Starting phenix.real_space_refine on Tue Mar 3 21:40:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kzo_0791/03_2026/6kzo_0791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kzo_0791/03_2026/6kzo_0791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6kzo_0791/03_2026/6kzo_0791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kzo_0791/03_2026/6kzo_0791_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kzo_0791/03_2026/6kzo_0791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kzo_0791/03_2026/6kzo_0791.map" } resolution = 3.3 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= 0.000 sd= 0.003 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 Ca 2 9.91 5 P 7 5.49 5 S 64 5.16 5 C 5503 2.51 5 N 1260 2.21 5 O 1402 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 7739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 967, 7739 Classifications: {'peptide': 967} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 28, 'TRANS': 938} Chain breaks: 12 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 499 Unusual residues: {' CA': 2, '3PE': 13, 'NAG': 5, 'Y01': 2} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 311 Unresolved non-hydrogen angles: 352 Unresolved non-hydrogen dihedrals: 327 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'3PE:plan-1': 6, '3PE:plan-2': 6} Unresolved non-hydrogen planarities: 37 Time building chain proxies: 2.12, per 1000 atoms: 0.26 Number of scatterers: 8238 At special positions: 0 Unit cell: (111.282, 121.101, 97.099, 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) Ca 2 19.99 S 64 16.00 P 7 15.00 O 1402 8.00 N 1260 7.00 C 5503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 104 " - pdb=" SG CYS A 889 " distance=1.95 Simple disulfide: pdb=" SG CYS A 271 " - pdb=" SG CYS A 282 " distance=1.91 Simple disulfide: pdb=" SG CYS A1418 " - pdb=" SG CYS A1432 " distance=2.02 Simple disulfide: pdb=" SG CYS A1747 " - pdb=" SG CYS A1753 " distance=2.02 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 Links applied NAG-ASN " NAG A2303 " - " ASN A 246 " " NAG A2304 " - " ASN A 322 " " NAG A2305 " - " ASN A1425 " " NAG A2306 " - " ASN A1428 " " NAG A2307 " - " ASN A1675 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 294.3 milliseconds 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 2 sheets defined 76.1% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 82 through 100 removed outlier: 3.695A pdb=" N ILE A 86 " --> pdb=" O TRP A 82 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER A 87 " --> pdb=" O PHE A 83 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 138 removed outlier: 3.554A pdb=" N ASP A 122 " --> pdb=" O GLN A 118 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 168 removed outlier: 3.506A pdb=" N LEU A 155 " --> pdb=" O THR A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.781A pdb=" N VAL A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 178 through 182' Processing helix chain 'A' and resid 183 through 188 Proline residue: A 187 - end of helix Processing helix chain 'A' and resid 189 through 194 removed outlier: 4.080A pdb=" N ARG A 193 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.917A pdb=" N LEU A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 233 removed outlier: 3.503A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL A 230 " --> pdb=" O GLY A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 3.744A pdb=" N GLN A 318 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 320 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 352 removed outlier: 3.611A pdb=" N TRP A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE A 345 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 367 removed outlier: 3.904A pdb=" N ILE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 382 removed outlier: 3.705A pdb=" N PHE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 removed outlier: 3.575A pdb=" N GLN A 397 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 761 removed outlier: 3.611A pdb=" N ILE A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 794 removed outlier: 4.039A pdb=" N GLU A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 805 removed outlier: 3.662A pdb=" N ILE A 803 " --> pdb=" O PRO A 799 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS A 804 " --> pdb=" O PHE A 800 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ASN A 805 " --> pdb=" O GLY A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 820 removed outlier: 3.805A pdb=" N ILE A 809 " --> pdb=" O ASN A 805 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE A 810 " --> pdb=" O PRO A 806 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY A 812 " --> pdb=" O ASN A 808 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 814 " --> pdb=" O PHE A 810 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL A 815 " --> pdb=" O ASP A 811 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP A 820 " --> pdb=" O VAL A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 837 removed outlier: 3.652A pdb=" N ARG A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 847 removed outlier: 3.905A pdb=" N VAL A 841 " --> pdb=" O LEU A 838 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS A 843 " --> pdb=" O ARG A 840 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ARG A 846 " --> pdb=" O LYS A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 861 removed outlier: 3.525A pdb=" N VAL A 856 " --> pdb=" O GLN A 852 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N THR A 861 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 887 removed outlier: 3.879A pdb=" N THR A 867 " --> pdb=" O ASP A 863 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N PHE A 868 " --> pdb=" O ASN A 864 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 874 " --> pdb=" O MET A 870 " (cutoff:3.500A) WARNING: missing atoms! removed outlier: 3.577A pdb=" N MET A 884 " --> pdb=" O SER A 880 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 921 removed outlier: 3.593A pdb=" N VAL A 914 " --> pdb=" O LEU A 910 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N THR A 915 " --> pdb=" O TRP A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 936 removed outlier: 4.002A pdb=" N VAL A 928 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASN A 931 " --> pdb=" O LYS A 927 " (cutoff:3.500A) Processing helix chain 'A' and resid 937 through 939 No H-bonds generated for 'chain 'A' and resid 937 through 939' Processing helix chain 'A' and resid 940 through 967 removed outlier: 4.120A pdb=" N PHE A 944 " --> pdb=" O ALA A 940 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 958 " --> pdb=" O VAL A 954 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 959 " --> pdb=" O LEU A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1273 removed outlier: 3.707A pdb=" N ILE A1262 " --> pdb=" O VAL A1258 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE A1268 " --> pdb=" O PHE A1264 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR A1269 " --> pdb=" O LEU A1265 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1310 removed outlier: 3.957A pdb=" N ILE A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A1308 " --> pdb=" O VAL A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1322 through 1342 removed outlier: 3.675A pdb=" N LEU A1326 " --> pdb=" O SER A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1345 No H-bonds generated for 'chain 'A' and resid 1343 through 1345' Processing helix chain 'A' and resid 1351 through 1361 Processing helix chain 'A' and resid 1362 through 1365 Proline residue: A1365 - end of helix No H-bonds generated for 'chain 'A' and resid 1362 through 1365' Processing helix chain 'A' and resid 1366 through 1372 removed outlier: 4.216A pdb=" N SER A1370 " --> pdb=" O LEU A1366 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A1371 " --> pdb=" O ARG A1367 " (cutoff:3.500A) Processing helix chain 'A' and resid 1372 through 1387 removed outlier: 3.520A pdb=" N VAL A1378 " --> pdb=" O GLY A1374 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N MET A1383 " --> pdb=" O VAL A1379 " (cutoff:3.500A) Processing helix chain 'A' and resid 1389 through 1411 removed outlier: 3.591A pdb=" N VAL A1394 " --> pdb=" O GLY A1390 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1395 " --> pdb=" O ASN A1391 " (cutoff:3.500A) Processing helix chain 'A' and resid 1428 through 1433 Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 3.890A pdb=" N MET A1454 " --> pdb=" O GLY A1450 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A1457 " --> pdb=" O LEU A1453 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A1459 " --> pdb=" O SER A1455 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA A1460 " --> pdb=" O LEU A1456 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1474 removed outlier: 3.533A pdb=" N ILE A1468 " --> pdb=" O GLY A1464 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP A1471 " --> pdb=" O ASP A1467 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1489 No H-bonds generated for 'chain 'A' and resid 1487 through 1489' Processing helix chain 'A' and resid 1490 through 1518 removed outlier: 3.570A pdb=" N PHE A1494 " --> pdb=" O MET A1490 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A1496 " --> pdb=" O LEU A1492 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A1497 " --> pdb=" O TYR A1493 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE A1500 " --> pdb=" O SER A1496 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE A1503 " --> pdb=" O LEU A1499 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASN A1516 " --> pdb=" O VAL A1512 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A1517 " --> pdb=" O VAL A1513 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N HIS A1518 " --> pdb=" O VAL A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1592 through 1606 removed outlier: 3.677A pdb=" N GLY A1596 " --> pdb=" O LEU A1592 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1638 removed outlier: 3.698A pdb=" N ILE A1626 " --> pdb=" O ILE A1622 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL A1629 " --> pdb=" O TYR A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1654 through 1676 removed outlier: 3.618A pdb=" N THR A1668 " --> pdb=" O ILE A1664 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU A1673 " --> pdb=" O LEU A1669 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A1674 " --> pdb=" O GLU A1670 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN A1675 " --> pdb=" O GLU A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1681 through 1691 removed outlier: 3.703A pdb=" N ILE A1685 " --> pdb=" O ASN A1681 " (cutoff:3.500A) Processing helix chain 'A' and resid 1692 through 1701 Processing helix chain 'A' and resid 1703 through 1716 removed outlier: 3.579A pdb=" N ARG A1707 " --> pdb=" O ALA A1703 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A1712 " --> pdb=" O ALA A1708 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL A1713 " --> pdb=" O LEU A1709 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET A1714 " --> pdb=" O LEU A1710 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A1716 " --> pdb=" O THR A1712 " (cutoff:3.500A) Processing helix chain 'A' and resid 1716 through 1742 removed outlier: 3.654A pdb=" N GLU A1740 " --> pdb=" O ALA A1736 " (cutoff:3.500A) Processing helix chain 'A' and resid 1766 through 1778 removed outlier: 3.872A pdb=" N LEU A1772 " --> pdb=" O ALA A1768 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE A1773 " --> pdb=" O PHE A1769 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG A1774 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A1776 " --> pdb=" O LEU A1772 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1787 removed outlier: 3.609A pdb=" N ILE A1784 " --> pdb=" O ASN A1780 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP A1787 " --> pdb=" O GLY A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1802 through 1837 removed outlier: 3.577A pdb=" N ILE A1806 " --> pdb=" O VAL A1802 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL A1812 " --> pdb=" O PHE A1808 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A1817 " --> pdb=" O LEU A1813 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A1823 " --> pdb=" O LEU A1819 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A1825 " --> pdb=" O ASN A1821 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS A1829 " --> pdb=" O ALA A1825 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU A1833 " --> pdb=" O LYS A1829 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A1834 " --> pdb=" O HIS A1830 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN A1835 " --> pdb=" O LEU A1831 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS A1836 " --> pdb=" O GLU A1832 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLU A1837 " --> pdb=" O GLU A1833 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 240 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 1416 through 1419 444 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.35 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1227 1.31 - 1.43: 2186 1.43 - 1.56: 4835 1.56 - 1.68: 34 1.68 - 1.81: 112 Bond restraints: 8394 Sorted by residual: bond pdb=" CAI Y01 A2321 " pdb=" CAZ Y01 A2321 " ideal model delta sigma weight residual 1.332 1.690 -0.358 2.00e-02 2.50e+03 3.21e+02 bond pdb=" CAI Y01 A2322 " pdb=" CAZ Y01 A2322 " ideal model delta sigma weight residual 1.332 1.688 -0.356 2.00e-02 2.50e+03 3.17e+02 bond pdb=" CAP Y01 A2321 " pdb=" CAQ Y01 A2321 " ideal model delta sigma weight residual 1.541 1.726 -0.185 2.00e-02 2.50e+03 8.52e+01 bond pdb=" CAP Y01 A2322 " pdb=" CAQ Y01 A2322 " ideal model delta sigma weight residual 1.541 1.723 -0.182 2.00e-02 2.50e+03 8.31e+01 bond pdb=" C21 3PE A2312 " pdb=" O21 3PE A2312 " ideal model delta sigma weight residual 1.316 1.465 -0.149 2.00e-02 2.50e+03 5.57e+01 ... (remaining 8389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 10335 2.27 - 4.53: 765 4.53 - 6.80: 141 6.80 - 9.07: 39 9.07 - 11.34: 13 Bond angle restraints: 11293 Sorted by residual: angle pdb=" N ALA A 334 " pdb=" CA ALA A 334 " pdb=" C ALA A 334 " ideal model delta sigma weight residual 111.36 122.16 -10.80 1.09e+00 8.42e-01 9.82e+01 angle pdb=" N VAL A1674 " pdb=" CA VAL A1674 " pdb=" C VAL A1674 " ideal model delta sigma weight residual 110.53 117.74 -7.21 9.40e-01 1.13e+00 5.89e+01 angle pdb=" N ASP A1447 " pdb=" CA ASP A1447 " pdb=" C ASP A1447 " ideal model delta sigma weight residual 111.14 119.16 -8.02 1.08e+00 8.57e-01 5.51e+01 angle pdb=" N GLU A 256 " pdb=" CA GLU A 256 " pdb=" C GLU A 256 " ideal model delta sigma weight residual 111.28 119.25 -7.97 1.09e+00 8.42e-01 5.35e+01 angle pdb=" N GLU A 327 " pdb=" CA GLU A 327 " pdb=" C GLU A 327 " ideal model delta sigma weight residual 111.28 119.13 -7.85 1.09e+00 8.42e-01 5.18e+01 ... (remaining 11288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.82: 4908 27.82 - 55.63: 277 55.63 - 83.45: 30 83.45 - 111.27: 9 111.27 - 139.08: 3 Dihedral angle restraints: 5227 sinusoidal: 2415 harmonic: 2812 Sorted by residual: dihedral pdb=" CB CYS A 271 " pdb=" SG CYS A 271 " pdb=" SG CYS A 282 " pdb=" CB CYS A 282 " ideal model delta sinusoidal sigma weight residual -86.00 -173.82 87.82 1 1.00e+01 1.00e-02 9.23e+01 dihedral pdb=" CB CYS A1747 " pdb=" SG CYS A1747 " pdb=" SG CYS A1753 " pdb=" CB CYS A1753 " ideal model delta sinusoidal sigma weight residual 93.00 139.61 -46.61 1 1.00e+01 1.00e-02 3.00e+01 dihedral pdb=" CA ASP A1787 " pdb=" C ASP A1787 " pdb=" N THR A1788 " pdb=" CA THR A1788 " ideal model delta harmonic sigma weight residual 180.00 154.26 25.74 0 5.00e+00 4.00e-02 2.65e+01 ... (remaining 5224 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.261: 1290 0.261 - 0.522: 22 0.522 - 0.783: 2 0.783 - 1.044: 1 1.044 - 1.304: 2 Chirality restraints: 1317 Sorted by residual: chirality pdb=" C1 NAG A2305 " pdb=" ND2 ASN A1425 " pdb=" C2 NAG A2305 " pdb=" O5 NAG A2305 " both_signs ideal model delta sigma weight residual False -2.40 -1.10 -1.30 2.00e-01 2.50e+01 4.25e+01 chirality pdb=" C1 NAG A2307 " pdb=" ND2 ASN A1675 " pdb=" C2 NAG A2307 " pdb=" O5 NAG A2307 " both_signs ideal model delta sigma weight residual False -2.40 -1.32 -1.08 2.00e-01 2.50e+01 2.93e+01 chirality pdb=" C1 NAG A2306 " pdb=" ND2 ASN A1428 " pdb=" C2 NAG A2306 " pdb=" O5 NAG A2306 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 1314 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1428 " -0.014 2.00e-02 2.50e+03 3.12e-01 1.21e+03 pdb=" CG ASN A1428 " -0.087 2.00e-02 2.50e+03 pdb=" OD1 ASN A1428 " 0.263 2.00e-02 2.50e+03 pdb=" ND2 ASN A1428 " -0.526 2.00e-02 2.50e+03 pdb=" C1 NAG A2306 " 0.363 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1425 " -0.203 2.00e-02 2.50e+03 2.14e-01 5.73e+02 pdb=" CG ASN A1425 " 0.090 2.00e-02 2.50e+03 pdb=" OD1 ASN A1425 " 0.071 2.00e-02 2.50e+03 pdb=" ND2 ASN A1425 " 0.316 2.00e-02 2.50e+03 pdb=" C1 NAG A2305 " -0.274 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2306 " -0.204 2.00e-02 2.50e+03 1.74e-01 3.79e+02 pdb=" C7 NAG A2306 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG A2306 " 0.034 2.00e-02 2.50e+03 pdb=" N2 NAG A2306 " 0.287 2.00e-02 2.50e+03 pdb=" O7 NAG A2306 " -0.158 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1065 2.74 - 3.28: 8442 3.28 - 3.82: 12205 3.82 - 4.36: 15371 4.36 - 4.90: 25841 Nonbonded interactions: 62924 Sorted by model distance: nonbonded pdb=" OD1 ASN A 213 " pdb=" C GLY A1705 " model vdw 2.196 3.270 nonbonded pdb=" N ASP A 907 " pdb=" OD1 ASP A 907 " model vdw 2.205 3.120 nonbonded pdb=" OD1 ASN A1425 " pdb=" O5 NAG A2305 " model vdw 2.215 3.040 nonbonded pdb=" OD1 ASN A 213 " pdb=" N MET A1706 " model vdw 2.246 3.120 nonbonded pdb=" O LEU A1710 " pdb=" CG1 VAL A1713 " model vdw 2.278 3.460 ... (remaining 62919 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.190 Set stop_for_unknowns flag: 0.010 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.160 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.014 0.358 8403 Z= 0.726 Angle : 1.570 33.644 11316 Z= 0.884 Chirality : 0.104 1.304 1317 Planarity : 0.011 0.174 1340 Dihedral : 16.980 139.084 3383 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 36.80 Ramachandran Plot: Outliers : 0.74 % Allowed : 3.29 % Favored : 95.96 % Rotamer: Outliers : 9.01 % Allowed : 12.98 % Favored : 78.01 % Cbeta Deviations : 0.33 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.27), residues: 941 helix: -0.54 (0.20), residues: 685 sheet: 0.10 (1.60), residues: 10 loop : -1.47 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1774 TYR 0.028 0.003 TYR A 258 PHE 0.029 0.003 PHE A1731 TRP 0.034 0.004 TRP A 233 HIS 0.007 0.002 HIS A1609 Details of bonding type rmsd covalent geometry : bond 0.01431 ( 8394) covalent geometry : angle 1.41452 (11293) SS BOND : bond 0.07350 ( 4) SS BOND : angle 16.89049 ( 8) hydrogen bonds : bond 0.31592 ( 444) hydrogen bonds : angle 8.92876 ( 1284) link_NAG-ASN : bond 0.04269 ( 5) link_NAG-ASN : angle 14.15828 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 199 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 ARG cc_start: 0.7721 (ttm110) cc_final: 0.6594 (mmt180) REVERT: A 283 ARG cc_start: 0.6676 (OUTLIER) cc_final: 0.5640 (ptp-170) REVERT: A 364 MET cc_start: 0.8800 (mtt) cc_final: 0.8460 (mtm) REVERT: A 759 SER cc_start: 0.9109 (OUTLIER) cc_final: 0.8840 (t) REVERT: A 833 LEU cc_start: 0.8904 (mt) cc_final: 0.8565 (pt) REVERT: A 862 MET cc_start: 0.8026 (mmm) cc_final: 0.7807 (tpp) REVERT: A 864 ASN cc_start: 0.8311 (OUTLIER) cc_final: 0.7721 (m-40) REVERT: A 1324 ASN cc_start: 0.8337 (OUTLIER) cc_final: 0.7193 (t0) REVERT: A 1355 ARG cc_start: 0.7714 (mtt180) cc_final: 0.7170 (ttp-170) REVERT: A 1506 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8438 (tp) REVERT: A 1515 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7205 (tp30) REVERT: A 1701 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.7051 (mmtp) REVERT: A 1714 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.7506 (tmm) REVERT: A 1831 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7513 (tm) outliers start: 77 outliers final: 39 residues processed: 264 average time/residue: 0.0881 time to fit residues: 31.9640 Evaluate side-chains 189 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 141 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 115 ARG Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 202 THR Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 271 CYS Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 759 SER Chi-restraints excluded: chain A residue 764 TYR Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 780 ILE Chi-restraints excluded: chain A residue 864 ASN Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 907 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1324 ASN Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1411 PHE Chi-restraints excluded: chain A residue 1445 ASN Chi-restraints excluded: chain A residue 1462 LYS Chi-restraints excluded: chain A residue 1463 ASP Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1620 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1712 THR Chi-restraints excluded: chain A residue 1714 MET Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1828 MET Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 ASN A 349 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 397 GLN A 773 ASN A 852 GLN A 952 ASN A1266 ASN A1291 ASN A1324 ASN A1409 GLN A1445 ASN A1481 GLN A1486 HIS A1516 ASN A1722 ASN A1780 ASN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.114988 restraints weight = 12278.912| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.80 r_work: 0.3236 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8403 Z= 0.181 Angle : 0.764 11.569 11316 Z= 0.371 Chirality : 0.047 0.400 1317 Planarity : 0.007 0.072 1340 Dihedral : 13.873 89.771 1697 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 5.61 % Allowed : 17.54 % Favored : 76.84 % 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: -0.35 (0.27), residues: 941 helix: 0.25 (0.20), residues: 680 sheet: -2.14 (0.95), residues: 22 loop : -1.15 (0.38), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1358 TYR 0.013 0.002 TYR A 258 PHE 0.022 0.002 PHE A 875 TRP 0.025 0.002 TRP A1439 HIS 0.004 0.001 HIS A 885 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 8394) covalent geometry : angle 0.73339 (11293) SS BOND : bond 0.00225 ( 4) SS BOND : angle 2.33913 ( 8) hydrogen bonds : bond 0.06866 ( 444) hydrogen bonds : angle 4.63018 ( 1284) link_NAG-ASN : bond 0.01155 ( 5) link_NAG-ASN : angle 5.73001 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 178 time to evaluate : 0.227 Fit side-chains REVERT: A 154 ARG cc_start: 0.7917 (ttm110) cc_final: 0.6414 (mmt180) REVERT: A 833 LEU cc_start: 0.8938 (mt) cc_final: 0.8633 (pt) REVERT: A 836 PHE cc_start: 0.8674 (OUTLIER) cc_final: 0.8293 (t80) REVERT: A 873 MET cc_start: 0.8783 (mmm) cc_final: 0.8435 (mmm) REVERT: A 1380 GLU cc_start: 0.8154 (tp30) cc_final: 0.7856 (tp30) REVERT: A 1470 TYR cc_start: 0.8795 (m-10) cc_final: 0.8264 (m-10) REVERT: A 1500 ILE cc_start: 0.8805 (pt) cc_final: 0.8585 (mt) REVERT: A 1515 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7763 (tp30) REVERT: A 1701 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.6951 (mmtp) REVERT: A 1714 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7783 (tmm) REVERT: A 1763 ARG cc_start: 0.8903 (ptt180) cc_final: 0.8656 (ptt90) REVERT: A 1824 ILE cc_start: 0.8967 (pt) cc_final: 0.8591 (mt) outliers start: 48 outliers final: 28 residues processed: 212 average time/residue: 0.0766 time to fit residues: 23.0554 Evaluate side-chains 179 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 147 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 870 MET Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1462 LYS Chi-restraints excluded: chain A residue 1463 ASP Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1714 MET Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 854 GLN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114569 restraints weight = 12223.040| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.83 r_work: 0.3230 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8403 Z= 0.144 Angle : 0.712 16.266 11316 Z= 0.334 Chirality : 0.046 0.457 1317 Planarity : 0.005 0.061 1340 Dihedral : 13.050 88.040 1642 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Rotamer: Outliers : 5.61 % Allowed : 19.30 % Favored : 75.09 % 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: 0.16 (0.27), residues: 941 helix: 0.69 (0.20), residues: 678 sheet: -2.41 (0.94), residues: 22 loop : -1.11 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.016 0.001 TYR A 764 PHE 0.019 0.001 PHE A 385 TRP 0.015 0.001 TRP A1439 HIS 0.003 0.001 HIS A1830 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8394) covalent geometry : angle 0.67162 (11293) SS BOND : bond 0.00199 ( 4) SS BOND : angle 1.70947 ( 8) hydrogen bonds : bond 0.05343 ( 444) hydrogen bonds : angle 4.22067 ( 1284) link_NAG-ASN : bond 0.01214 ( 5) link_NAG-ASN : angle 6.39152 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 162 time to evaluate : 0.306 Fit side-chains REVERT: A 154 ARG cc_start: 0.7819 (ttm110) cc_final: 0.6580 (mmt-90) REVERT: A 197 MET cc_start: 0.8897 (mmm) cc_final: 0.8631 (mpp) REVERT: A 833 LEU cc_start: 0.8991 (mt) cc_final: 0.8637 (pt) REVERT: A 836 PHE cc_start: 0.8717 (OUTLIER) cc_final: 0.8305 (t80) REVERT: A 1254 MET cc_start: 0.7759 (tpp) cc_final: 0.7543 (tpp) REVERT: A 1355 ARG cc_start: 0.7838 (mtt180) cc_final: 0.7422 (mtp85) REVERT: A 1380 GLU cc_start: 0.8080 (tp30) cc_final: 0.7708 (tp30) REVERT: A 1431 ASP cc_start: 0.8516 (t0) cc_final: 0.8190 (t0) REVERT: A 1470 TYR cc_start: 0.8768 (m-10) cc_final: 0.8339 (m-10) REVERT: A 1515 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: A 1701 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.7143 (mmtp) REVERT: A 1717 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7399 (tp) REVERT: A 1763 ARG cc_start: 0.8870 (ptt180) cc_final: 0.8616 (ptt90) REVERT: A 1831 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7286 (mt) outliers start: 48 outliers final: 29 residues processed: 193 average time/residue: 0.0696 time to fit residues: 20.0791 Evaluate side-chains 181 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1462 LYS Chi-restraints excluded: chain A residue 1463 ASP Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1657 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1717 LEU Chi-restraints excluded: chain A residue 1723 LEU Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1826 VAL Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 31 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 18 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 70 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A1653 ASN A1816 GLN ** A1830 HIS ** 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 = 0.3689 r_free = 0.3689 target = 0.139378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.116281 restraints weight = 12419.572| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.79 r_work: 0.3249 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8403 Z= 0.124 Angle : 0.636 11.256 11316 Z= 0.300 Chirality : 0.043 0.321 1317 Planarity : 0.004 0.056 1340 Dihedral : 12.045 87.984 1633 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.87 % Favored : 97.02 % Rotamer: Outliers : 4.91 % Allowed : 21.75 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.28), residues: 941 helix: 1.04 (0.20), residues: 685 sheet: -2.39 (0.91), residues: 22 loop : -1.12 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.013 0.001 TYR A 764 PHE 0.024 0.001 PHE A 875 TRP 0.012 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8394) covalent geometry : angle 0.61073 (11293) SS BOND : bond 0.00306 ( 4) SS BOND : angle 1.56860 ( 8) hydrogen bonds : bond 0.04383 ( 444) hydrogen bonds : angle 3.95822 ( 1284) link_NAG-ASN : bond 0.00591 ( 5) link_NAG-ASN : angle 4.83968 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 155 time to evaluate : 0.316 Fit side-chains REVERT: A 115 ARG cc_start: 0.7514 (tpp-160) cc_final: 0.7237 (mmp80) REVERT: A 154 ARG cc_start: 0.7704 (ttm110) cc_final: 0.6225 (mmt180) REVERT: A 208 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8671 (mm) REVERT: A 751 ILE cc_start: 0.8546 (mm) cc_final: 0.8087 (mp) REVERT: A 833 LEU cc_start: 0.8952 (mt) cc_final: 0.8603 (pt) REVERT: A 836 PHE cc_start: 0.8699 (OUTLIER) cc_final: 0.8288 (t80) REVERT: A 1254 MET cc_start: 0.7960 (tpp) cc_final: 0.7638 (tpp) REVERT: A 1380 GLU cc_start: 0.8366 (tp30) cc_final: 0.8153 (tp30) REVERT: A 1470 TYR cc_start: 0.8758 (m-10) cc_final: 0.8410 (m-10) REVERT: A 1515 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: A 1661 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7856 (mt) REVERT: A 1701 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.7231 (mmtp) REVERT: A 1763 ARG cc_start: 0.8794 (ptt180) cc_final: 0.8529 (ptt90) REVERT: A 1831 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7439 (mt) outliers start: 42 outliers final: 19 residues processed: 182 average time/residue: 0.0741 time to fit residues: 19.8696 Evaluate side-chains 173 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 836 PHE Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1515 GLU Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 47 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 81 optimal weight: 0.9980 chunk 39 optimal weight: 0.1980 chunk 84 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 349 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.139511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.115251 restraints weight = 12391.060| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.88 r_work: 0.3249 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8403 Z= 0.129 Angle : 0.637 10.471 11316 Z= 0.299 Chirality : 0.042 0.309 1317 Planarity : 0.004 0.054 1340 Dihedral : 11.474 87.800 1623 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 5.85 % Allowed : 21.17 % Favored : 72.98 % 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: 0.90 (0.28), residues: 941 helix: 1.23 (0.20), residues: 685 sheet: -2.79 (1.39), residues: 12 loop : -0.93 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 189 TYR 0.012 0.001 TYR A1807 PHE 0.023 0.001 PHE A 875 TRP 0.008 0.001 TRP A 911 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8394) covalent geometry : angle 0.61447 (11293) SS BOND : bond 0.00284 ( 4) SS BOND : angle 1.40772 ( 8) hydrogen bonds : bond 0.04239 ( 444) hydrogen bonds : angle 3.89268 ( 1284) link_NAG-ASN : bond 0.00463 ( 5) link_NAG-ASN : angle 4.51925 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 154 time to evaluate : 0.292 Fit side-chains REVERT: A 154 ARG cc_start: 0.7748 (ttm110) cc_final: 0.6221 (mmt180) REVERT: A 197 MET cc_start: 0.8941 (mmm) cc_final: 0.8631 (mpp) REVERT: A 793 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8489 (mmmm) REVERT: A 833 LEU cc_start: 0.8969 (mt) cc_final: 0.8585 (pt) REVERT: A 1254 MET cc_start: 0.7845 (tpp) cc_final: 0.7474 (tpp) REVERT: A 1380 GLU cc_start: 0.8395 (tp30) cc_final: 0.8182 (tp30) REVERT: A 1406 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8696 (tt) REVERT: A 1470 TYR cc_start: 0.8774 (m-10) cc_final: 0.8456 (m-10) REVERT: A 1515 GLU cc_start: 0.8136 (pp20) cc_final: 0.7839 (tp30) REVERT: A 1661 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7918 (mt) REVERT: A 1701 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.7162 (mmtp) REVERT: A 1763 ARG cc_start: 0.8804 (ptt180) cc_final: 0.8526 (ptt90) REVERT: A 1831 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7499 (mt) outliers start: 50 outliers final: 28 residues processed: 188 average time/residue: 0.0753 time to fit residues: 20.7721 Evaluate side-chains 182 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 848 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 887 PHE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.115496 restraints weight = 12197.580| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.87 r_work: 0.3265 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8403 Z= 0.133 Angle : 0.650 11.236 11316 Z= 0.302 Chirality : 0.042 0.303 1317 Planarity : 0.004 0.051 1340 Dihedral : 11.308 87.164 1620 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 5.03 % Allowed : 21.99 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.28), residues: 941 helix: 1.28 (0.20), residues: 691 sheet: -2.43 (0.97), residues: 22 loop : -0.79 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1695 TYR 0.012 0.001 TYR A 258 PHE 0.024 0.001 PHE A 875 TRP 0.008 0.001 TRP A 911 HIS 0.002 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 8394) covalent geometry : angle 0.62974 (11293) SS BOND : bond 0.00894 ( 4) SS BOND : angle 2.42572 ( 8) hydrogen bonds : bond 0.04161 ( 444) hydrogen bonds : angle 3.85234 ( 1284) link_NAG-ASN : bond 0.00474 ( 5) link_NAG-ASN : angle 4.12160 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 152 time to evaluate : 0.282 Fit side-chains REVERT: A 154 ARG cc_start: 0.7730 (ttm110) cc_final: 0.6282 (mmt180) REVERT: A 763 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7824 (mm-30) REVERT: A 793 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8491 (mmmm) REVERT: A 833 LEU cc_start: 0.8951 (mt) cc_final: 0.8581 (pt) REVERT: A 873 MET cc_start: 0.8759 (mmm) cc_final: 0.8417 (mmm) REVERT: A 1380 GLU cc_start: 0.8375 (tp30) cc_final: 0.8148 (tp30) REVERT: A 1406 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 1470 TYR cc_start: 0.8787 (m-10) cc_final: 0.8446 (m-10) REVERT: A 1515 GLU cc_start: 0.8218 (pp20) cc_final: 0.7870 (tp30) REVERT: A 1661 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7941 (mt) REVERT: A 1701 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.7161 (mmtp) REVERT: A 1763 ARG cc_start: 0.8802 (ptt180) cc_final: 0.8542 (ptt90) REVERT: A 1831 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7517 (mt) outliers start: 43 outliers final: 27 residues processed: 179 average time/residue: 0.0730 time to fit residues: 19.4002 Evaluate side-chains 179 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1600 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 70 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 51 optimal weight: 0.0010 chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 45 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A1816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.138800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114583 restraints weight = 12305.523| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 1.99 r_work: 0.3255 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8403 Z= 0.126 Angle : 0.649 12.143 11316 Z= 0.304 Chirality : 0.042 0.294 1317 Planarity : 0.004 0.050 1340 Dihedral : 11.106 86.082 1616 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 4.44 % Allowed : 23.16 % Favored : 72.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.28), residues: 941 helix: 1.36 (0.20), residues: 690 sheet: -2.45 (1.34), residues: 12 loop : -0.65 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1695 TYR 0.014 0.001 TYR A 361 PHE 0.025 0.001 PHE A 875 TRP 0.015 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8394) covalent geometry : angle 0.63216 (11293) SS BOND : bond 0.00517 ( 4) SS BOND : angle 2.41929 ( 8) hydrogen bonds : bond 0.04030 ( 444) hydrogen bonds : angle 3.89000 ( 1284) link_NAG-ASN : bond 0.00410 ( 5) link_NAG-ASN : angle 3.76028 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 0.194 Fit side-chains REVERT: A 154 ARG cc_start: 0.7586 (ttm110) cc_final: 0.6119 (mmt180) REVERT: A 197 MET cc_start: 0.8988 (mmm) cc_final: 0.8647 (mpp) REVERT: A 763 GLU cc_start: 0.8249 (mm-30) cc_final: 0.7896 (mm-30) REVERT: A 793 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8383 (mmmm) REVERT: A 833 LEU cc_start: 0.8966 (mt) cc_final: 0.8510 (pt) REVERT: A 873 MET cc_start: 0.8729 (mmm) cc_final: 0.8441 (mmm) REVERT: A 965 GLU cc_start: 0.8397 (tt0) cc_final: 0.8191 (tt0) REVERT: A 1380 GLU cc_start: 0.8127 (tp30) cc_final: 0.7915 (tp30) REVERT: A 1406 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8550 (tt) REVERT: A 1437 TYR cc_start: 0.8472 (m-80) cc_final: 0.8246 (m-80) REVERT: A 1470 TYR cc_start: 0.8574 (m-10) cc_final: 0.8333 (m-10) REVERT: A 1515 GLU cc_start: 0.8436 (pp20) cc_final: 0.7833 (tp30) REVERT: A 1661 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 1701 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.6986 (mmtp) REVERT: A 1763 ARG cc_start: 0.8809 (ptt180) cc_final: 0.8501 (ptt90) REVERT: A 1831 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7517 (mt) outliers start: 38 outliers final: 26 residues processed: 173 average time/residue: 0.0758 time to fit residues: 19.2415 Evaluate side-chains 180 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 150 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 33 optimal weight: 4.9990 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 chunk 40 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A1830 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.139405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115113 restraints weight = 12176.936| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.99 r_work: 0.3259 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8403 Z= 0.120 Angle : 0.632 12.506 11316 Z= 0.297 Chirality : 0.041 0.296 1317 Planarity : 0.004 0.049 1340 Dihedral : 10.963 84.616 1614 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 4.44 % Allowed : 23.63 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.40 (0.28), residues: 941 helix: 1.50 (0.20), residues: 690 sheet: -1.92 (1.52), residues: 10 loop : -0.52 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1695 TYR 0.011 0.001 TYR A1807 PHE 0.023 0.001 PHE A 875 TRP 0.010 0.001 TRP A1439 HIS 0.002 0.001 HIS A1830 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8394) covalent geometry : angle 0.61918 (11293) SS BOND : bond 0.00203 ( 4) SS BOND : angle 2.14588 ( 8) hydrogen bonds : bond 0.03883 ( 444) hydrogen bonds : angle 3.82716 ( 1284) link_NAG-ASN : bond 0.00417 ( 5) link_NAG-ASN : angle 3.15212 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.313 Fit side-chains REVERT: A 154 ARG cc_start: 0.7593 (ttm110) cc_final: 0.6009 (mmt180) REVERT: A 197 MET cc_start: 0.9017 (mmm) cc_final: 0.8685 (mpp) REVERT: A 199 ILE cc_start: 0.7988 (mm) cc_final: 0.7604 (mt) REVERT: A 763 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 793 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8404 (mmmm) REVERT: A 833 LEU cc_start: 0.8942 (mt) cc_final: 0.8481 (pt) REVERT: A 873 MET cc_start: 0.8696 (mmm) cc_final: 0.8390 (mmm) REVERT: A 965 GLU cc_start: 0.8394 (tt0) cc_final: 0.8193 (tt0) REVERT: A 1254 MET cc_start: 0.7623 (tpp) cc_final: 0.7153 (tpp) REVERT: A 1361 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.7984 (mtm-85) REVERT: A 1380 GLU cc_start: 0.8119 (tp30) cc_final: 0.7909 (tp30) REVERT: A 1470 TYR cc_start: 0.8628 (m-10) cc_final: 0.8404 (m-10) REVERT: A 1515 GLU cc_start: 0.8404 (pp20) cc_final: 0.7832 (tp30) REVERT: A 1661 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7917 (mt) REVERT: A 1701 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.7103 (mmtp) REVERT: A 1763 ARG cc_start: 0.8798 (ptt180) cc_final: 0.8483 (ptt90) REVERT: A 1831 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7481 (mt) outliers start: 38 outliers final: 25 residues processed: 176 average time/residue: 0.0835 time to fit residues: 21.0870 Evaluate side-chains 179 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1361 ARG Chi-restraints excluded: chain A residue 1366 LEU Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 32 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A1816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.138901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.114473 restraints weight = 12113.195| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.90 r_work: 0.3249 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.4275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8403 Z= 0.145 Angle : 0.656 13.093 11316 Z= 0.310 Chirality : 0.042 0.299 1317 Planarity : 0.004 0.048 1340 Dihedral : 11.042 86.356 1613 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 4.44 % Allowed : 23.51 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.28), residues: 941 helix: 1.46 (0.20), residues: 689 sheet: -2.26 (1.37), residues: 10 loop : -0.62 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1695 TYR 0.013 0.001 TYR A1807 PHE 0.025 0.001 PHE A 875 TRP 0.010 0.001 TRP A1439 HIS 0.004 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8394) covalent geometry : angle 0.64351 (11293) SS BOND : bond 0.00527 ( 4) SS BOND : angle 2.38454 ( 8) hydrogen bonds : bond 0.04068 ( 444) hydrogen bonds : angle 3.86179 ( 1284) link_NAG-ASN : bond 0.00413 ( 5) link_NAG-ASN : angle 3.14167 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.307 Fit side-chains REVERT: A 154 ARG cc_start: 0.7635 (ttm110) cc_final: 0.6178 (mmt180) REVERT: A 763 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7651 (mm-30) REVERT: A 793 LYS cc_start: 0.8779 (mmmm) cc_final: 0.8379 (mmmm) REVERT: A 833 LEU cc_start: 0.8961 (mt) cc_final: 0.8530 (pt) REVERT: A 873 MET cc_start: 0.8691 (mmm) cc_final: 0.8378 (mmm) REVERT: A 1361 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.8075 (mtm-85) REVERT: A 1406 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8713 (tt) REVERT: A 1470 TYR cc_start: 0.8823 (m-10) cc_final: 0.8608 (m-10) REVERT: A 1515 GLU cc_start: 0.8303 (pp20) cc_final: 0.7764 (tp30) REVERT: A 1701 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.7253 (mmtp) REVERT: A 1763 ARG cc_start: 0.8796 (ptt180) cc_final: 0.8506 (ptt90) REVERT: A 1831 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7574 (mt) outliers start: 38 outliers final: 27 residues processed: 167 average time/residue: 0.0803 time to fit residues: 19.3050 Evaluate side-chains 177 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 146 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1361 ARG Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1690 VAL Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1772 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 81 optimal weight: 0.0270 chunk 18 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.140154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.115751 restraints weight = 12062.136| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 1.83 r_work: 0.3265 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8403 Z= 0.132 Angle : 0.659 13.359 11316 Z= 0.310 Chirality : 0.042 0.296 1317 Planarity : 0.004 0.048 1340 Dihedral : 10.978 85.629 1613 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 4.09 % Allowed : 24.09 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.28), residues: 941 helix: 1.48 (0.20), residues: 690 sheet: -2.60 (1.29), residues: 10 loop : -0.57 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 189 TYR 0.011 0.001 TYR A1807 PHE 0.025 0.001 PHE A 875 TRP 0.012 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8394) covalent geometry : angle 0.64793 (11293) SS BOND : bond 0.00300 ( 4) SS BOND : angle 2.36680 ( 8) hydrogen bonds : bond 0.03957 ( 444) hydrogen bonds : angle 3.86762 ( 1284) link_NAG-ASN : bond 0.00419 ( 5) link_NAG-ASN : angle 2.88106 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1882 Ramachandran restraints generated. 941 Oldfield, 0 Emsley, 941 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.294 Fit side-chains REVERT: A 154 ARG cc_start: 0.7639 (ttm110) cc_final: 0.6156 (mmt180) REVERT: A 197 MET cc_start: 0.8906 (mmm) cc_final: 0.8641 (mpp) REVERT: A 763 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 793 LYS cc_start: 0.8788 (mmmm) cc_final: 0.8399 (mmmm) REVERT: A 833 LEU cc_start: 0.8955 (mt) cc_final: 0.8541 (pt) REVERT: A 873 MET cc_start: 0.8698 (mmm) cc_final: 0.8388 (mmm) REVERT: A 1470 TYR cc_start: 0.8813 (m-10) cc_final: 0.8610 (m-10) REVERT: A 1515 GLU cc_start: 0.8239 (pp20) cc_final: 0.7775 (tp30) REVERT: A 1701 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.7283 (mmtp) REVERT: A 1763 ARG cc_start: 0.8780 (ptt180) cc_final: 0.8500 (ptt90) REVERT: A 1831 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7606 (mt) outliers start: 35 outliers final: 28 residues processed: 169 average time/residue: 0.0786 time to fit residues: 19.3505 Evaluate side-chains 177 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASP Chi-restraints excluded: chain A residue 164 MET Chi-restraints excluded: chain A residue 196 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 881 ILE Chi-restraints excluded: chain A residue 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1332 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1375 LEU Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1514 VAL Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 VAL Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1725 LEU Chi-restraints excluded: chain A residue 1772 LEU Chi-restraints excluded: chain A residue 1799 TYR Chi-restraints excluded: chain A residue 1820 VAL Chi-restraints excluded: chain A residue 1831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 72 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 37 optimal weight: 0.0030 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A1816 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.116135 restraints weight = 12145.523| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.96 r_work: 0.3261 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8403 Z= 0.122 Angle : 0.651 12.687 11316 Z= 0.305 Chirality : 0.041 0.293 1317 Planarity : 0.004 0.048 1340 Dihedral : 10.755 84.642 1613 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 3.86 % Allowed : 24.33 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.28), residues: 941 helix: 1.58 (0.20), residues: 691 sheet: -2.94 (1.28), residues: 10 loop : -0.47 (0.40), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1358 TYR 0.011 0.001 TYR A 258 PHE 0.024 0.001 PHE A 875 TRP 0.014 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8394) covalent geometry : angle 0.64182 (11293) SS BOND : bond 0.00321 ( 4) SS BOND : angle 2.10109 ( 8) hydrogen bonds : bond 0.03821 ( 444) hydrogen bonds : angle 3.80458 ( 1284) link_NAG-ASN : bond 0.00388 ( 5) link_NAG-ASN : angle 2.75504 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2202.69 seconds wall clock time: 38 minutes 19.12 seconds (2299.12 seconds total)