Starting phenix.real_space_refine on Thu Feb 13 08:59:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kzo_0791/02_2025/6kzo_0791_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kzo_0791/02_2025/6kzo_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kzo_0791/02_2025/6kzo_0791.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kzo_0791/02_2025/6kzo_0791.map" model { file = "/net/cci-nas-00/data/ceres_data/6kzo_0791/02_2025/6kzo_0791_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kzo_0791/02_2025/6kzo_0791_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.61, per 1000 atoms: 0.68 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: 2.21 Conformation dependent library (CDL) restraints added in 918.9 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: 0.82 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: 2.27 Time building geometry restraints manager: 2.55 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.360 ------------------------------------------------------------------------------- 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 8394 Z= 0.870 Angle : 1.415 11.337 11293 Z= 0.841 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 : 36.78 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.27), 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 TRP 0.034 0.004 TRP A 233 HIS 0.007 0.002 HIS A1609 PHE 0.029 0.003 PHE A1731 TYR 0.028 0.003 TYR A 258 ARG 0.015 0.001 ARG A1774 *********************** 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 : 0.883 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: 0.8564 (pt) REVERT: A 862 MET cc_start: 0.8026 (mmm) cc_final: 0.7808 (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: 0.7052 (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: 0.2071 time to fit residues: 74.3624 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 : 0.880 ------------------------------------------------------------------------------- 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 81 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 397 GLN A 773 ASN A 852 GLN A 854 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.116163 restraints weight = 12182.230| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.78 r_work: 0.3250 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8394 Z= 0.230 Angle : 0.730 11.371 11293 Z= 0.359 Chirality : 0.046 0.403 1317 Planarity : 0.007 0.070 1340 Dihedral : 13.824 89.773 1697 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 5.96 % Allowed : 16.84 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.27), residues: 941 helix: 0.27 (0.20), residues: 678 sheet: -2.16 (0.94), residues: 22 loop : -1.14 (0.38), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1439 HIS 0.005 0.001 HIS A 885 PHE 0.023 0.002 PHE A 875 TYR 0.013 0.002 TYR A 258 ARG 0.005 0.001 ARG A1358 *********************** 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 232 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 181 time to evaluate : 0.915 Fit side-chains REVERT: A 154 ARG cc_start: 0.7897 (ttm110) cc_final: 0.6463 (mmt-90) REVERT: A 833 LEU cc_start: 0.8938 (mt) cc_final: 0.8630 (pt) REVERT: A 836 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.8271 (t80) REVERT: A 873 MET cc_start: 0.8814 (mmm) cc_final: 0.8447 (mmm) REVERT: A 1380 GLU cc_start: 0.8157 (tp30) cc_final: 0.7855 (tp30) REVERT: A 1470 TYR cc_start: 0.8766 (m-10) cc_final: 0.8231 (m-10) REVERT: A 1515 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7760 (tp30) REVERT: A 1699 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8651 (pp) REVERT: A 1701 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.6948 (mmtp) REVERT: A 1714 MET cc_start: 0.8046 (OUTLIER) cc_final: 0.7804 (tmm) REVERT: A 1763 ARG cc_start: 0.8898 (ptt180) cc_final: 0.8646 (ptt90) REVERT: A 1824 ILE cc_start: 0.8931 (pt) cc_final: 0.8619 (mt) REVERT: A 1831 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7292 (mt) outliers start: 51 outliers final: 26 residues processed: 215 average time/residue: 0.1823 time to fit residues: 55.0352 Evaluate side-chains 185 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 153 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 ASP 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 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 848 LEU 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 1384 SER Chi-restraints excluded: chain A residue 1426 ILE 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 1699 LEU 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 69 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3664 r_free = 0.3664 target = 0.137318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.114300 restraints weight = 12435.186| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.79 r_work: 0.3230 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8394 Z= 0.222 Angle : 0.668 13.066 11293 Z= 0.326 Chirality : 0.044 0.364 1317 Planarity : 0.005 0.060 1340 Dihedral : 12.633 87.226 1638 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.81 % Rotamer: Outliers : 5.26 % Allowed : 19.18 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.27), residues: 941 helix: 0.72 (0.20), residues: 678 sheet: -2.41 (0.89), residues: 22 loop : -1.08 (0.40), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1439 HIS 0.003 0.001 HIS A1830 PHE 0.020 0.002 PHE A 385 TYR 0.016 0.001 TYR A 764 ARG 0.005 0.000 ARG A 189 *********************** 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 205 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 0.856 Fit side-chains REVERT: A 115 ARG cc_start: 0.7498 (tpp-160) cc_final: 0.7215 (mmp80) REVERT: A 197 MET cc_start: 0.8919 (mmm) cc_final: 0.8637 (mpp) REVERT: A 833 LEU cc_start: 0.8967 (mt) cc_final: 0.8628 (pt) REVERT: A 836 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.8291 (t80) REVERT: A 863 ASP cc_start: 0.8408 (m-30) cc_final: 0.8179 (m-30) REVERT: A 1254 MET cc_start: 0.7908 (tpp) cc_final: 0.7676 (tpp) REVERT: A 1355 ARG cc_start: 0.7915 (mtt180) cc_final: 0.7535 (mtp85) REVERT: A 1380 GLU cc_start: 0.8137 (tp30) cc_final: 0.7765 (tp30) REVERT: A 1431 ASP cc_start: 0.8484 (t0) cc_final: 0.8208 (t0) REVERT: A 1470 TYR cc_start: 0.8787 (m-10) cc_final: 0.8418 (m-10) REVERT: A 1515 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: A 1701 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.7314 (mmtp) REVERT: A 1763 ARG cc_start: 0.8839 (ptt180) cc_final: 0.8591 (ptt90) REVERT: A 1824 ILE cc_start: 0.8942 (pt) cc_final: 0.8635 (mt) REVERT: A 1828 MET cc_start: 0.8496 (tpp) cc_final: 0.8094 (mpp) REVERT: A 1831 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7249 (mt) outliers start: 45 outliers final: 27 residues processed: 189 average time/residue: 0.1643 time to fit residues: 45.1769 Evaluate side-chains 180 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 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 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 1303 THR Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1384 SER 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 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 56 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 A1816 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.136137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.113439 restraints weight = 12361.601| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.70 r_work: 0.3214 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8394 Z= 0.254 Angle : 0.642 10.166 11293 Z= 0.313 Chirality : 0.045 0.338 1317 Planarity : 0.005 0.055 1340 Dihedral : 12.738 95.559 1629 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.98 % Favored : 96.92 % Rotamer: Outliers : 5.85 % Allowed : 21.29 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 941 helix: 0.90 (0.20), residues: 683 sheet: -2.44 (0.90), residues: 22 loop : -1.24 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1439 HIS 0.004 0.001 HIS A1442 PHE 0.022 0.002 PHE A 875 TYR 0.014 0.002 TYR A1807 ARG 0.004 0.000 ARG A 189 *********************** 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 202 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.913 Fit side-chains REVERT: A 154 ARG cc_start: 0.8006 (mtt90) cc_final: 0.5820 (mmt180) REVERT: A 208 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8746 (mm) REVERT: A 357 VAL cc_start: 0.9067 (OUTLIER) cc_final: 0.8517 (m) REVERT: A 833 LEU cc_start: 0.8935 (mt) cc_final: 0.8616 (pt) REVERT: A 836 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8260 (t80) REVERT: A 1254 MET cc_start: 0.7994 (tpp) cc_final: 0.7720 (tpp) REVERT: A 1355 ARG cc_start: 0.7961 (mtt180) cc_final: 0.7573 (mtp85) REVERT: A 1380 GLU cc_start: 0.8337 (tp30) cc_final: 0.7933 (tp30) REVERT: A 1470 TYR cc_start: 0.8748 (m-10) cc_final: 0.8378 (m-10) REVERT: A 1515 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7874 (tp30) REVERT: A 1701 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.7246 (mmtp) REVERT: A 1763 ARG cc_start: 0.8805 (ptt180) cc_final: 0.8564 (ptt90) REVERT: A 1824 ILE cc_start: 0.8996 (pt) cc_final: 0.8654 (mt) REVERT: A 1828 MET cc_start: 0.8564 (tpp) cc_final: 0.8149 (mpp) REVERT: A 1831 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7455 (mt) outliers start: 50 outliers final: 32 residues processed: 186 average time/residue: 0.1682 time to fit residues: 45.2292 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 : 0.961 ------------------------------------------------------------------------------- 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 208 LEU 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 351 ILE Chi-restraints excluded: chain A residue 357 VAL 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 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 1332 LEU Chi-restraints excluded: chain A residue 1350 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1418 CYS Chi-restraints excluded: chain A residue 1426 ILE 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 1617 ASP Chi-restraints excluded: chain A residue 1629 VAL Chi-restraints excluded: chain A residue 1636 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 5 optimal weight: 0.0040 chunk 67 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3674 r_free = 0.3674 target = 0.138108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.115625 restraints weight = 12062.430| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.67 r_work: 0.3270 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8394 Z= 0.177 Angle : 0.610 9.042 11293 Z= 0.294 Chirality : 0.042 0.320 1317 Planarity : 0.004 0.053 1340 Dihedral : 12.076 89.695 1625 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.19 % Favored : 96.71 % Rotamer: Outliers : 5.50 % Allowed : 21.64 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 941 helix: 1.16 (0.20), residues: 685 sheet: -2.77 (1.33), residues: 12 loop : -1.01 (0.38), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1439 HIS 0.002 0.001 HIS A1830 PHE 0.024 0.001 PHE A 875 TYR 0.010 0.001 TYR A1807 ARG 0.002 0.000 ARG A 189 *********************** 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 199 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 152 time to evaluate : 0.882 Fit side-chains REVERT: A 154 ARG cc_start: 0.8044 (mtt90) cc_final: 0.5772 (mmt180) REVERT: A 197 MET cc_start: 0.8829 (mmm) cc_final: 0.8492 (mpp) REVERT: A 208 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8783 (mm) REVERT: A 357 VAL cc_start: 0.9083 (OUTLIER) cc_final: 0.8695 (m) REVERT: A 833 LEU cc_start: 0.8944 (mt) cc_final: 0.8593 (pt) REVERT: A 873 MET cc_start: 0.8686 (mmm) cc_final: 0.8361 (mmm) REVERT: A 1254 MET cc_start: 0.7894 (tpp) cc_final: 0.7616 (tpp) REVERT: A 1380 GLU cc_start: 0.8330 (tp30) cc_final: 0.8129 (tp30) REVERT: A 1406 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8715 (tt) REVERT: A 1470 TYR cc_start: 0.8733 (m-10) cc_final: 0.8412 (m-10) REVERT: A 1515 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7851 (tp30) REVERT: A 1701 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.7214 (mmtp) REVERT: A 1763 ARG cc_start: 0.8773 (ptt180) cc_final: 0.8518 (ptt180) REVERT: A 1824 ILE cc_start: 0.8908 (pt) cc_final: 0.8702 (mt) REVERT: A 1828 MET cc_start: 0.8522 (tpp) cc_final: 0.8161 (mpp) REVERT: A 1831 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7485 (mt) outliers start: 47 outliers final: 27 residues processed: 184 average time/residue: 0.1598 time to fit residues: 43.2136 Evaluate side-chains 182 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 CYS 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 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 924 ASP Chi-restraints excluded: chain A residue 1265 LEU Chi-restraints excluded: chain A residue 1303 THR Chi-restraints excluded: chain A residue 1339 LEU Chi-restraints excluded: chain A residue 1350 ILE 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 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 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 1723 LEU 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 16 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 70 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 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 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 = 0.3685 r_free = 0.3685 target = 0.137526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113241 restraints weight = 12222.735| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.98 r_work: 0.3229 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8394 Z= 0.222 Angle : 0.630 9.481 11293 Z= 0.301 Chirality : 0.043 0.310 1317 Planarity : 0.004 0.051 1340 Dihedral : 12.152 89.955 1623 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 5.61 % Allowed : 21.87 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.28), residues: 941 helix: 1.19 (0.20), residues: 690 sheet: -2.57 (1.28), residues: 12 loop : -0.87 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 911 HIS 0.003 0.001 HIS A1442 PHE 0.025 0.001 PHE A 875 TYR 0.014 0.001 TYR A1807 ARG 0.005 0.000 ARG A1695 *********************** 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 199 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 151 time to evaluate : 0.884 Fit side-chains REVERT: A 154 ARG cc_start: 0.8008 (mtt90) cc_final: 0.5783 (mmt180) REVERT: A 357 VAL cc_start: 0.8989 (OUTLIER) cc_final: 0.8740 (t) REVERT: A 793 LYS cc_start: 0.8735 (mmmm) cc_final: 0.8399 (mmmm) REVERT: A 833 LEU cc_start: 0.9010 (mt) cc_final: 0.8536 (pt) REVERT: A 873 MET cc_start: 0.8712 (mmm) cc_final: 0.8379 (mmm) REVERT: A 1254 MET cc_start: 0.7653 (tpp) cc_final: 0.7368 (tpp) REVERT: A 1380 GLU cc_start: 0.8118 (tp30) cc_final: 0.7706 (tp30) REVERT: A 1406 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8585 (tt) REVERT: A 1470 TYR cc_start: 0.8558 (m-10) cc_final: 0.8306 (m-10) REVERT: A 1515 GLU cc_start: 0.8447 (pp20) cc_final: 0.7843 (tp30) REVERT: A 1616 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8043 (tp) REVERT: A 1701 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.6986 (mmtp) REVERT: A 1763 ARG cc_start: 0.8828 (ptt180) cc_final: 0.8530 (ptt90) REVERT: A 1824 ILE cc_start: 0.8810 (pt) cc_final: 0.8502 (mt) REVERT: A 1828 MET cc_start: 0.8642 (tpp) cc_final: 0.8194 (tpp) REVERT: A 1831 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7463 (mt) outliers start: 48 outliers final: 29 residues processed: 186 average time/residue: 0.1696 time to fit residues: 45.3534 Evaluate side-chains 185 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 0.828 ------------------------------------------------------------------------------- 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 357 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 784 SER 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 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 1350 ILE 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 1616 LEU 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 1723 LEU 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 72 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 80 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 6 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 = 0.3693 r_free = 0.3693 target = 0.138235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113854 restraints weight = 12198.804| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 2.00 r_work: 0.3223 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8394 Z= 0.199 Angle : 0.635 10.603 11293 Z= 0.301 Chirality : 0.043 0.304 1317 Planarity : 0.004 0.049 1340 Dihedral : 12.042 89.313 1618 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.81 % Rotamer: Outliers : 5.15 % Allowed : 22.46 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.28), residues: 941 helix: 1.30 (0.20), residues: 690 sheet: -2.54 (1.25), residues: 12 loop : -0.76 (0.39), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1439 HIS 0.004 0.001 HIS A1442 PHE 0.024 0.001 PHE A 875 TYR 0.012 0.001 TYR A 258 ARG 0.003 0.000 ARG A 283 *********************** 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 193 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 1.088 Fit side-chains REVERT: A 154 ARG cc_start: 0.7823 (mtt90) cc_final: 0.5645 (mmt180) REVERT: A 197 MET cc_start: 0.8990 (mmm) cc_final: 0.8647 (mpp) REVERT: A 357 VAL cc_start: 0.8971 (OUTLIER) cc_final: 0.8754 (t) REVERT: A 763 GLU cc_start: 0.8343 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 833 LEU cc_start: 0.9006 (mt) cc_final: 0.8534 (pt) REVERT: A 1361 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8054 (mtm-85) REVERT: A 1406 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8578 (tt) REVERT: A 1470 TYR cc_start: 0.8572 (m-10) cc_final: 0.8335 (m-10) REVERT: A 1515 GLU cc_start: 0.8413 (pp20) cc_final: 0.7754 (tp30) REVERT: A 1701 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.7006 (mmtp) REVERT: A 1763 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8516 (ptt90) REVERT: A 1831 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7480 (mt) outliers start: 44 outliers final: 32 residues processed: 178 average time/residue: 0.1847 time to fit residues: 48.0645 Evaluate side-chains 182 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 251 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 784 SER 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 858 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 1339 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 1418 CYS 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 1690 VAL Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1699 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP 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 1831 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3698 r_free = 0.3698 target = 0.138491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114150 restraints weight = 12287.685| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.00 r_work: 0.3243 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8394 Z= 0.181 Angle : 0.623 11.917 11293 Z= 0.294 Chirality : 0.042 0.296 1317 Planarity : 0.004 0.049 1340 Dihedral : 11.746 89.559 1616 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.81 % Rotamer: Outliers : 5.61 % Allowed : 22.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 941 helix: 1.43 (0.20), residues: 690 sheet: -1.99 (1.26), residues: 10 loop : -0.69 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 82 HIS 0.003 0.001 HIS A1442 PHE 0.025 0.001 PHE A 875 TYR 0.010 0.001 TYR A1807 ARG 0.003 0.000 ARG A1695 *********************** 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 201 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 153 time to evaluate : 0.929 Fit side-chains REVERT: A 154 ARG cc_start: 0.7814 (mtt90) cc_final: 0.5601 (mmt180) REVERT: A 197 MET cc_start: 0.9023 (mmm) cc_final: 0.8689 (mpp) REVERT: A 199 ILE cc_start: 0.7997 (mm) cc_final: 0.7606 (mt) REVERT: A 251 LEU cc_start: 0.7267 (OUTLIER) cc_final: 0.6831 (pp) REVERT: A 357 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8548 (m) REVERT: A 754 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7543 (mp) REVERT: A 763 GLU cc_start: 0.8302 (mm-30) cc_final: 0.7995 (mm-30) REVERT: A 833 LEU cc_start: 0.8986 (mt) cc_final: 0.8514 (pt) REVERT: A 834 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8364 (mtp-110) REVERT: A 1254 MET cc_start: 0.7742 (tpp) cc_final: 0.7257 (tpp) REVERT: A 1361 ARG cc_start: 0.8475 (mtm110) cc_final: 0.8097 (mtm-85) REVERT: A 1406 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8572 (tt) REVERT: A 1470 TYR cc_start: 0.8659 (m-10) cc_final: 0.8375 (m-10) REVERT: A 1515 GLU cc_start: 0.8395 (pp20) cc_final: 0.7846 (tp30) REVERT: A 1701 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.7122 (mmtp) REVERT: A 1763 ARG cc_start: 0.8796 (ptt180) cc_final: 0.8477 (ptt90) REVERT: A 1831 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7551 (mt) outliers start: 48 outliers final: 30 residues processed: 186 average time/residue: 0.1830 time to fit residues: 48.4950 Evaluate side-chains 186 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 848 LEU 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 1339 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 1418 CYS 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 1699 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1723 LEU 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 1826 VAL 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 69 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A1653 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.138236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113730 restraints weight = 12387.530| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.89 r_work: 0.3239 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8394 Z= 0.231 Angle : 0.668 12.583 11293 Z= 0.316 Chirality : 0.043 0.293 1317 Planarity : 0.004 0.048 1340 Dihedral : 11.745 89.162 1613 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.29 % Favored : 96.60 % Rotamer: Outliers : 4.80 % Allowed : 23.51 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 941 helix: 1.40 (0.20), residues: 689 sheet: -2.32 (1.17), residues: 10 loop : -0.74 (0.39), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1439 HIS 0.004 0.001 HIS A1442 PHE 0.025 0.001 PHE A 875 TYR 0.013 0.001 TYR A1807 ARG 0.002 0.000 ARG A1695 *********************** 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 189 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 148 time to evaluate : 0.859 Fit side-chains REVERT: A 115 ARG cc_start: 0.7939 (tpp-160) cc_final: 0.7414 (mmp-170) REVERT: A 154 ARG cc_start: 0.7925 (mtt90) cc_final: 0.5675 (mmt180) REVERT: A 763 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7857 (mm-30) REVERT: A 833 LEU cc_start: 0.8986 (mt) cc_final: 0.8546 (pt) REVERT: A 834 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8523 (mtp-110) REVERT: A 873 MET cc_start: 0.8806 (mmm) cc_final: 0.8387 (mmm) REVERT: A 1361 ARG cc_start: 0.8427 (mtm110) cc_final: 0.8153 (mtm-85) REVERT: A 1406 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8755 (tt) REVERT: A 1470 TYR cc_start: 0.8820 (m-10) cc_final: 0.8603 (m-10) REVERT: A 1515 GLU cc_start: 0.8237 (pp20) cc_final: 0.7787 (tp30) REVERT: A 1701 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.7292 (mmtp) REVERT: A 1763 ARG cc_start: 0.8810 (ptt180) cc_final: 0.8524 (ptt90) REVERT: A 1831 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7591 (mt) outliers start: 41 outliers final: 29 residues processed: 176 average time/residue: 0.1912 time to fit residues: 47.0602 Evaluate side-chains 180 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 777 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 848 LEU 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 1418 CYS 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 1699 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1723 LEU 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 1831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 87 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 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 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 = 0.139183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.114903 restraints weight = 12059.451| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.85 r_work: 0.3254 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8394 Z= 0.203 Angle : 0.664 12.854 11293 Z= 0.311 Chirality : 0.043 0.296 1317 Planarity : 0.004 0.049 1340 Dihedral : 11.624 89.054 1613 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.08 % Favored : 96.81 % Rotamer: Outliers : 4.21 % Allowed : 24.09 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.28), residues: 941 helix: 1.44 (0.20), residues: 690 sheet: -2.10 (1.25), residues: 10 loop : -0.69 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 PHE 0.024 0.001 PHE A 875 TYR 0.011 0.001 TYR A 258 ARG 0.002 0.000 ARG A1695 ********************** 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 187 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 0.982 Fit side-chains REVERT: A 115 ARG cc_start: 0.7935 (tpp-160) cc_final: 0.7419 (mmp-170) REVERT: A 154 ARG cc_start: 0.7916 (mtt90) cc_final: 0.5660 (mmt180) REVERT: A 197 MET cc_start: 0.8911 (mmm) cc_final: 0.8636 (mpp) REVERT: A 763 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7806 (mm-30) REVERT: A 833 LEU cc_start: 0.8955 (mt) cc_final: 0.8547 (pt) REVERT: A 834 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8520 (mtp-110) REVERT: A 1254 MET cc_start: 0.7784 (tpp) cc_final: 0.7359 (tpp) REVERT: A 1361 ARG cc_start: 0.8421 (mtm110) cc_final: 0.8159 (mtm-85) REVERT: A 1406 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8737 (tt) REVERT: A 1470 TYR cc_start: 0.8841 (m-10) cc_final: 0.8611 (m-10) REVERT: A 1515 GLU cc_start: 0.8233 (pp20) cc_final: 0.7796 (tp30) REVERT: A 1701 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.7335 (mmtp) REVERT: A 1763 ARG cc_start: 0.8799 (ptt180) cc_final: 0.8516 (ptt90) REVERT: A 1831 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7601 (mt) outliers start: 36 outliers final: 29 residues processed: 173 average time/residue: 0.1888 time to fit residues: 46.1222 Evaluate side-chains 181 residues out of total 861 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 148 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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 351 ILE Chi-restraints excluded: chain A residue 777 ILE Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 788 LEU Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 834 ARG Chi-restraints excluded: chain A residue 848 LEU 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 1699 LEU Chi-restraints excluded: chain A residue 1701 LYS Chi-restraints excluded: chain A residue 1711 ASP Chi-restraints excluded: chain A residue 1723 LEU 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 1831 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 1 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 2 optimal weight: 0.1980 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.140002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114807 restraints weight = 12198.592| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.95 r_work: 0.3239 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8394 Z= 0.213 Angle : 0.669 12.696 11293 Z= 0.314 Chirality : 0.043 0.297 1317 Planarity : 0.004 0.048 1340 Dihedral : 11.568 88.168 1613 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.40 % Favored : 96.49 % Rotamer: Outliers : 4.56 % Allowed : 23.74 % Favored : 71.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.28), residues: 941 helix: 1.43 (0.20), residues: 690 sheet: -2.37 (1.28), residues: 10 loop : -0.69 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1439 HIS 0.003 0.001 HIS A1442 PHE 0.024 0.001 PHE A 875 TYR 0.012 0.001 TYR A1807 ARG 0.002 0.000 ARG A1695 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4382.15 seconds wall clock time: 78 minutes 29.36 seconds (4709.36 seconds total)