8135 (ttt) cc_final: 0.7675 (mmp) REVERT: A 122 MET cc_start: 0.8877 (tmm) cc_final: 0.8605 (tmm) REVERT: A 153 PHE cc_start: 0.8526 (t80) cc_final: 0.8055 (t80) REVERT: A 360 MET cc_start: 0.8293 (tpp) cc_final: 0.7390 (tpp) REVERT: A 487 MET cc_start: 0.8122 (tmm) cc_final: 0.7724 (tmm) REVERT: A 579 CYS cc_start: 0.7752 (t) cc_final: 0.7410 (t) REVERT: A 849 MET cc_start: 0.7623 (mpp) cc_final: 0.7065 (mpp) REVERT: A 893 MET cc_start: 0.7100 (mmm) cc_final: 0.6663 (tmm) REVERT: A 1209 MET cc_start: 0.8755 (ppp) cc_final: 0.8294 (ptt) REVERT: A 1662 GLU cc_start: 0.7241 (mm-30) cc_final: 0.7020 (mm-30) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 0.2601 time to fit residues: 49.9658 Evaluate side-chains 89 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 132 optimal weight: 0.0060 chunk 15 optimal weight: 0.0980 chunk 48 optimal weight: 7.9990 chunk 126 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 chunk 139 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 97 optimal weight: 4.9990 overall best weight: 1.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.088995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.072870 restraints weight = 62321.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.074605 restraints weight = 37941.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.075785 restraints weight = 26954.420| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.2186 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= 0.129 Angle : 0.621 8.875 21303 Z= 0.310 Chirality : 0.041 0.318 2477 Planarity : 0.004 0.044 2337 Dihedral : 16.555 84.280 3318 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.21), residues: 1549 helix: -0.07 (0.20), residues: 689 sheet: -1.10 (0.37), residues: 166 loop : -1.09 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1634 HIS 0.005 0.001 HIS A1519 PHE 0.035 0.002 PHE A1648 TYR 0.015 0.001 TYR A 754 ARG 0.007 0.000 ARG A 808 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 635) hydrogen bonds : angle 4.69604 ( 1713) covalent geometry : bond 0.00283 (15376) covalent geometry : angle 0.62132 (21303) ********************** 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 139 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.702 Fit side-chains REVERT: A 208 MET cc_start: 0.6871 (mmp) cc_final: 0.6418 (tpp) REVERT: A 288 MET cc_start: 0.8316 (tmm) cc_final: 0.8106 (tmm) REVERT: A 360 MET cc_start: 0.8244 (tpp) cc_final: 0.7444 (tpp) REVERT: A 487 MET cc_start: 0.7988 (tmm) cc_final: 0.7625 (tmm) REVERT: A 579 CYS cc_start: 0.7645 (t) cc_final: 0.7326 (t) REVERT: A 849 MET cc_start: 0.7750 (mpp) cc_final: 0.7218 (mpp) REVERT: A 1031 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7002 (mtp85) REVERT: A 1662 GLU cc_start: 0.7216 (mm-30) cc_final: 0.6963 (mm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2741 time to fit residues: 61.1036 Evaluate side-chains 98 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 12 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 157 optimal weight: 0.3980 chunk 99 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.089692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073547 restraints weight = 62607.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.075352 restraints weight = 37655.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.076410 restraints weight = 26466.623| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15376 Z= 0.118 Angle : 0.605 8.388 21303 Z= 0.301 Chirality : 0.040 0.295 2477 Planarity : 0.004 0.042 2337 Dihedral : 16.453 84.748 3318 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.22), residues: 1549 helix: 0.04 (0.20), residues: 695 sheet: -1.34 (0.38), residues: 159 loop : -1.00 (0.25), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1634 HIS 0.003 0.001 HIS A1519 PHE 0.017 0.001 PHE A 49 TYR 0.016 0.001 TYR A 705 ARG 0.010 0.000 ARG A1330 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 635) hydrogen bonds : angle 4.63342 ( 1713) covalent geometry : bond 0.00257 (15376) covalent geometry : angle 0.60474 (21303) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4602.54 seconds wall clock time: 85 minutes 25.75 seconds (5125.75 seconds total)