Starting phenix.real_space_refine on Fri Jul 3 10:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eop_28451/07_2026/8eop_28451.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 63 5.16 5 C 8504 2.51 5 N 2320 2.21 5 O 2370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13265 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1687, 13050 Classifications: {'peptide': 1687} Link IDs: {'PTRANS': 105, 'TRANS': 1581} Chain breaks: 9 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 148 Unusual residues: {' MG': 2, 'ATP': 2, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 2.47, per 1000 atoms: 0.19 Number of scatterers: 13265 At special positions: 0 Unit cell: (159.131, 147.574, 105.791, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 63 16.00 P 6 15.00 Mg 2 11.99 O 2370 8.00 N 2320 7.00 C 8504 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 81 " distance=2.03 Simple disulfide: pdb=" SG CYS A 75 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 267 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A1347 " - pdb=" SG CYS A1359 " distance=2.03 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 BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A2201 " - " ASN A 78 " " NAG A2202 " - " ASN A 98 " " NAG A2203 " - " ASN A 312 " " NAG A2204 " - " ASN A 340 " " NAG A2205 " - " ASN A1518 " " NAG A2206 " - " ASN A1457 " " NAG B 1 " - " ASN A1386 " " NAG C 1 " - " ASN A1381 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 534.0 milliseconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3094 Finding SS restraints... Secondary structure from input PDB file: 79 helices and 10 sheets defined 60.2% alpha, 4.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.533A pdb=" N GLN A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 31 removed outlier: 4.238A pdb=" N LEU A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 removed outlier: 3.695A pdb=" N SER A 45 " --> pdb=" O ALA A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.606A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.954A pdb=" N ALA A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 126 Processing helix chain 'A' and resid 183 through 194 Processing helix chain 'A' and resid 198 through 208 Processing helix chain 'A' and resid 215 through 225 removed outlier: 3.803A pdb=" N LEU A 219 " --> pdb=" O GLY A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 275 Processing helix chain 'A' and resid 277 through 292 removed outlier: 4.777A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.532A pdb=" N LEU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 319 through 340 removed outlier: 3.829A pdb=" N ASP A 323 " --> pdb=" O THR A 319 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 342 through 354 removed outlier: 3.611A pdb=" N MET A 354 " --> pdb=" O ARG A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 Processing helix chain 'A' and resid 387 through 407 removed outlier: 3.928A pdb=" N LEU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 429 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 496 through 502 removed outlier: 3.741A pdb=" N TRP A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 502 " --> pdb=" O TYR A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 520 Processing helix chain 'A' and resid 540 through 558 removed outlier: 3.870A pdb=" N ARG A 544 " --> pdb=" O ASP A 540 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG A 548 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER A 549 " --> pdb=" O VAL A 545 " (cutoff:3.500A) Proline residue: A 551 - end of helix removed outlier: 4.052A pdb=" N TRP A 558 " --> pdb=" O LEU A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 575 removed outlier: 3.550A pdb=" N THR A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 584 removed outlier: 3.738A pdb=" N MET A 584 " --> pdb=" O THR A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 617 Proline residue: A 602 - end of helix Processing helix chain 'A' and resid 624 through 647 removed outlier: 3.788A pdb=" N VAL A 628 " --> pdb=" O HIS A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 659 Processing helix chain 'A' and resid 661 through 666 Processing helix chain 'A' and resid 668 through 677 removed outlier: 3.723A pdb=" N VAL A 672 " --> pdb=" O TYR A 668 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 690 Processing helix chain 'A' and resid 692 through 710 Processing helix chain 'A' and resid 732 through 755 Processing helix chain 'A' and resid 846 through 855 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 916 through 928 Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.540A pdb=" N LEU A 940 " --> pdb=" O THR A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 955 Processing helix chain 'A' and resid 971 through 985 removed outlier: 3.823A pdb=" N GLY A 977 " --> pdb=" O ALA A 973 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR A 985 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1005 Processing helix chain 'A' and resid 1021 through 1027 Processing helix chain 'A' and resid 1140 through 1151 Processing helix chain 'A' and resid 1213 through 1235 removed outlier: 3.712A pdb=" N THR A1217 " --> pdb=" O GLY A1213 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU A1221 " --> pdb=" O THR A1217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU A1226 " --> pdb=" O GLN A1222 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N SER A1235 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1235 through 1244 removed outlier: 3.969A pdb=" N LEU A1239 " --> pdb=" O SER A1235 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL A1244 " --> pdb=" O PHE A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1244 through 1259 removed outlier: 3.579A pdb=" N VAL A1250 " --> pdb=" O PRO A1246 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE A1259 " --> pdb=" O VAL A1255 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1290 through 1305 removed outlier: 3.523A pdb=" N ALA A1294 " --> pdb=" O ASP A1290 " (cutoff:3.500A) Processing helix chain 'A' and resid 1310 through 1314 Processing helix chain 'A' and resid 1324 through 1334 Processing helix chain 'A' and resid 1388 through 1402 removed outlier: 3.788A pdb=" N VAL A1392 " --> pdb=" O SER A1388 " (cutoff:3.500A) Proline residue: A1396 - end of helix Processing helix chain 'A' and resid 1428 through 1441 removed outlier: 3.507A pdb=" N LEU A1432 " --> pdb=" O SER A1428 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A1433 " --> pdb=" O GLY A1429 " (cutoff:3.500A) Processing helix chain 'A' and resid 1449 through 1466 removed outlier: 4.099A pdb=" N ASP A1466 " --> pdb=" O ALA A1462 " (cutoff:3.500A) Processing helix chain 'A' and resid 1482 through 1499 Processing helix chain 'A' and resid 1533 through 1549 removed outlier: 3.704A pdb=" N PHE A1548 " --> pdb=" O PHE A1544 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL A1549 " --> pdb=" O ALA A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1550 through 1552 No H-bonds generated for 'chain 'A' and resid 1550 through 1552' Processing helix chain 'A' and resid 1553 through 1563 removed outlier: 4.363A pdb=" N LEU A1557 " --> pdb=" O PHE A1553 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1573 removed outlier: 3.546A pdb=" N GLN A1569 " --> pdb=" O ALA A1565 " (cutoff:3.500A) Processing helix chain 'A' and resid 1575 through 1605 removed outlier: 3.766A pdb=" N LEU A1592 " --> pdb=" O MET A1588 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL A1593 " --> pdb=" O CYS A1589 " (cutoff:3.500A) Proline residue: A1594 - end of helix Processing helix chain 'A' and resid 1615 through 1631 removed outlier: 3.818A pdb=" N THR A1631 " --> pdb=" O GLY A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1632 through 1634 No H-bonds generated for 'chain 'A' and resid 1632 through 1634' Processing helix chain 'A' and resid 1635 through 1639 removed outlier: 3.627A pdb=" N PHE A1639 " --> pdb=" O PRO A1636 " (cutoff:3.500A) Processing helix chain 'A' and resid 1643 through 1671 removed outlier: 3.566A pdb=" N ALA A1647 " --> pdb=" O VAL A1643 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY A1662 " --> pdb=" O ILE A1658 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1688 removed outlier: 3.856A pdb=" N GLN A1686 " --> pdb=" O ARG A1682 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL A1687 " --> pdb=" O ILE A1683 " (cutoff:3.500A) Processing helix chain 'A' and resid 1693 through 1698 removed outlier: 3.525A pdb=" N GLY A1697 " --> pdb=" O HIS A1693 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1717 removed outlier: 3.624A pdb=" N MET A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N VAL A1704 " --> pdb=" O LEU A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1753 Proline residue: A1742 - end of helix removed outlier: 4.295A pdb=" N LEU A1745 " --> pdb=" O GLY A1741 " (cutoff:3.500A) Processing helix chain 'A' and resid 1774 through 1786 Processing helix chain 'A' and resid 1832 through 1842 removed outlier: 3.831A pdb=" N GLY A1842 " --> pdb=" O ARG A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1861 through 1868 removed outlier: 4.388A pdb=" N SER A1868 " --> pdb=" O ALA A1864 " (cutoff:3.500A) Processing helix chain 'A' and resid 1883 through 1896 Processing helix chain 'A' and resid 1898 through 1900 No H-bonds generated for 'chain 'A' and resid 1898 through 1900' Processing helix chain 'A' and resid 1901 through 1913 removed outlier: 3.828A pdb=" N LEU A1913 " --> pdb=" O GLY A1909 " (cutoff:3.500A) Processing helix chain 'A' and resid 1922 through 1926 removed outlier: 3.611A pdb=" N TYR A1926 " --> pdb=" O ALA A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1927 through 1941 removed outlier: 3.741A pdb=" N ALA A1939 " --> pdb=" O ALA A1935 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU A1940 " --> pdb=" O THR A1936 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A1941 " --> pdb=" O ALA A1937 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1975 Processing helix chain 'A' and resid 2008 through 2016 Processing helix chain 'A' and resid 2094 through 2104 removed outlier: 3.773A pdb=" N GLN A2104 " --> pdb=" O PHE A2100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 51 removed outlier: 3.641A pdb=" N LEU A 49 " --> pdb=" O ASP A 539 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 537 " --> pdb=" O HIS A 51 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 removed outlier: 3.730A pdb=" N ILE A1473 " --> pdb=" O TYR A 528 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N SER A1284 " --> pdb=" O LEU A1419 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 439 through 441 removed outlier: 3.787A pdb=" N ARG A 463 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 807 through 813 removed outlier: 3.511A pdb=" N ARG A 810 " --> pdb=" O SER A 864 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 864 " --> pdb=" O ARG A 810 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU A 812 " --> pdb=" O GLY A 862 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N GLY A 862 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 883 through 884 removed outlier: 6.614A pdb=" N GLY A 884 " --> pdb=" O ILE A 962 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL A 961 " --> pdb=" O ILE A 992 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N SER A 994 " --> pdb=" O VAL A 961 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N THR A 837 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ALA A 838 " --> pdb=" O ALA A1009 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N VAL A1011 " --> pdb=" O ALA A 838 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU A 840 " --> pdb=" O VAL A1011 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N CYS A1018 " --> pdb=" O VAL A1010 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ALA A1012 " --> pdb=" O LEU A1016 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU A1016 " --> pdb=" O ALA A1012 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1372 through 1373 Processing sheet with id=AA7, first strand: chain 'A' and resid 1814 through 1817 removed outlier: 3.953A pdb=" N LEU A1815 " --> pdb=" O LEU A1795 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU A1793 " --> pdb=" O ILE A1817 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LEU A1798 " --> pdb=" O ARG A1848 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG A1848 " --> pdb=" O LEU A1798 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS A1856 " --> pdb=" O LEU A1853 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1822 through 1823 Processing sheet with id=AA9, first strand: chain 'A' and resid 1870 through 1872 removed outlier: 7.171A pdb=" N GLY A1870 " --> pdb=" O PHE A1948 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 1998 through 1999 659 hydrogen bonds defined for protein. 1929 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: 2.00 Time building geometry restraints manager: 1.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4312 1.34 - 1.46: 2808 1.46 - 1.58: 6355 1.58 - 1.70: 8 1.70 - 1.82: 95 Bond restraints: 13578 Sorted by residual: bond pdb=" CA ALA A1919 " pdb=" CB ALA A1919 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.54e-02 4.22e+03 7.25e+00 bond pdb=" N ASP A1920 " pdb=" CA ASP A1920 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.29e-02 6.01e+03 6.56e+00 bond pdb=" CA SER A1916 " pdb=" CB SER A1916 " ideal model delta sigma weight residual 1.530 1.490 0.040 1.69e-02 3.50e+03 5.69e+00 bond pdb=" N SER A1916 " pdb=" CA SER A1916 " ideal model delta sigma weight residual 1.457 1.488 -0.030 1.29e-02 6.01e+03 5.45e+00 bond pdb=" C ARG A 880 " pdb=" N PRO A 881 " ideal model delta sigma weight residual 1.334 1.352 -0.018 8.40e-03 1.42e+04 4.74e+00 ... (remaining 13573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 17940 1.66 - 3.32: 442 3.32 - 4.98: 77 4.98 - 6.64: 13 6.64 - 8.30: 2 Bond angle restraints: 18474 Sorted by residual: angle pdb=" N ILE A 559 " pdb=" CA ILE A 559 " pdb=" C ILE A 559 " ideal model delta sigma weight residual 113.71 109.79 3.92 9.50e-01 1.11e+00 1.70e+01 angle pdb=" N ILE A 879 " pdb=" CA ILE A 879 " pdb=" C ILE A 879 " ideal model delta sigma weight residual 112.96 109.37 3.59 1.00e+00 1.00e+00 1.29e+01 angle pdb=" CB ARG A 350 " pdb=" CG ARG A 350 " pdb=" CD ARG A 350 " ideal model delta sigma weight residual 111.30 119.24 -7.94 2.30e+00 1.89e-01 1.19e+01 angle pdb=" N VAL A 915 " pdb=" CA VAL A 915 " pdb=" C VAL A 915 " ideal model delta sigma weight residual 106.21 109.07 -2.86 1.07e+00 8.73e-01 7.13e+00 angle pdb=" C ASN A 98 " pdb=" N ASP A 99 " pdb=" CA ASP A 99 " ideal model delta sigma weight residual 121.54 126.60 -5.06 1.91e+00 2.74e-01 7.01e+00 ... (remaining 18469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7221 17.77 - 35.54: 629 35.54 - 53.31: 102 53.31 - 71.08: 11 71.08 - 88.85: 8 Dihedral angle restraints: 7971 sinusoidal: 3166 harmonic: 4805 Sorted by residual: dihedral pdb=" CB CYS A1347 " pdb=" SG CYS A1347 " pdb=" SG CYS A1359 " pdb=" CB CYS A1359 " ideal model delta sinusoidal sigma weight residual 93.00 165.23 -72.23 1 1.00e+01 1.00e-02 6.67e+01 dihedral pdb=" CA SER A 385 " pdb=" C SER A 385 " pdb=" N TRP A 386 " pdb=" CA TRP A 386 " ideal model delta harmonic sigma weight residual -180.00 -162.88 -17.12 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CB GLU A 752 " pdb=" CG GLU A 752 " pdb=" CD GLU A 752 " pdb=" OE1 GLU A 752 " ideal model delta sinusoidal sigma weight residual 0.00 -88.85 88.85 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 7968 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2016 0.089 - 0.178: 107 0.178 - 0.266: 2 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 2128 Sorted by residual: chirality pdb=" C1 NAG A2202 " pdb=" ND2 ASN A 98 " pdb=" C2 NAG A2202 " pdb=" O5 NAG A2202 " both_signs ideal model delta sigma weight residual False -2.40 -1.96 -0.44 2.00e-01 2.50e+01 4.93e+00 chirality pdb=" C1 NAG A2206 " pdb=" ND2 ASN A1457 " pdb=" C2 NAG A2206 " pdb=" O5 NAG A2206 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.29e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 2125 not shown) Planarity restraints: 2352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A1915 " -0.017 2.00e-02 2.50e+03 3.37e-02 1.13e+01 pdb=" C LEU A1915 " 0.058 2.00e-02 2.50e+03 pdb=" O LEU A1915 " -0.022 2.00e-02 2.50e+03 pdb=" N SER A1916 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A1366 " 0.049 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO A1367 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A1367 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO A1367 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 979 " 0.016 2.00e-02 2.50e+03 1.32e-02 4.34e+00 pdb=" CG TRP A 979 " -0.035 2.00e-02 2.50e+03 pdb=" CD1 TRP A 979 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A 979 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 979 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 979 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 979 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 979 " 0.003 2.00e-02 2.50e+03 ... (remaining 2349 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 95 2.58 - 3.16: 10744 3.16 - 3.74: 20057 3.74 - 4.32: 24867 4.32 - 4.90: 42638 Nonbonded interactions: 98401 Sorted by model distance: nonbonded pdb="MG MG A2208 " pdb=" O1B ATP A2210 " model vdw 2.001 2.170 nonbonded pdb="MG MG A2208 " pdb=" O1G ATP A2210 " model vdw 2.008 2.170 nonbonded pdb=" OE1 GLN A1874 " pdb="MG MG A2209 " model vdw 2.053 2.170 nonbonded pdb=" OG1 THR A1834 " pdb="MG MG A2209 " model vdw 2.057 2.170 nonbonded pdb=" O2G ATP A2207 " pdb="MG MG A2209 " model vdw 2.213 2.170 ... (remaining 98396 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.740 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13593 Z= 0.147 Angle : 0.632 9.657 18515 Z= 0.308 Chirality : 0.042 0.444 2128 Planarity : 0.004 0.073 2344 Dihedral : 13.385 88.854 4865 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.64 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.22), residues: 1667 helix: 1.69 (0.18), residues: 917 sheet: -1.72 (0.51), residues: 114 loop : -1.88 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 350 TYR 0.010 0.001 TYR A 17 PHE 0.011 0.001 PHE A 866 TRP 0.035 0.001 TRP A 979 HIS 0.003 0.001 HIS A 882 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 (13578) covalent geometry : angle 0.61585 / 0.30 (18474) SS BOND : bond 0.00130 / 0.06 ( 4) SS BOND : angle 0.87346 / 0.57 ( 8) hydrogen bonds : bond 0.14177 / 9.94 ( 659) hydrogen bonds : angle 5.17770 / 3.77 ( 1929) link_BETA1-4 : bond 0.00421 / 0.20 ( 3) link_BETA1-4 : angle 1.28350 / 0.76 ( 9) link_NAG-ASN : bond 0.00929 / 0.66 ( 8) link_NAG-ASN : angle 3.91288 / 2.63 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 MET cc_start: 0.8242 (mmp) cc_final: 0.7989 (mmp) REVERT: A 323 ASP cc_start: 0.6558 (m-30) cc_final: 0.6309 (t70) REVERT: A 386 TRP cc_start: 0.4469 (m-10) cc_final: 0.3751 (m-10) REVERT: A 615 LYS cc_start: 0.7122 (tptt) cc_final: 0.6675 (tptp) REVERT: A 975 ARG cc_start: 0.7136 (mtt180) cc_final: 0.6898 (mtt90) REVERT: A 1372 VAL cc_start: 0.6604 (t) cc_final: 0.6002 (m) REVERT: A 1615 ASN cc_start: 0.6762 (p0) cc_final: 0.6012 (m-40) REVERT: A 1686 GLN cc_start: 0.7534 (mm-40) cc_final: 0.6909 (mt0) REVERT: A 1739 ILE cc_start: 0.8281 (tp) cc_final: 0.8079 (tt) REVERT: A 1750 LEU cc_start: 0.7204 (tt) cc_final: 0.6288 (mt) REVERT: A 1799 THR cc_start: 0.8070 (t) cc_final: 0.7667 (m) REVERT: A 1962 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7561 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1140 time to fit residues: 39.1582 Evaluate side-chains 152 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 152 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.0670 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN A 353 GLN A 390 HIS A 395 HIS A 477 ASN A 718 ASN A1675 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.172907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.136049 restraints weight = 19153.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.136359 restraints weight = 19008.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137335 restraints weight = 15608.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137780 restraints weight = 12757.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.137819 restraints weight = 11753.753| |-----------------------------------------------------------------------------| r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13593 Z= 0.122 Angle : 0.606 9.244 18515 Z= 0.292 Chirality : 0.039 0.292 2128 Planarity : 0.005 0.106 2344 Dihedral : 4.449 69.263 1838 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.01 % Allowed : 8.63 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.21), residues: 1667 helix: 1.87 (0.18), residues: 925 sheet: -1.61 (0.52), residues: 114 loop : -1.99 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1885 TYR 0.014 0.001 TYR A1926 PHE 0.022 0.001 PHE A 303 TRP 0.016 0.001 TRP A 328 HIS 0.011 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (13578) covalent geometry : angle 0.59553 / 0.29 (18474) SS BOND : bond 0.00241 / 0.12 ( 4) SS BOND : angle 1.11621 / 0.80 ( 8) hydrogen bonds : bond 0.04231 / 2.88 ( 659) hydrogen bonds : angle 4.02567 / 2.91 ( 1929) link_BETA1-4 : bond 0.00390 / 0.18 ( 3) link_BETA1-4 : angle 1.43598 / 0.82 ( 9) link_NAG-ASN : bond 0.00786 / 0.52 ( 8) link_NAG-ASN : angle 3.08356 / 2.21 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6936 (tmm) cc_final: 0.5305 (mmm) REVERT: A 16 MET cc_start: 0.8155 (mmp) cc_final: 0.7905 (mmp) REVERT: A 291 ILE cc_start: 0.6302 (mm) cc_final: 0.5933 (mm) REVERT: A 292 LEU cc_start: 0.6757 (mt) cc_final: 0.6397 (mp) REVERT: A 294 LYS cc_start: 0.7456 (mmtt) cc_final: 0.7139 (mmtp) REVERT: A 312 ASN cc_start: 0.6902 (t0) cc_final: 0.6698 (t0) REVERT: A 581 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8151 (mtp) REVERT: A 615 LYS cc_start: 0.7166 (tptt) cc_final: 0.6826 (tptp) REVERT: A 1615 ASN cc_start: 0.6556 (p0) cc_final: 0.5779 (m-40) REVERT: A 1686 GLN cc_start: 0.7492 (mm-40) cc_final: 0.6794 (tt0) REVERT: A 1750 LEU cc_start: 0.7544 (tt) cc_final: 0.6622 (mt) REVERT: A 1799 THR cc_start: 0.8050 (t) cc_final: 0.7769 (m) REVERT: A 1962 ARG cc_start: 0.7848 (ttm110) cc_final: 0.7450 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7204 (t70) cc_final: 0.6898 (t-90) outliers start: 14 outliers final: 9 residues processed: 171 average time/residue: 0.1023 time to fit residues: 25.6637 Evaluate side-chains 148 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 138 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 0.0670 chunk 78 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 109 optimal weight: 4.9990 chunk 141 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 HIS A 395 HIS A 710 GLN A1313 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.174086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.139437 restraints weight = 19436.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138442 restraints weight = 22870.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139776 restraints weight = 22174.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139964 restraints weight = 16403.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.140265 restraints weight = 14533.266| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13593 Z= 0.138 Angle : 0.602 9.504 18515 Z= 0.293 Chirality : 0.040 0.243 2128 Planarity : 0.005 0.047 2344 Dihedral : 4.529 72.833 1838 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.01 % Allowed : 12.23 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.21), residues: 1667 helix: 1.84 (0.17), residues: 930 sheet: -1.75 (0.52), residues: 114 loop : -1.99 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1210 TYR 0.023 0.001 TYR A1926 PHE 0.016 0.001 PHE A 303 TRP 0.023 0.001 TRP A 484 HIS 0.007 0.001 HIS A 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (13578) covalent geometry : angle 0.59587 / 0.29 (18474) SS BOND : bond 0.00388 / 0.19 ( 4) SS BOND : angle 1.38303 / 0.97 ( 8) hydrogen bonds : bond 0.04349 / 2.93 ( 659) hydrogen bonds : angle 3.86401 / 2.79 ( 1929) link_BETA1-4 : bond 0.00466 / 0.20 ( 3) link_BETA1-4 : angle 1.29123 / 0.79 ( 9) link_NAG-ASN : bond 0.00576 / 0.35 ( 8) link_NAG-ASN : angle 2.27367 / 1.69 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 MET cc_start: 0.6881 (tmm) cc_final: 0.5305 (mmm) REVERT: A 16 MET cc_start: 0.8135 (mmp) cc_final: 0.7819 (mmt) REVERT: A 30 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7813 (mp) REVERT: A 291 ILE cc_start: 0.6354 (mm) cc_final: 0.6118 (mm) REVERT: A 581 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8258 (mtp) REVERT: A 615 LYS cc_start: 0.7289 (tptt) cc_final: 0.6874 (tptp) REVERT: A 876 MET cc_start: 0.7550 (ppp) cc_final: 0.7218 (ppp) REVERT: A 1615 ASN cc_start: 0.6478 (p0) cc_final: 0.5741 (m-40) REVERT: A 1686 GLN cc_start: 0.7431 (mm-40) cc_final: 0.6775 (tt0) REVERT: A 1750 LEU cc_start: 0.7627 (tt) cc_final: 0.6786 (mt) REVERT: A 1799 THR cc_start: 0.8254 (t) cc_final: 0.7818 (m) REVERT: A 1852 VAL cc_start: 0.8354 (OUTLIER) cc_final: 0.8111 (m) REVERT: A 1962 ARG cc_start: 0.7717 (ttm110) cc_final: 0.7346 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7004 (t70) cc_final: 0.6782 (t-90) outliers start: 28 outliers final: 18 residues processed: 165 average time/residue: 0.0964 time to fit residues: 23.5809 Evaluate side-chains 158 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 532 MET Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 754 VAL Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 19 optimal weight: 0.0570 chunk 69 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 126 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 HIS A 395 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.174938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.140169 restraints weight = 19363.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.138942 restraints weight = 25048.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.140280 restraints weight = 22216.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.140924 restraints weight = 15116.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.140925 restraints weight = 14614.941| |-----------------------------------------------------------------------------| r_work (final): 0.3658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13593 Z= 0.113 Angle : 0.573 9.561 18515 Z= 0.275 Chirality : 0.039 0.249 2128 Planarity : 0.005 0.076 2344 Dihedral : 4.466 69.178 1838 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.23 % Allowed : 14.46 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.21), residues: 1667 helix: 1.97 (0.17), residues: 930 sheet: -1.73 (0.52), residues: 114 loop : -1.97 (0.23), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1349 TYR 0.020 0.001 TYR A1926 PHE 0.014 0.001 PHE A 303 TRP 0.015 0.001 TRP A 558 HIS 0.004 0.001 HIS A 395 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13578) covalent geometry : angle 0.56577 / 0.27 (18474) SS BOND : bond 0.00428 / 0.21 ( 4) SS BOND : angle 1.34882 / 0.98 ( 8) hydrogen bonds : bond 0.03723 / 2.51 ( 659) hydrogen bonds : angle 3.73926 / 2.71 ( 1929) link_BETA1-4 : bond 0.00445 / 0.20 ( 3) link_BETA1-4 : angle 1.25621 / 0.74 ( 9) link_NAG-ASN : bond 0.00508 / 0.33 ( 8) link_NAG-ASN : angle 2.38219 / 1.73 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 8 MET cc_start: 0.6870 (tmm) cc_final: 0.5305 (mmm) REVERT: A 16 MET cc_start: 0.8098 (mmp) cc_final: 0.7781 (tpp) REVERT: A 30 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7778 (mp) REVERT: A 291 ILE cc_start: 0.6448 (mm) cc_final: 0.6165 (mm) REVERT: A 312 ASN cc_start: 0.6581 (t0) cc_final: 0.6252 (t0) REVERT: A 581 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8172 (mtp) REVERT: A 615 LYS cc_start: 0.7209 (tptt) cc_final: 0.6838 (tptp) REVERT: A 1210 ARG cc_start: 0.6477 (mtt-85) cc_final: 0.6269 (mmt90) REVERT: A 1615 ASN cc_start: 0.6352 (p0) cc_final: 0.5704 (m-40) REVERT: A 1686 GLN cc_start: 0.7413 (mm-40) cc_final: 0.6771 (tt0) REVERT: A 1750 LEU cc_start: 0.7630 (tt) cc_final: 0.6786 (mt) REVERT: A 1799 THR cc_start: 0.8114 (t) cc_final: 0.7746 (m) REVERT: A 1852 VAL cc_start: 0.8336 (OUTLIER) cc_final: 0.8095 (m) REVERT: A 1962 ARG cc_start: 0.7746 (ttm110) cc_final: 0.7351 (ptp-170) REVERT: A 2011 HIS cc_start: 0.7019 (t70) cc_final: 0.6800 (t-90) outliers start: 31 outliers final: 20 residues processed: 169 average time/residue: 0.1000 time to fit residues: 25.2332 Evaluate side-chains 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1852 VAL Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 134 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 58 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 109 optimal weight: 0.0020 chunk 5 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.175765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.141712 restraints weight = 19318.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.140584 restraints weight = 23757.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.142070 restraints weight = 20398.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141760 restraints weight = 15944.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.142040 restraints weight = 13900.460| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 13593 Z= 0.106 Angle : 0.562 9.726 18515 Z= 0.269 Chirality : 0.038 0.217 2128 Planarity : 0.004 0.066 2344 Dihedral : 4.406 67.800 1838 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.66 % Allowed : 14.46 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1667 helix: 2.10 (0.17), residues: 923 sheet: -1.68 (0.52), residues: 114 loop : -1.94 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1210 TYR 0.019 0.001 TYR A1926 PHE 0.013 0.001 PHE A 303 TRP 0.016 0.001 TRP A 558 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13578) covalent geometry : angle 0.55686 / 0.27 (18474) SS BOND : bond 0.00460 / 0.23 ( 4) SS BOND : angle 1.34553 / 1.00 ( 8) hydrogen bonds : bond 0.03443 / 2.31 ( 659) hydrogen bonds : angle 3.63952 / 2.63 ( 1929) link_BETA1-4 : bond 0.00487 / 0.22 ( 3) link_BETA1-4 : angle 1.21917 / 0.72 ( 9) link_NAG-ASN : bond 0.00487 / 0.31 ( 8) link_NAG-ASN : angle 2.00911 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 146 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 16 MET cc_start: 0.8074 (mmp) cc_final: 0.7792 (tpp) REVERT: A 30 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.7779 (mp) REVERT: A 291 ILE cc_start: 0.6421 (mm) cc_final: 0.6176 (mm) REVERT: A 312 ASN cc_start: 0.6490 (t0) cc_final: 0.6248 (t0) REVERT: A 477 ASN cc_start: 0.7449 (OUTLIER) cc_final: 0.7176 (m110) REVERT: A 581 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8162 (mtp) REVERT: A 615 LYS cc_start: 0.7105 (tptt) cc_final: 0.6804 (tptp) REVERT: A 876 MET cc_start: 0.7471 (ppp) cc_final: 0.7252 (ppp) REVERT: A 1349 ARG cc_start: 0.5819 (mtt180) cc_final: 0.5529 (mtm180) REVERT: A 1353 ARG cc_start: 0.5733 (OUTLIER) cc_final: 0.3773 (ptt180) REVERT: A 1615 ASN cc_start: 0.6156 (p0) cc_final: 0.5711 (m-40) REVERT: A 1750 LEU cc_start: 0.7654 (tt) cc_final: 0.6830 (mt) REVERT: A 1799 THR cc_start: 0.8138 (t) cc_final: 0.7839 (m) REVERT: A 1886 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6855 (mp0) REVERT: A 1962 ARG cc_start: 0.7716 (ttm110) cc_final: 0.7344 (ptp-170) outliers start: 37 outliers final: 22 residues processed: 169 average time/residue: 0.1033 time to fit residues: 25.6916 Evaluate side-chains 163 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 347 MET Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 143 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 150 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 75 optimal weight: 0.0770 chunk 144 optimal weight: 3.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.176391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.144540 restraints weight = 19180.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.143315 restraints weight = 25893.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.144525 restraints weight = 23546.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144688 restraints weight = 18599.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.144769 restraints weight = 16851.905| |-----------------------------------------------------------------------------| r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13593 Z= 0.136 Angle : 0.589 9.917 18515 Z= 0.284 Chirality : 0.040 0.220 2128 Planarity : 0.005 0.076 2344 Dihedral : 4.502 69.141 1838 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.88 % Allowed : 15.04 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1667 helix: 2.03 (0.17), residues: 930 sheet: -1.88 (0.51), residues: 114 loop : -1.95 (0.24), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1349 TYR 0.018 0.001 TYR A1926 PHE 0.015 0.001 PHE A1486 TRP 0.016 0.001 TRP A 558 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (13578) covalent geometry : angle 0.58314 / 0.28 (18474) SS BOND : bond 0.00468 / 0.23 ( 4) SS BOND : angle 1.54727 / 1.13 ( 8) hydrogen bonds : bond 0.04092 / 2.76 ( 659) hydrogen bonds : angle 3.72903 / 2.70 ( 1929) link_BETA1-4 : bond 0.00581 / 0.28 ( 3) link_BETA1-4 : angle 1.26254 / 0.76 ( 9) link_NAG-ASN : bond 0.00451 / 0.28 ( 8) link_NAG-ASN : angle 2.01521 / 1.53 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 138 time to evaluate : 0.501 Fit side-chains REVERT: A 8 MET cc_start: 0.6807 (tmm) cc_final: 0.5246 (mmm) REVERT: A 16 MET cc_start: 0.8068 (mmp) cc_final: 0.7862 (tpp) REVERT: A 30 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7896 (mp) REVERT: A 291 ILE cc_start: 0.6470 (mm) cc_final: 0.6224 (mm) REVERT: A 477 ASN cc_start: 0.7383 (OUTLIER) cc_final: 0.7101 (m110) REVERT: A 581 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: A 876 MET cc_start: 0.7565 (ppp) cc_final: 0.7345 (ppp) REVERT: A 1353 ARG cc_start: 0.5692 (OUTLIER) cc_final: 0.3708 (ptt180) REVERT: A 1372 VAL cc_start: 0.6183 (t) cc_final: 0.5523 (m) REVERT: A 1615 ASN cc_start: 0.6123 (p0) cc_final: 0.5679 (m-40) REVERT: A 1750 LEU cc_start: 0.7708 (tt) cc_final: 0.6917 (mt) REVERT: A 1799 THR cc_start: 0.8264 (t) cc_final: 0.7885 (m) REVERT: A 1850 GLU cc_start: 0.5597 (mp0) cc_final: 0.5346 (tp30) REVERT: A 1886 GLU cc_start: 0.7424 (OUTLIER) cc_final: 0.6901 (mp0) REVERT: A 1962 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7309 (ptp-170) outliers start: 40 outliers final: 24 residues processed: 166 average time/residue: 0.1161 time to fit residues: 28.3805 Evaluate side-chains 159 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1432 LEU Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1599 VAL Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1844 THR Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 69 optimal weight: 0.9980 chunk 117 optimal weight: 0.0470 chunk 91 optimal weight: 0.4980 chunk 40 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS A 890 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.173915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138676 restraints weight = 19366.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137818 restraints weight = 21047.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.139121 restraints weight = 17663.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.139346 restraints weight = 14037.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.139443 restraints weight = 13057.334| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13593 Z= 0.108 Angle : 0.571 10.171 18515 Z= 0.273 Chirality : 0.039 0.221 2128 Planarity : 0.005 0.135 2344 Dihedral : 4.436 67.013 1838 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.59 % Allowed : 16.19 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1667 helix: 2.17 (0.17), residues: 923 sheet: -1.76 (0.51), residues: 114 loop : -1.93 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 922 TYR 0.018 0.001 TYR A1926 PHE 0.012 0.001 PHE A 303 TRP 0.013 0.001 TRP A 558 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (13578) covalent geometry : angle 0.56644 / 0.27 (18474) SS BOND : bond 0.00487 / 0.24 ( 4) SS BOND : angle 1.42115 / 1.06 ( 8) hydrogen bonds : bond 0.03482 / 2.35 ( 659) hydrogen bonds : angle 3.61732 / 2.62 ( 1929) link_BETA1-4 : bond 0.00461 / 0.20 ( 3) link_BETA1-4 : angle 1.22195 / 0.72 ( 9) link_NAG-ASN : bond 0.00487 / 0.32 ( 8) link_NAG-ASN : angle 1.93044 / 1.48 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 142 time to evaluate : 0.500 Fit side-chains REVERT: A 8 MET cc_start: 0.6800 (tmm) cc_final: 0.5214 (mmm) REVERT: A 16 MET cc_start: 0.8100 (mmp) cc_final: 0.7893 (tpp) REVERT: A 291 ILE cc_start: 0.6428 (mm) cc_final: 0.6178 (mm) REVERT: A 477 ASN cc_start: 0.7336 (OUTLIER) cc_final: 0.7033 (m110) REVERT: A 581 MET cc_start: 0.8455 (OUTLIER) cc_final: 0.8181 (mtp) REVERT: A 876 MET cc_start: 0.7538 (ppp) cc_final: 0.7303 (ppp) REVERT: A 1353 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.3517 (ptt180) REVERT: A 1372 VAL cc_start: 0.6045 (t) cc_final: 0.5364 (m) REVERT: A 1615 ASN cc_start: 0.6151 (p0) cc_final: 0.5665 (m-40) REVERT: A 1750 LEU cc_start: 0.7619 (tt) cc_final: 0.6814 (mt) REVERT: A 1799 THR cc_start: 0.8275 (t) cc_final: 0.7853 (m) REVERT: A 1886 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: A 1962 ARG cc_start: 0.7799 (ttm110) cc_final: 0.7337 (ptp-170) outliers start: 36 outliers final: 23 residues processed: 170 average time/residue: 0.1042 time to fit residues: 26.9215 Evaluate side-chains 157 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Chi-restraints excluded: chain A residue 1969 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 80 optimal weight: 0.1980 chunk 6 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 112 optimal weight: 6.9990 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.173642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.139195 restraints weight = 19200.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138333 restraints weight = 22391.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139688 restraints weight = 19247.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.139759 restraints weight = 14653.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139962 restraints weight = 14280.360| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13593 Z= 0.113 Angle : 0.593 13.409 18515 Z= 0.281 Chirality : 0.039 0.224 2128 Planarity : 0.004 0.045 2344 Dihedral : 4.409 67.574 1838 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 2.52 % Allowed : 16.55 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.22), residues: 1667 helix: 2.16 (0.17), residues: 934 sheet: -1.74 (0.54), residues: 104 loop : -1.92 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 922 TYR 0.018 0.001 TYR A1926 PHE 0.012 0.001 PHE A1486 TRP 0.020 0.001 TRP A 558 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (13578) covalent geometry : angle 0.58828 / 0.28 (18474) SS BOND : bond 0.00498 / 0.25 ( 4) SS BOND : angle 1.51737 / 1.13 ( 8) hydrogen bonds : bond 0.03562 / 2.40 ( 659) hydrogen bonds : angle 3.61343 / 2.62 ( 1929) link_BETA1-4 : bond 0.00529 / 0.23 ( 3) link_BETA1-4 : angle 1.22948 / 0.73 ( 9) link_NAG-ASN : bond 0.00449 / 0.29 ( 8) link_NAG-ASN : angle 1.91205 / 1.47 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.499 Fit side-chains REVERT: A 8 MET cc_start: 0.6815 (tmm) cc_final: 0.5255 (mmm) REVERT: A 16 MET cc_start: 0.8100 (mmp) cc_final: 0.7894 (tpp) REVERT: A 291 ILE cc_start: 0.6438 (mm) cc_final: 0.6189 (mm) REVERT: A 477 ASN cc_start: 0.7324 (OUTLIER) cc_final: 0.7032 (m110) REVERT: A 581 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8174 (mtp) REVERT: A 876 MET cc_start: 0.7573 (ppp) cc_final: 0.7351 (ppp) REVERT: A 1353 ARG cc_start: 0.5421 (OUTLIER) cc_final: 0.3494 (ptt180) REVERT: A 1372 VAL cc_start: 0.6004 (t) cc_final: 0.5338 (m) REVERT: A 1615 ASN cc_start: 0.6104 (p0) cc_final: 0.5685 (m-40) REVERT: A 1738 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6892 (p) REVERT: A 1750 LEU cc_start: 0.7621 (tt) cc_final: 0.6827 (mt) REVERT: A 1799 THR cc_start: 0.8249 (t) cc_final: 0.7838 (m) REVERT: A 1886 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: A 1962 ARG cc_start: 0.7763 (ttm110) cc_final: 0.7314 (ptp-170) REVERT: A 1985 MET cc_start: 0.7121 (ptt) cc_final: 0.6314 (mmp) outliers start: 35 outliers final: 25 residues processed: 162 average time/residue: 0.1129 time to fit residues: 27.5447 Evaluate side-chains 160 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1142 ILE Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1738 VAL Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1844 THR Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS A 890 ASN A1675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.137935 restraints weight = 19435.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136667 restraints weight = 22826.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138335 restraints weight = 19376.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138477 restraints weight = 15466.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138692 restraints weight = 14367.271| |-----------------------------------------------------------------------------| r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13593 Z= 0.120 Angle : 0.601 13.341 18515 Z= 0.285 Chirality : 0.039 0.224 2128 Planarity : 0.004 0.048 2344 Dihedral : 4.431 67.568 1838 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.59 % Allowed : 16.55 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1667 helix: 2.18 (0.18), residues: 928 sheet: -1.76 (0.51), residues: 114 loop : -1.93 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 922 TYR 0.017 0.001 TYR A1926 PHE 0.013 0.001 PHE A1486 TRP 0.048 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 (13578) covalent geometry : angle 0.59568 / 0.28 (18474) SS BOND : bond 0.00406 / 0.20 ( 4) SS BOND : angle 1.48916 / 1.10 ( 8) hydrogen bonds : bond 0.03699 / 2.49 ( 659) hydrogen bonds : angle 3.64721 / 2.65 ( 1929) link_BETA1-4 : bond 0.00431 / 0.18 ( 3) link_BETA1-4 : angle 1.24742 / 0.74 ( 9) link_NAG-ASN : bond 0.00459 / 0.30 ( 8) link_NAG-ASN : angle 1.94938 / 1.49 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.500 Fit side-chains REVERT: A 8 MET cc_start: 0.6823 (tmm) cc_final: 0.5243 (mmm) REVERT: A 16 MET cc_start: 0.8109 (mmp) cc_final: 0.7904 (tpp) REVERT: A 291 ILE cc_start: 0.6486 (mm) cc_final: 0.6244 (mm) REVERT: A 477 ASN cc_start: 0.7301 (OUTLIER) cc_final: 0.6971 (m110) REVERT: A 485 ASP cc_start: 0.7462 (m-30) cc_final: 0.7092 (t0) REVERT: A 581 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8228 (mtp) REVERT: A 876 MET cc_start: 0.7604 (ppp) cc_final: 0.7376 (ppp) REVERT: A 1353 ARG cc_start: 0.5410 (OUTLIER) cc_final: 0.3556 (ptt180) REVERT: A 1372 VAL cc_start: 0.6022 (t) cc_final: 0.5344 (m) REVERT: A 1615 ASN cc_start: 0.6118 (p0) cc_final: 0.5687 (m-40) REVERT: A 1664 MET cc_start: 0.7797 (ttp) cc_final: 0.7561 (ttp) REVERT: A 1750 LEU cc_start: 0.7632 (tt) cc_final: 0.6826 (mt) REVERT: A 1798 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8376 (mp) REVERT: A 1799 THR cc_start: 0.8174 (t) cc_final: 0.7793 (m) REVERT: A 1886 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6917 (mp0) REVERT: A 1962 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7412 (ptp-170) outliers start: 36 outliers final: 29 residues processed: 165 average time/residue: 0.1117 time to fit residues: 27.9688 Evaluate side-chains 168 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 134 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 890 ASN Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1844 THR Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 33 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 80 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS A 890 ASN A1675 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.172938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138175 restraints weight = 19349.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136764 restraints weight = 22899.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138198 restraints weight = 20492.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138645 restraints weight = 15062.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.138690 restraints weight = 14359.123| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 13593 Z= 0.167 Angle : 0.813 59.199 18515 Z= 0.446 Chirality : 0.041 0.620 2128 Planarity : 0.005 0.062 2344 Dihedral : 4.459 67.575 1838 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.66 % Allowed : 16.76 % Favored : 80.58 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1667 helix: 2.18 (0.18), residues: 928 sheet: -1.77 (0.51), residues: 114 loop : -1.94 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 922 TYR 0.016 0.001 TYR A1926 PHE 0.013 0.001 PHE A1486 TRP 0.036 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13578) covalent geometry : angle 0.80962 / 0.45 (18474) SS BOND : bond 0.00398 / 0.20 ( 4) SS BOND : angle 1.47718 / 1.09 ( 8) hydrogen bonds : bond 0.03686 / 2.48 ( 659) hydrogen bonds : angle 3.65082 / 2.65 ( 1929) link_BETA1-4 : bond 0.00400 / 0.19 ( 3) link_BETA1-4 : angle 1.26782 / 0.76 ( 9) link_NAG-ASN : bond 0.00459 / 0.30 ( 8) link_NAG-ASN : angle 1.94592 / 1.48 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 135 time to evaluate : 0.514 Fit side-chains REVERT: A 8 MET cc_start: 0.6814 (tmm) cc_final: 0.5240 (mmm) REVERT: A 291 ILE cc_start: 0.6483 (mm) cc_final: 0.6243 (mm) REVERT: A 477 ASN cc_start: 0.7295 (OUTLIER) cc_final: 0.6974 (m110) REVERT: A 485 ASP cc_start: 0.7463 (m-30) cc_final: 0.7096 (t0) REVERT: A 581 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8219 (mtp) REVERT: A 876 MET cc_start: 0.7617 (ppp) cc_final: 0.7384 (ppp) REVERT: A 1353 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.3564 (ptt180) REVERT: A 1372 VAL cc_start: 0.6036 (t) cc_final: 0.5356 (m) REVERT: A 1615 ASN cc_start: 0.6094 (p0) cc_final: 0.5679 (m-40) REVERT: A 1664 MET cc_start: 0.7817 (ttp) cc_final: 0.7562 (ttp) REVERT: A 1750 LEU cc_start: 0.7635 (tt) cc_final: 0.6835 (mt) REVERT: A 1798 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8359 (mp) REVERT: A 1799 THR cc_start: 0.8193 (t) cc_final: 0.7793 (m) REVERT: A 1886 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.6891 (mp0) REVERT: A 1962 ARG cc_start: 0.7761 (ttm110) cc_final: 0.7403 (ptp-170) outliers start: 37 outliers final: 29 residues processed: 165 average time/residue: 0.1117 time to fit residues: 27.7069 Evaluate side-chains 167 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 TYR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 438 VAL Chi-restraints excluded: chain A residue 477 ASN Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 581 MET Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 ASP Chi-restraints excluded: chain A residue 839 PHE Chi-restraints excluded: chain A residue 894 ASP Chi-restraints excluded: chain A residue 925 GLN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 930 VAL Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 970 VAL Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1255 VAL Chi-restraints excluded: chain A residue 1353 ARG Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1435 SER Chi-restraints excluded: chain A residue 1458 LEU Chi-restraints excluded: chain A residue 1541 CYS Chi-restraints excluded: chain A residue 1668 VAL Chi-restraints excluded: chain A residue 1689 LEU Chi-restraints excluded: chain A residue 1729 VAL Chi-restraints excluded: chain A residue 1793 LEU Chi-restraints excluded: chain A residue 1798 LEU Chi-restraints excluded: chain A residue 1837 PHE Chi-restraints excluded: chain A residue 1844 THR Chi-restraints excluded: chain A residue 1886 GLU Chi-restraints excluded: chain A residue 1891 LEU Chi-restraints excluded: chain A residue 1910 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 73 optimal weight: 40.0000 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 chunk 161 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 53 optimal weight: 1.9990 chunk 112 optimal weight: 0.0770 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 HIS ** A 890 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1675 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.172900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137745 restraints weight = 19279.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.136577 restraints weight = 22421.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.137920 restraints weight = 20200.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.138136 restraints weight = 15470.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.138388 restraints weight = 13619.993| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 13593 Z= 0.167 Angle : 0.813 59.199 18515 Z= 0.446 Chirality : 0.041 0.620 2128 Planarity : 0.005 0.062 2344 Dihedral : 4.459 67.575 1838 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.45 % Allowed : 16.83 % Favored : 80.72 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.22), residues: 1667 helix: 2.18 (0.18), residues: 928 sheet: -1.77 (0.51), residues: 114 loop : -1.94 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 922 TYR 0.016 0.001 TYR A1926 PHE 0.013 0.001 PHE A1486 TRP 0.036 0.001 TRP A 979 HIS 0.003 0.001 HIS A 717 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (13578) covalent geometry : angle 0.80960 / 0.45 (18474) SS BOND : bond 0.00398 / 0.20 ( 4) SS BOND : angle 1.47718 / 1.09 ( 8) hydrogen bonds : bond 0.03686 / 2.48 ( 659) hydrogen bonds : angle 3.65082 / 2.65 ( 1929) link_BETA1-4 : bond 0.00400 / 0.19 ( 3) link_BETA1-4 : angle 1.26782 / 0.76 ( 9) link_NAG-ASN : bond 0.00459 / 0.30 ( 8) link_NAG-ASN : angle 1.94592 / 1.48 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2070.37 seconds wall clock time: 36 minutes 32.63 seconds (2192.63 seconds total)