Starting phenix.real_space_refine on Fri Jul 3 19:05:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bao_12126/07_2026/7bao_12126.cif" } resolution = 2.7 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= 0.004 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: 5 Type Number sf(0) Gaussians Ca 3 9.91 5 S 74 5.16 5 C 9635 2.51 5 N 2640 2.21 5 O 2954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 15306 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 15093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1904, 15093 Classifications: {'peptide': 1904} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 74, 'TRANS': 1829} Chain breaks: 4 Chain: "B" 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: "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: "D" 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: "E" 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: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 101 Unusual residues: {' CA': 3, 'NAG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 2.93, per 1000 atoms: 0.19 Number of scatterers: 15306 At special positions: 0 Unit cell: (120.406, 147.35, 121.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 3 19.99 S 74 16.00 O 2954 8.00 N 2640 7.00 C 9635 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 838 " - pdb=" SG CYS A 857 " distance=2.04 Simple disulfide: pdb=" SG CYS A 852 " - pdb=" SG CYS A 863 " distance=2.04 Simple disulfide: pdb=" SG CYS A 858 " - pdb=" SG CYS A 869 " distance=2.04 Simple disulfide: pdb=" SG CYS A1011 " - pdb=" SG CYS A1145 " distance=2.02 Simple disulfide: pdb=" SG CYS A1035 " - pdb=" SG CYS A2524 " distance=2.04 Simple disulfide: pdb=" SG CYS A1217 " - pdb=" SG CYS A1220 " distance=2.03 Simple disulfide: pdb=" SG CYS A1237 " - pdb=" SG CYS A1545 " distance=2.04 Simple disulfide: pdb=" SG CYS A1328 " - pdb=" SG CYS A1336 " distance=2.03 Simple disulfide: pdb=" SG CYS A1395 " - pdb=" SG CYS A1448 " distance=2.03 Simple disulfide: pdb=" SG CYS A1513 " - pdb=" SG CYS A1521 " distance=2.03 Simple disulfide: pdb=" SG CYS A1515 " - pdb=" SG CYS A1523 " distance=2.04 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 C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2801 " - " ASN A1705 " " NAG A2802 " - " ASN A1799 " " NAG A2803 " - " ASN A1884 " " NAG A2804 " - " ASN A1259 " " NAG A2805 " - " ASN A1741 " " NAG A2806 " - " ASN A1985 " " NAG A2807 " - " ASN A2188 " " NAG B 1 " - " ASN A1609 " " NAG C 1 " - " ASN A2328 " " NAG D 1 " - " ASN A2646 " " NAG E 1 " - " ASN A 940 " Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 605.2 milliseconds 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3508 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 23 sheets defined 9.6% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 850 through 860 Proline residue: A 855 - end of helix removed outlier: 3.706A pdb=" N LEU A 859 " --> pdb=" O ASP A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 881 removed outlier: 3.819A pdb=" N GLU A 881 " --> pdb=" O ASP A 877 " (cutoff:3.500A) Processing helix chain 'A' and resid 894 through 900 removed outlier: 3.634A pdb=" N ILE A 898 " --> pdb=" O PHE A 894 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 949 Processing helix chain 'A' and resid 1197 through 1199 No H-bonds generated for 'chain 'A' and resid 1197 through 1199' Processing helix chain 'A' and resid 1271 through 1280 removed outlier: 4.358A pdb=" N HIS A1275 " --> pdb=" O ARG A1272 " (cutoff:3.500A) Proline residue: A1277 - end of helix Processing helix chain 'A' and resid 1402 through 1404 No H-bonds generated for 'chain 'A' and resid 1402 through 1404' Processing helix chain 'A' and resid 2401 through 2405 Processing helix chain 'A' and resid 2434 through 2438 Processing helix chain 'A' and resid 2452 through 2456 Processing helix chain 'A' and resid 2465 through 2470 removed outlier: 3.752A pdb=" N THR A2469 " --> pdb=" O LYS A2465 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP A2470 " --> pdb=" O CYS A2466 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2465 through 2470' Processing helix chain 'A' and resid 2471 through 2479 removed outlier: 3.505A pdb=" N THR A2477 " --> pdb=" O SER A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2481 through 2485 Processing helix chain 'A' and resid 2500 through 2506 Processing helix chain 'A' and resid 2506 through 2511 removed outlier: 4.060A pdb=" N GLN A2511 " --> pdb=" O GLN A2507 " (cutoff:3.500A) Processing helix chain 'A' and resid 2520 through 2533 removed outlier: 3.706A pdb=" N CYS A2524 " --> pdb=" O LEU A2520 " (cutoff:3.500A) Processing helix chain 'A' and resid 2539 through 2543 Processing helix chain 'A' and resid 2590 through 2599 Processing helix chain 'A' and resid 2625 through 2633 removed outlier: 3.517A pdb=" N ILE A2631 " --> pdb=" O GLY A2627 " (cutoff:3.500A) Processing helix chain 'A' and resid 2682 through 2712 removed outlier: 3.547A pdb=" N LYS A2687 " --> pdb=" O LEU A2683 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU A2712 " --> pdb=" O GLN A2708 " (cutoff:3.500A) Processing helix chain 'A' and resid 2721 through 2732 removed outlier: 3.521A pdb=" N GLN A2726 " --> pdb=" O GLU A2722 " (cutoff:3.500A) Processing helix chain 'A' and resid 2748 through 2752 Processing helix chain 'A' and resid 2754 through 2756 No H-bonds generated for 'chain 'A' and resid 2754 through 2756' Processing sheet with id=AA1, first strand: chain 'A' and resid 959 through 965 removed outlier: 8.251A pdb=" N PHE A 994 " --> pdb=" O ALA A 921 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL A 923 " --> pdb=" O PHE A 994 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 959 through 965 Processing sheet with id=AA3, first strand: chain 'A' and resid 951 through 953 removed outlier: 3.701A pdb=" N GLU A 975 " --> pdb=" O ASN A 940 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1022 through 1025 Processing sheet with id=AA5, first strand: chain 'A' and resid 1041 through 1042 Processing sheet with id=AA6, first strand: chain 'A' and resid 1100 through 1107 Processing sheet with id=AA7, first strand: chain 'A' and resid 1178 through 1180 Processing sheet with id=AA8, first strand: chain 'A' and resid 1202 through 1203 removed outlier: 3.625A pdb=" N ARG A1559 " --> pdb=" O ASP A1554 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER A1541 " --> pdb=" O ALA A1553 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1222 through 1223 removed outlier: 6.635A pdb=" N ILE A1251 " --> pdb=" O ILE A1263 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1283 through 1285 removed outlier: 4.212A pdb=" N VAL A1292 " --> pdb=" O ILE A1305 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU A1294 " --> pdb=" O PHE A1303 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A1322 " --> pdb=" O VAL A1302 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1350 through 1355 removed outlier: 4.936A pdb=" N GLY A1352 " --> pdb=" O VAL A1364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1399 through 1400 removed outlier: 7.110A pdb=" N VAL A1429 " --> pdb=" O VAL A1441 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL A1423 " --> pdb=" O LEU A1430 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP A1411 " --> pdb=" O LEU A1424 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1470 through 1475 removed outlier: 6.485A pdb=" N ALA A1484 " --> pdb=" O THR A1471 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N LEU A1473 " --> pdb=" O TYR A1482 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TYR A1482 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE A1494 " --> pdb=" O VAL A1506 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1569 through 1570 removed outlier: 3.872A pdb=" N PHE A1569 " --> pdb=" O GLU A1577 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A1586 " --> pdb=" O THR A1598 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR A1598 " --> pdb=" O LEU A1586 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU A1588 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N LEU A1596 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ASN A1609 " --> pdb=" O LEU A1596 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR A1598 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU A1607 " --> pdb=" O ASP A1623 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASP A1623 " --> pdb=" O LEU A1607 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASN A1609 " --> pdb=" O ILE A1621 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ILE A1621 " --> pdb=" O ASN A1609 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR A1611 " --> pdb=" O THR A1619 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A1617 " --> pdb=" O THR A1613 " (cutoff:3.500A) removed outlier: 10.442A pdb=" N ASP A1617 " --> pdb=" O ARG A1633 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ARG A1633 " --> pdb=" O ASP A1617 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N THR A1619 " --> pdb=" O VAL A1631 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN A1630 " --> pdb=" O LEU A1642 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LEU A1642 " --> pdb=" O ASN A1630 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARG A1632 " --> pdb=" O LEU A1640 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU A1640 " --> pdb=" O VAL A1652 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TRP A1651 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL A1663 " --> pdb=" O TRP A1651 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A1653 " --> pdb=" O LYS A1661 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS A1661 " --> pdb=" O MET A1673 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A1671 " --> pdb=" O VAL A1663 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N MET A1672 " --> pdb=" O LYS A1685 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A1685 " --> pdb=" O MET A1672 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR A1674 " --> pdb=" O ALA A1683 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LEU A1681 " --> pdb=" O HIS A1676 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N LEU A1681 " --> pdb=" O TYR A1697 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N TYR A1697 " --> pdb=" O LEU A1681 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N ALA A1683 " --> pdb=" O TYR A1695 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A1694 " --> pdb=" O VAL A1706 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A1706 " --> pdb=" O PHE A1694 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU A1696 " --> pdb=" O THR A1704 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N THR A1704 " --> pdb=" O PHE A1716 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP A1719 " --> pdb=" O HIS A1725 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL A1724 " --> pdb=" O THR A1740 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1740 " --> pdb=" O VAL A1724 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A1828 " --> pdb=" O ARG A1816 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A1826 " --> pdb=" O GLU A1818 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU A1839 " --> pdb=" O LEU A1831 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL A1833 " --> pdb=" O ASN A1837 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN A1837 " --> pdb=" O VAL A1833 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1782 through 1784 Processing sheet with id=AB7, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 6.718A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A1944 " --> pdb=" O VAL A1956 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A1956 " --> pdb=" O ILE A1944 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A1946 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A1989 " --> pdb=" O THR A2001 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A2001 " --> pdb=" O ILE A1989 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A1991 " --> pdb=" O LEU A1999 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG A2009 " --> pdb=" O TYR A2025 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR A2025 " --> pdb=" O ARG A2009 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A2029 " --> pdb=" O LEU A2046 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A2046 " --> pdb=" O LYS A2029 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER A2031 " --> pdb=" O ILE A2044 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A2044 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A2033 " --> pdb=" O LYS A2042 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1883 through 1887 removed outlier: 6.718A pdb=" N ASN A1884 " --> pdb=" O ILE A1896 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A1896 " --> pdb=" O ASN A1884 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N THR A1886 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A1894 " --> pdb=" O MET A1905 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A1905 " --> pdb=" O ALA A1894 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N SER A1902 " --> pdb=" O PHE A1918 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N PHE A1918 " --> pdb=" O SER A1902 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A1904 " --> pdb=" O ARG A1916 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG A1916 " --> pdb=" O ARG A1904 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLU A1906 " --> pdb=" O THR A1914 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N THR A1914 " --> pdb=" O TYR A1926 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A1944 " --> pdb=" O VAL A1956 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N VAL A1956 " --> pdb=" O ILE A1944 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N GLU A1946 " --> pdb=" O SER A1954 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N SER A1954 " --> pdb=" O LEU A1966 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A1989 " --> pdb=" O THR A2001 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR A2001 " --> pdb=" O ILE A1989 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A1991 " --> pdb=" O LEU A1999 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N LEU A1999 " --> pdb=" O TYR A2012 " (cutoff:3.500A) removed outlier: 8.012A pdb=" N ARG A2009 " --> pdb=" O TYR A2025 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N TYR A2025 " --> pdb=" O ARG A2009 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILE A2011 " --> pdb=" O THR A2023 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR A2023 " --> pdb=" O ILE A2011 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS A2013 " --> pdb=" O ALA A2021 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ALA A2021 " --> pdb=" O PHE A2032 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS A2029 " --> pdb=" O LEU A2046 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A2046 " --> pdb=" O LYS A2029 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N SER A2031 " --> pdb=" O ILE A2044 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A2044 " --> pdb=" O SER A2031 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR A2033 " --> pdb=" O LYS A2042 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A2042 " --> pdb=" O TYR A2057 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N THR A2052 " --> pdb=" O PHE A2071 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE A2071 " --> pdb=" O THR A2052 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR A2054 " --> pdb=" O PHE A2069 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE A2069 " --> pdb=" O THR A2054 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ARG A2056 " --> pdb=" O GLN A2067 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLN A2067 " --> pdb=" O ARG A2056 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A2058 " --> pdb=" O ASP A2065 " (cutoff:3.500A) removed outlier: 10.540A pdb=" N LEU A2063 " --> pdb=" O TYR A2085 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N TYR A2085 " --> pdb=" O LEU A2063 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASP A2065 " --> pdb=" O TYR A2083 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ARG A2080 " --> pdb=" O ALA A2096 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ALA A2096 " --> pdb=" O ARG A2080 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ASP A2082 " --> pdb=" O MET A2094 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N MET A2094 " --> pdb=" O ASP A2082 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASN A2084 " --> pdb=" O THR A2092 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N THR A2092 " --> pdb=" O TYR A2108 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU A2107 " --> pdb=" O PHE A2120 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N PHE A2120 " --> pdb=" O LEU A2107 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N ARG A2109 " --> pdb=" O GLU A2118 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N GLU A2118 " --> pdb=" O VAL A2125 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN A2132 " --> pdb=" O LYS A2143 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A2153 " --> pdb=" O HIS A2144 " (cutoff:3.500A) removed outlier: 5.544A pdb=" N LYS A2152 " --> pdb=" O VAL A2168 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR A2164 " --> pdb=" O TYR A2156 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE A2158 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LEU A2162 " --> pdb=" O ILE A2158 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A2178 " --> pdb=" O GLN A2169 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL A2177 " --> pdb=" O TYR A2194 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARG A2191 " --> pdb=" O ILE A2207 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A2207 " --> pdb=" O ARG A2191 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER A2193 " --> pdb=" O VAL A2205 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N VAL A2205 " --> pdb=" O SER A2193 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLU A2195 " --> pdb=" O GLN A2203 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A2207 " --> pdb=" O PRO A2211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2216 through 2217 removed outlier: 6.657A pdb=" N SER A2216 " --> pdb=" O HIS A2224 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N HIS A2224 " --> pdb=" O LEU A2237 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU A2248 " --> pdb=" O PRO A2236 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ARG A2238 " --> pdb=" O THR A2246 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N THR A2246 " --> pdb=" O TYR A2253 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLN A2252 " --> pdb=" O ARG A2264 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG A2264 " --> pdb=" O GLN A2252 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS A2254 " --> pdb=" O ARG A2262 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ARG A2262 " --> pdb=" O PHE A2269 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LYS A2279 " --> pdb=" O GLU A2270 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILE A2278 " --> pdb=" O TYR A2291 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER A2288 " --> pdb=" O SER A2304 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N SER A2304 " --> pdb=" O SER A2288 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG A2290 " --> pdb=" O SER A2302 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER A2302 " --> pdb=" O ARG A2290 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ARG A2292 " --> pdb=" O VAL A2300 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N VAL A2300 " --> pdb=" O PHE A2312 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N HIS A2325 " --> pdb=" O PHE A2313 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU A2333 " --> pdb=" O ASN A2328 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA A2347 " --> pdb=" O TYR A2338 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N PHE A2346 " --> pdb=" O ILE A2358 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N GLU A2355 " --> pdb=" O SER A2371 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N SER A2371 " --> pdb=" O GLU A2355 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N TYR A2357 " --> pdb=" O VAL A2369 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N VAL A2369 " --> pdb=" O TYR A2357 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ALA A2359 " --> pdb=" O LEU A2367 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N LEU A2367 " --> pdb=" O GLN A2379 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N GLN A2379 " --> pdb=" O LEU A2367 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL A2369 " --> pdb=" O ILE A2377 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET A2390 " --> pdb=" O LEU A2381 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2406 through 2408 removed outlier: 4.064A pdb=" N LEU A2413 " --> pdb=" O ASP A2408 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2570 through 2574 Processing sheet with id=AC3, first strand: chain 'A' and resid 2602 through 2603 Processing sheet with id=AC4, first strand: chain 'A' and resid 2602 through 2603 removed outlier: 6.165A pdb=" N ASP A2615 " --> pdb=" O CYS A2674 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N ASN A2676 " --> pdb=" O ASP A2615 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N HIS A2617 " --> pdb=" O ASN A2676 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ARG A2678 " --> pdb=" O HIS A2617 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N PHE A2619 " --> pdb=" O ARG A2678 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2737 through 2741 546 hydrogen bonds defined for protein. 1401 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: 4.43 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4945 1.33 - 1.46: 3725 1.46 - 1.58: 6846 1.58 - 1.71: 0 1.71 - 1.84: 119 Bond restraints: 15635 Sorted by residual: bond pdb=" CG1 ILE A1989 " pdb=" CD1 ILE A1989 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" N LEU A 862 " pdb=" CA LEU A 862 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.23e-02 6.61e+03 9.93e+00 bond pdb=" CG ARG A1976 " pdb=" CD ARG A1976 " ideal model delta sigma weight residual 1.520 1.441 0.079 3.00e-02 1.11e+03 6.96e+00 bond pdb=" CB VAL A2423 " pdb=" CG2 VAL A2423 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.44e+00 bond pdb=" CB ARG A2008 " pdb=" CG ARG A2008 " ideal model delta sigma weight residual 1.520 1.446 0.074 3.00e-02 1.11e+03 6.00e+00 ... (remaining 15630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 20566 2.58 - 5.16: 568 5.16 - 7.74: 55 7.74 - 10.32: 9 10.32 - 12.90: 1 Bond angle restraints: 21199 Sorted by residual: angle pdb=" C ASN A 874 " pdb=" N PRO A 875 " pdb=" CA PRO A 875 " ideal model delta sigma weight residual 119.56 115.12 4.44 1.02e+00 9.61e-01 1.90e+01 angle pdb=" N VAL A1321 " pdb=" CA VAL A1321 " pdb=" C VAL A1321 " ideal model delta sigma weight residual 113.42 108.52 4.90 1.17e+00 7.31e-01 1.75e+01 angle pdb=" CB ARG A2244 " pdb=" CG ARG A2244 " pdb=" CD ARG A2244 " ideal model delta sigma weight residual 111.30 101.77 9.53 2.30e+00 1.89e-01 1.72e+01 angle pdb=" CA ASP A 847 " pdb=" CB ASP A 847 " pdb=" CG ASP A 847 " ideal model delta sigma weight residual 112.60 116.52 -3.92 1.00e+00 1.00e+00 1.54e+01 angle pdb=" N GLN A1823 " pdb=" CA GLN A1823 " pdb=" C GLN A1823 " ideal model delta sigma weight residual 108.34 113.39 -5.05 1.31e+00 5.83e-01 1.48e+01 ... (remaining 21194 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 8457 17.75 - 35.50: 633 35.50 - 53.25: 81 53.25 - 71.00: 19 71.00 - 88.76: 15 Dihedral angle restraints: 9205 sinusoidal: 3705 harmonic: 5500 Sorted by residual: dihedral pdb=" CA TYR A2025 " pdb=" C TYR A2025 " pdb=" N ASP A2026 " pdb=" CA ASP A2026 " ideal model delta harmonic sigma weight residual -180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA ASN A1557 " pdb=" C ASN A1557 " pdb=" N ILE A1558 " pdb=" CA ILE A1558 " ideal model delta harmonic sigma weight residual -180.00 -150.27 -29.73 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ASN A2657 " pdb=" C ASN A2657 " pdb=" N GLY A2658 " pdb=" CA GLY A2658 " ideal model delta harmonic sigma weight residual 180.00 150.85 29.15 0 5.00e+00 4.00e-02 3.40e+01 ... (remaining 9202 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2201 0.112 - 0.223: 164 0.223 - 0.335: 6 0.335 - 0.446: 1 0.446 - 0.558: 1 Chirality restraints: 2373 Sorted by residual: chirality pdb=" CB ILE A1989 " pdb=" CA ILE A1989 " pdb=" CG1 ILE A1989 " pdb=" CG2 ILE A1989 " both_signs ideal model delta sigma weight residual False 2.64 2.09 0.56 2.00e-01 2.50e+01 7.77e+00 chirality pdb=" CB VAL A2534 " pdb=" CA VAL A2534 " pdb=" CG1 VAL A2534 " pdb=" CG2 VAL A2534 " both_signs ideal model delta sigma weight residual False -2.63 -2.19 -0.43 2.00e-01 2.50e+01 4.72e+00 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 940 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.42e+00 ... (remaining 2370 not shown) Planarity restraints: 2748 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1865 " 0.020 2.00e-02 2.50e+03 2.15e-02 9.27e+00 pdb=" CG TYR A1865 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR A1865 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR A1865 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR A1865 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR A1865 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A1865 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1865 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A1145 " -0.048 5.00e-02 4.00e+02 7.42e-02 8.81e+00 pdb=" N PRO A1146 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A1146 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A1146 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A2085 " -0.013 2.00e-02 2.50e+03 1.98e-02 7.86e+00 pdb=" CG TYR A2085 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TYR A2085 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR A2085 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A2085 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR A2085 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A2085 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A2085 " 0.003 2.00e-02 2.50e+03 ... (remaining 2745 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 194 2.64 - 3.20: 13259 3.20 - 3.77: 21581 3.77 - 4.33: 31837 4.33 - 4.90: 54680 Nonbonded interactions: 121551 Sorted by model distance: nonbonded pdb=" NH1 ARG A1300 " pdb=" OD1 ASN A1349 " model vdw 2.075 3.120 nonbonded pdb=" NH1 ARG A1300 " pdb=" O THR A1348 " model vdw 2.124 3.120 nonbonded pdb=" OG1 THR A2006 " pdb=" OD2 ASP A2258 " model vdw 2.141 3.040 nonbonded pdb=" OG SER A2744 " pdb=" OE1 GLN A2747 " model vdw 2.146 3.040 nonbonded pdb=" NE2 GLN A2119 " pdb=" O GLY A2121 " model vdw 2.168 3.120 ... (remaining 121546 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.150 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:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8758 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 : 0.011 0.139 15661 Z= 0.465 Angle : 1.011 12.898 21266 Z= 0.551 Chirality : 0.064 0.558 2373 Planarity : 0.006 0.074 2737 Dihedral : 12.982 88.755 5664 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.06 % Allowed : 0.42 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.18), residues: 1894 helix: -2.35 (0.41), residues: 109 sheet: -0.14 (0.21), residues: 601 loop : -1.70 (0.17), residues: 1184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.002 ARG A2427 TYR 0.052 0.003 TYR A1865 PHE 0.045 0.003 PHE A2069 TRP 0.041 0.003 TRP A 990 HIS 0.015 0.003 HIS A2000 Details of bonding type rmsd/Z covalent geometry : bond 0.01093 / 0.47 (15635) covalent geometry : angle 1.00165 / 0.55 (21199) SS BOND : bond 0.00768 / 0.43 ( 11) SS BOND : angle 2.01727 / 1.09 ( 22) hydrogen bonds : bond 0.24494 / 16.06 ( 476) hydrogen bonds : angle 9.17524 / 6.48 ( 1401) link_BETA1-4 : bond 0.00387 / 0.19 ( 4) link_BETA1-4 : angle 1.78924 / 1.11 ( 12) link_NAG-ASN : bond 0.00668 / 0.40 ( 11) link_NAG-ASN : angle 3.17742 / 1.93 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 180 time to evaluate : 0.605 Fit side-chains revert: symmetry clash REVERT: A 945 ASN cc_start: 0.8281 (p0) cc_final: 0.8072 (p0) REVERT: A 1363 PHE cc_start: 0.8961 (p90) cc_final: 0.8692 (p90) REVERT: A 1440 ILE cc_start: 0.8668 (mm) cc_final: 0.8195 (tt) REVERT: A 1673 MET cc_start: 0.9015 (mpp) cc_final: 0.8664 (mpp) REVERT: A 1748 PHE cc_start: 0.7767 (t80) cc_final: 0.7423 (t80) REVERT: A 1905 MET cc_start: 0.8078 (mpp) cc_final: 0.7673 (mpt) outliers start: 1 outliers final: 2 residues processed: 181 average time/residue: 0.6382 time to fit residues: 126.1488 Evaluate side-chains 135 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 133 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 877 ASP Chi-restraints excluded: chain A residue 896 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 50.0000 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1262 ASN A1419 ASN A1427 ASN A1668 HIS A2087 ASN A2095 GLN A2252 GLN A2403 HIS A2588 ASN A2651 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.145842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.101484 restraints weight = 21020.927| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.47 r_work: 0.3142 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8948 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15661 Z= 0.140 Angle : 0.688 9.648 21266 Z= 0.358 Chirality : 0.048 0.296 2373 Planarity : 0.005 0.063 2737 Dihedral : 5.929 87.635 2110 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.74 % Allowed : 6.98 % Favored : 91.28 % 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: -1.05 (0.19), residues: 1894 helix: -0.39 (0.49), residues: 103 sheet: 0.22 (0.21), residues: 609 loop : -1.27 (0.17), residues: 1182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1371 TYR 0.020 0.001 TYR A2085 PHE 0.014 0.001 PHE A2069 TRP 0.013 0.001 TRP A1874 HIS 0.006 0.001 HIS A2000 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15635) covalent geometry : angle 0.68219 / 0.36 (21199) SS BOND : bond 0.00301 / 0.16 ( 11) SS BOND : angle 0.88103 / 0.51 ( 22) hydrogen bonds : bond 0.04920 / 3.39 ( 476) hydrogen bonds : angle 6.06170 / 4.31 ( 1401) link_BETA1-4 : bond 0.00375 / 0.18 ( 4) link_BETA1-4 : angle 1.00086 / 0.61 ( 12) link_NAG-ASN : bond 0.00275 / 0.15 ( 11) link_NAG-ASN : angle 2.32707 / 1.40 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.377 Fit side-chains REVERT: A 853 MET cc_start: 0.7925 (mmp) cc_final: 0.7334 (mtm) REVERT: A 945 ASN cc_start: 0.8202 (p0) cc_final: 0.7760 (p0) REVERT: A 948 LEU cc_start: 0.9150 (mt) cc_final: 0.8895 (pt) REVERT: A 1425 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (p0) REVERT: A 1440 ILE cc_start: 0.8544 (mm) cc_final: 0.8305 (tt) REVERT: A 1673 MET cc_start: 0.9350 (mpp) cc_final: 0.8821 (mpp) REVERT: A 1748 PHE cc_start: 0.8272 (t80) cc_final: 0.8004 (t80) REVERT: A 1905 MET cc_start: 0.8647 (mpp) cc_final: 0.8205 (mpt) REVERT: A 2219 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8730 (mt) REVERT: A 2470 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7692 (t0) outliers start: 29 outliers final: 8 residues processed: 176 average time/residue: 0.5357 time to fit residues: 104.8290 Evaluate side-chains 142 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1425 ASP Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2470 ASP Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 101 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 169 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 chunk 144 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1262 ASN A1419 ASN A1496 GLN A1571 ASN A2087 ASN A2588 ASN A2676 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.147215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103374 restraints weight = 21237.465| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.46 r_work: 0.3168 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15661 Z= 0.114 Angle : 0.623 9.682 21266 Z= 0.320 Chirality : 0.046 0.277 2373 Planarity : 0.005 0.054 2737 Dihedral : 5.085 33.027 2106 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.16 % Allowed : 10.58 % Favored : 87.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.63 (0.19), residues: 1894 helix: 0.58 (0.52), residues: 103 sheet: 0.51 (0.21), residues: 616 loop : -1.06 (0.18), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1371 TYR 0.015 0.001 TYR A2025 PHE 0.010 0.001 PHE A1569 TRP 0.008 0.001 TRP A1874 HIS 0.007 0.001 HIS A 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (15635) covalent geometry : angle 0.61391 / 0.32 (21199) SS BOND : bond 0.00204 / 0.11 ( 11) SS BOND : angle 0.75464 / 0.44 ( 22) hydrogen bonds : bond 0.04129 / 2.82 ( 476) hydrogen bonds : angle 5.42522 / 3.86 ( 1401) link_BETA1-4 : bond 0.00321 / 0.16 ( 4) link_BETA1-4 : angle 1.09775 / 0.65 ( 12) link_NAG-ASN : bond 0.00218 / 0.12 ( 11) link_NAG-ASN : angle 2.69924 / 1.68 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 0.447 Fit side-chains REVERT: A 853 MET cc_start: 0.7907 (mmp) cc_final: 0.7413 (mtm) REVERT: A 1368 MET cc_start: 0.8353 (mtm) cc_final: 0.8125 (ptp) REVERT: A 1425 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7918 (p0) REVERT: A 1673 MET cc_start: 0.9321 (mpp) cc_final: 0.8872 (mpp) REVERT: A 1748 PHE cc_start: 0.8247 (t80) cc_final: 0.8004 (t80) REVERT: A 1905 MET cc_start: 0.8643 (mpp) cc_final: 0.8109 (mpt) REVERT: A 2087 ASN cc_start: 0.7609 (t0) cc_final: 0.7397 (t160) REVERT: A 2106 ASP cc_start: 0.8704 (OUTLIER) cc_final: 0.8436 (m-30) REVERT: A 2219 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8861 (mt) outliers start: 36 outliers final: 14 residues processed: 182 average time/residue: 0.5310 time to fit residues: 107.6511 Evaluate side-chains 151 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1425 ASP Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1739 THR Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 2106 ASP Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 102 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 128 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 159 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 169 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN A1668 HIS A2608 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.144031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099295 restraints weight = 21158.763| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.46 r_work: 0.3105 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15661 Z= 0.215 Angle : 0.702 10.150 21266 Z= 0.358 Chirality : 0.049 0.275 2373 Planarity : 0.005 0.055 2737 Dihedral : 5.239 29.958 2106 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.47 % Allowed : 12.39 % Favored : 85.15 % 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 (0.19), residues: 1894 helix: 0.76 (0.51), residues: 103 sheet: 0.63 (0.21), residues: 598 loop : -1.08 (0.17), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2008 TYR 0.024 0.002 TYR A1865 PHE 0.014 0.002 PHE A2069 TRP 0.010 0.001 TRP A 990 HIS 0.006 0.001 HIS A2000 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.22 (15635) covalent geometry : angle 0.69116 / 0.36 (21199) SS BOND : bond 0.00252 / 0.14 ( 11) SS BOND : angle 1.15489 / 0.69 ( 22) hydrogen bonds : bond 0.04601 / 3.14 ( 476) hydrogen bonds : angle 5.45019 / 3.88 ( 1401) link_BETA1-4 : bond 0.00297 / 0.14 ( 4) link_BETA1-4 : angle 1.22996 / 0.75 ( 12) link_NAG-ASN : bond 0.00269 / 0.15 ( 11) link_NAG-ASN : angle 3.07580 / 1.90 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.7994 (mmp) cc_final: 0.7511 (mtm) REVERT: A 1060 ARG cc_start: 0.8500 (mtm-85) cc_final: 0.8101 (mtp180) REVERT: A 1368 MET cc_start: 0.8383 (mtm) cc_final: 0.8155 (ptp) REVERT: A 1673 MET cc_start: 0.9360 (mpp) cc_final: 0.8821 (mpp) REVERT: A 1748 PHE cc_start: 0.8270 (t80) cc_final: 0.8016 (t80) REVERT: A 1934 VAL cc_start: 0.9035 (OUTLIER) cc_final: 0.8824 (t) REVERT: A 1995 ASP cc_start: 0.8246 (OUTLIER) cc_final: 0.8044 (p0) REVERT: A 2035 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: A 2219 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8927 (mt) REVERT: A 2355 GLU cc_start: 0.8165 (OUTLIER) cc_final: 0.7893 (mm-30) outliers start: 41 outliers final: 21 residues processed: 171 average time/residue: 0.5232 time to fit residues: 99.9037 Evaluate side-chains 159 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 133 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1240 ASP Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1354 THR Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1934 VAL Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2642 GLU Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 87 optimal weight: 0.0870 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 186 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 117 optimal weight: 0.0970 chunk 47 optimal weight: 10.0000 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN A1668 HIS A2087 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.145261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.100577 restraints weight = 21122.459| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.46 r_work: 0.3124 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15661 Z= 0.146 Angle : 0.638 10.886 21266 Z= 0.325 Chirality : 0.046 0.271 2373 Planarity : 0.004 0.055 2737 Dihedral : 5.013 29.163 2106 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.59 % Allowed : 13.35 % Favored : 84.06 % 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: -0.48 (0.19), residues: 1894 helix: 0.92 (0.52), residues: 105 sheet: 0.63 (0.21), residues: 616 loop : -1.00 (0.18), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1371 TYR 0.015 0.001 TYR A2025 PHE 0.013 0.001 PHE A1363 TRP 0.009 0.001 TRP A1874 HIS 0.006 0.001 HIS A2438 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (15635) covalent geometry : angle 0.62798 / 0.32 (21199) SS BOND : bond 0.00251 / 0.14 ( 11) SS BOND : angle 0.84490 / 0.51 ( 22) hydrogen bonds : bond 0.04047 / 2.75 ( 476) hydrogen bonds : angle 5.28279 / 3.76 ( 1401) link_BETA1-4 : bond 0.00388 / 0.19 ( 4) link_BETA1-4 : angle 1.16255 / 0.71 ( 12) link_NAG-ASN : bond 0.00222 / 0.11 ( 11) link_NAG-ASN : angle 2.82406 / 1.75 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.8033 (mmp) cc_final: 0.7543 (mtm) REVERT: A 1060 ARG cc_start: 0.8490 (mtm-85) cc_final: 0.8035 (mtm180) REVERT: A 1319 GLU cc_start: 0.7595 (tp30) cc_final: 0.7178 (mp0) REVERT: A 1577 GLU cc_start: 0.8413 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 1673 MET cc_start: 0.9335 (mpp) cc_final: 0.8808 (mpp) REVERT: A 1748 PHE cc_start: 0.8278 (t80) cc_final: 0.8055 (t80) REVERT: A 1905 MET cc_start: 0.8582 (mpp) cc_final: 0.8026 (mpt) REVERT: A 1995 ASP cc_start: 0.8211 (OUTLIER) cc_final: 0.7994 (p0) REVERT: A 2035 ASP cc_start: 0.8065 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: A 2160 ARG cc_start: 0.8670 (mtp85) cc_final: 0.8292 (mmt-90) REVERT: A 2219 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.8995 (mt) REVERT: A 2355 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7889 (mm-30) REVERT: A 2588 ASN cc_start: 0.8133 (t0) cc_final: 0.7275 (p0) REVERT: A 2701 GLN cc_start: 0.8595 (OUTLIER) cc_final: 0.8339 (mt0) outliers start: 43 outliers final: 21 residues processed: 175 average time/residue: 0.5134 time to fit residues: 100.3351 Evaluate side-chains 164 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1240 ASP Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1665 THR Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1835 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2461 SER Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 81 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 136 optimal weight: 0.9990 chunk 163 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 151 optimal weight: 0.6980 chunk 161 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN A1668 HIS A2087 ASN A2523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.145556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.100790 restraints weight = 21129.180| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.47 r_work: 0.3128 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8959 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15661 Z= 0.136 Angle : 0.630 12.557 21266 Z= 0.320 Chirality : 0.046 0.271 2373 Planarity : 0.004 0.055 2737 Dihedral : 4.897 32.672 2106 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.89 % Allowed : 13.89 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.37 (0.19), residues: 1894 helix: 1.28 (0.53), residues: 103 sheet: 0.68 (0.20), residues: 626 loop : -0.94 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2160 TYR 0.015 0.001 TYR A2025 PHE 0.016 0.001 PHE A1363 TRP 0.009 0.001 TRP A1874 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (15635) covalent geometry : angle 0.62110 / 0.32 (21199) SS BOND : bond 0.00245 / 0.13 ( 11) SS BOND : angle 0.72860 / 0.44 ( 22) hydrogen bonds : bond 0.03864 / 2.63 ( 476) hydrogen bonds : angle 5.18399 / 3.68 ( 1401) link_BETA1-4 : bond 0.00359 / 0.17 ( 4) link_BETA1-4 : angle 1.12088 / 0.67 ( 12) link_NAG-ASN : bond 0.00220 / 0.11 ( 11) link_NAG-ASN : angle 2.68800 / 1.66 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 150 time to evaluate : 0.535 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.8037 (mmp) cc_final: 0.7521 (mtt) REVERT: A 1060 ARG cc_start: 0.8441 (mtm-85) cc_final: 0.8147 (mtm180) REVERT: A 1319 GLU cc_start: 0.7607 (tp30) cc_final: 0.7230 (mp0) REVERT: A 1577 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8153 (mt-10) REVERT: A 1673 MET cc_start: 0.9338 (mpp) cc_final: 0.8814 (mpp) REVERT: A 1748 PHE cc_start: 0.8259 (t80) cc_final: 0.8004 (t80) REVERT: A 1995 ASP cc_start: 0.8218 (OUTLIER) cc_final: 0.7995 (p0) REVERT: A 2035 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7762 (m-30) REVERT: A 2087 ASN cc_start: 0.7659 (t0) cc_final: 0.7428 (t160) REVERT: A 2160 ARG cc_start: 0.8666 (mtp85) cc_final: 0.8311 (mmt-90) REVERT: A 2219 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9016 (mt) REVERT: A 2355 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7880 (mm-30) REVERT: A 2588 ASN cc_start: 0.8058 (t0) cc_final: 0.7169 (p0) outliers start: 48 outliers final: 27 residues processed: 188 average time/residue: 0.4697 time to fit residues: 99.1935 Evaluate side-chains 171 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1240 ASP Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1321 VAL Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1665 THR Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1692 THR Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1754 ASP Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2027 THR Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 1 optimal weight: 0.3980 chunk 105 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 170 optimal weight: 4.9990 chunk 118 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 152 optimal weight: 0.6980 chunk 24 optimal weight: 7.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN A1668 HIS A2132 GLN A2403 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.146623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.102057 restraints weight = 20970.040| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.47 r_work: 0.3147 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15661 Z= 0.108 Angle : 0.601 12.517 21266 Z= 0.304 Chirality : 0.045 0.272 2373 Planarity : 0.004 0.056 2737 Dihedral : 4.715 30.251 2106 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.65 % Allowed : 14.43 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.24 (0.19), residues: 1894 helix: 1.32 (0.54), residues: 105 sheet: 0.75 (0.21), residues: 628 loop : -0.85 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1371 TYR 0.014 0.001 TYR A2025 PHE 0.018 0.001 PHE A 974 TRP 0.009 0.001 TRP A1874 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (15635) covalent geometry : angle 0.59290 / 0.30 (21199) SS BOND : bond 0.00191 / 0.11 ( 11) SS BOND : angle 0.61744 / 0.37 ( 22) hydrogen bonds : bond 0.03579 / 2.42 ( 476) hydrogen bonds : angle 5.07127 / 3.59 ( 1401) link_BETA1-4 : bond 0.00355 / 0.18 ( 4) link_BETA1-4 : angle 1.07102 / 0.64 ( 12) link_NAG-ASN : bond 0.00209 / 0.11 ( 11) link_NAG-ASN : angle 2.52533 / 1.57 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.547 Fit side-chains REVERT: A 853 MET cc_start: 0.8048 (mmp) cc_final: 0.7527 (mtt) REVERT: A 1060 ARG cc_start: 0.8427 (mtm-85) cc_final: 0.8119 (mtm180) REVERT: A 1319 GLU cc_start: 0.7629 (tp30) cc_final: 0.7240 (mp0) REVERT: A 1673 MET cc_start: 0.9327 (mpp) cc_final: 0.9044 (mpp) REVERT: A 1748 PHE cc_start: 0.8228 (t80) cc_final: 0.7988 (t80) REVERT: A 1905 MET cc_start: 0.8559 (mpp) cc_final: 0.7998 (mpt) REVERT: A 1995 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7973 (p0) REVERT: A 2035 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7722 (m-30) REVERT: A 2087 ASN cc_start: 0.7592 (t0) cc_final: 0.7352 (t160) REVERT: A 2219 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9023 (mt) REVERT: A 2355 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7879 (mm-30) REVERT: A 2588 ASN cc_start: 0.8043 (t0) cc_final: 0.7172 (p0) REVERT: A 2701 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8362 (mt0) outliers start: 44 outliers final: 17 residues processed: 183 average time/residue: 0.4670 time to fit residues: 95.7404 Evaluate side-chains 161 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 139 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1263 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 146 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 92 optimal weight: 0.8980 chunk 161 optimal weight: 0.0040 chunk 137 optimal weight: 0.0470 chunk 76 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 53 optimal weight: 2.9990 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1427 ASN A1668 HIS A2132 GLN A2342 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.146209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.101911 restraints weight = 21033.776| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.48 r_work: 0.3163 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15661 Z= 0.101 Angle : 0.653 28.348 21266 Z= 0.316 Chirality : 0.045 0.281 2373 Planarity : 0.004 0.055 2737 Dihedral : 4.595 29.926 2106 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.70 % Favored : 95.25 % Rotamer: Outliers : 2.04 % Allowed : 15.51 % Favored : 82.44 % 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: -0.15 (0.19), residues: 1894 helix: 1.46 (0.54), residues: 105 sheet: 0.85 (0.21), residues: 623 loop : -0.81 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A2659 TYR 0.014 0.001 TYR A2025 PHE 0.016 0.001 PHE A 974 TRP 0.008 0.001 TRP A1874 HIS 0.008 0.001 HIS A2438 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.10 (15635) covalent geometry : angle 0.61711 / 0.31 (21199) SS BOND : bond 0.00173 / 0.10 ( 11) SS BOND : angle 0.54633 / 0.33 ( 22) hydrogen bonds : bond 0.03374 / 2.27 ( 476) hydrogen bonds : angle 4.96307 / 3.51 ( 1401) link_BETA1-4 : bond 0.00507 / 0.25 ( 4) link_BETA1-4 : angle 1.05878 / 0.62 ( 12) link_NAG-ASN : bond 0.00319 / 0.16 ( 11) link_NAG-ASN : angle 5.43512 / 3.56 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 0.621 Fit side-chains REVERT: A 853 MET cc_start: 0.8085 (mmp) cc_final: 0.7596 (mtt) REVERT: A 1060 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.8006 (mtm180) REVERT: A 1319 GLU cc_start: 0.7680 (tp30) cc_final: 0.7304 (mp0) REVERT: A 1673 MET cc_start: 0.9317 (mpp) cc_final: 0.9054 (mpp) REVERT: A 1748 PHE cc_start: 0.8198 (t80) cc_final: 0.7967 (t80) REVERT: A 1905 MET cc_start: 0.8539 (mpp) cc_final: 0.7981 (mpt) REVERT: A 1995 ASP cc_start: 0.8201 (OUTLIER) cc_final: 0.7970 (p0) REVERT: A 2035 ASP cc_start: 0.7981 (OUTLIER) cc_final: 0.7691 (m-30) REVERT: A 2087 ASN cc_start: 0.7532 (t0) cc_final: 0.7306 (t160) REVERT: A 2160 ARG cc_start: 0.8629 (mtp85) cc_final: 0.8236 (mmt-90) REVERT: A 2219 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9046 (mt) REVERT: A 2355 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7858 (mm-30) REVERT: A 2588 ASN cc_start: 0.7986 (t0) cc_final: 0.7207 (p0) REVERT: A 2701 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8306 (mt0) outliers start: 34 outliers final: 17 residues processed: 171 average time/residue: 0.5608 time to fit residues: 106.7674 Evaluate side-chains 162 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 952 THR Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1642 LEU Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1958 MET Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2035 ASP Chi-restraints excluded: chain A residue 2219 LEU Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 142 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 65 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 165 optimal weight: 0.0370 chunk 59 optimal weight: 9.9990 chunk 150 optimal weight: 0.3980 chunk 82 optimal weight: 0.0070 chunk 17 optimal weight: 0.2980 chunk 105 optimal weight: 0.1980 overall best weight: 0.1876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 984 HIS A1668 HIS A1725 HIS A2132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.148971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.104927 restraints weight = 21050.422| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.46 r_work: 0.3195 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 15661 Z= 0.094 Angle : 0.584 12.701 21266 Z= 0.295 Chirality : 0.044 0.272 2373 Planarity : 0.004 0.055 2737 Dihedral : 4.375 30.716 2106 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.68 % Allowed : 16.12 % Favored : 82.20 % 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: 0.02 (0.19), residues: 1894 helix: 1.74 (0.55), residues: 103 sheet: 0.94 (0.20), residues: 640 loop : -0.72 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A2659 TYR 0.013 0.001 TYR A2025 PHE 0.015 0.001 PHE A 974 TRP 0.008 0.001 TRP A1813 HIS 0.008 0.001 HIS A2438 Details of bonding type rmsd/Z covalent geometry : bond 0.00204 / 0.09 (15635) covalent geometry : angle 0.57335 / 0.29 (21199) SS BOND : bond 0.00132 / 0.07 ( 11) SS BOND : angle 0.43367 / 0.26 ( 22) hydrogen bonds : bond 0.03125 / 2.08 ( 476) hydrogen bonds : angle 4.78544 / 3.37 ( 1401) link_BETA1-4 : bond 0.00389 / 0.20 ( 4) link_BETA1-4 : angle 1.00491 / 0.57 ( 12) link_NAG-ASN : bond 0.00227 / 0.12 ( 11) link_NAG-ASN : angle 2.85846 / 1.84 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 166 time to evaluate : 0.589 Fit side-chains REVERT: A 853 MET cc_start: 0.8049 (mmp) cc_final: 0.7596 (mtt) REVERT: A 1060 ARG cc_start: 0.8340 (mtm-85) cc_final: 0.8093 (mtp180) REVERT: A 1319 GLU cc_start: 0.7683 (tp30) cc_final: 0.7288 (mp0) REVERT: A 1673 MET cc_start: 0.9301 (mpp) cc_final: 0.8908 (mpp) REVERT: A 1748 PHE cc_start: 0.8166 (t80) cc_final: 0.7923 (t80) REVERT: A 1905 MET cc_start: 0.8549 (mpp) cc_final: 0.8016 (mpt) REVERT: A 1995 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7949 (p0) REVERT: A 2035 ASP cc_start: 0.7923 (t0) cc_final: 0.7707 (m-30) REVERT: A 2087 ASN cc_start: 0.7432 (t0) cc_final: 0.7206 (t160) REVERT: A 2160 ARG cc_start: 0.8603 (mtp85) cc_final: 0.8280 (tpp80) REVERT: A 2355 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7838 (mm-30) REVERT: A 2588 ASN cc_start: 0.7892 (t0) cc_final: 0.7038 (p0) REVERT: A 2701 GLN cc_start: 0.8528 (OUTLIER) cc_final: 0.8284 (mt0) outliers start: 28 outliers final: 18 residues processed: 186 average time/residue: 0.5126 time to fit residues: 107.0708 Evaluate side-chains 168 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 834 MET Chi-restraints excluded: chain A residue 990 TRP Chi-restraints excluded: chain A residue 999 ILE Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1503 ILE Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1770 LEU Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2519 ILE Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2665 ASP Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 157 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 16 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN A1427 ASN A1668 HIS A1725 HIS A1960 ASN A2132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.144640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.099522 restraints weight = 21282.742| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.49 r_work: 0.3103 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15661 Z= 0.199 Angle : 0.685 12.906 21266 Z= 0.348 Chirality : 0.048 0.265 2373 Planarity : 0.005 0.055 2737 Dihedral : 4.826 30.427 2106 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.68 % Allowed : 16.30 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.19), residues: 1894 helix: 1.37 (0.53), residues: 105 sheet: 0.86 (0.20), residues: 631 loop : -0.80 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1371 TYR 0.016 0.002 TYR A1865 PHE 0.013 0.002 PHE A2120 TRP 0.020 0.002 TRP A1105 HIS 0.007 0.001 HIS A2438 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (15635) covalent geometry : angle 0.67651 / 0.35 (21199) SS BOND : bond 0.00251 / 0.15 ( 11) SS BOND : angle 0.70519 / 0.42 ( 22) hydrogen bonds : bond 0.04151 / 2.81 ( 476) hydrogen bonds : angle 5.12882 / 3.62 ( 1401) link_BETA1-4 : bond 0.00289 / 0.14 ( 4) link_BETA1-4 : angle 1.21445 / 0.73 ( 12) link_NAG-ASN : bond 0.00231 / 0.13 ( 11) link_NAG-ASN : angle 2.66307 / 1.71 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3788 Ramachandran restraints generated. 1894 Oldfield, 0 Emsley, 1894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.568 Fit side-chains revert: symmetry clash REVERT: A 853 MET cc_start: 0.8066 (mmp) cc_final: 0.7579 (mtt) REVERT: A 1060 ARG cc_start: 0.8443 (mtm-85) cc_final: 0.8222 (mtm180) REVERT: A 1319 GLU cc_start: 0.7672 (tp30) cc_final: 0.7287 (mp0) REVERT: A 1673 MET cc_start: 0.9366 (mpp) cc_final: 0.8880 (mpp) REVERT: A 1748 PHE cc_start: 0.8196 (t80) cc_final: 0.7982 (t80) REVERT: A 1905 MET cc_start: 0.8595 (mpp) cc_final: 0.8085 (mpt) REVERT: A 1995 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7982 (p0) REVERT: A 2035 ASP cc_start: 0.8063 (t0) cc_final: 0.7765 (m-30) REVERT: A 2160 ARG cc_start: 0.8719 (mtp85) cc_final: 0.8352 (mmt-90) REVERT: A 2355 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7904 (mm-30) REVERT: A 2507 GLN cc_start: 0.9045 (OUTLIER) cc_final: 0.8774 (tt0) REVERT: A 2588 ASN cc_start: 0.8130 (t0) cc_final: 0.7369 (p0) REVERT: A 2701 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8335 (mt0) outliers start: 28 outliers final: 13 residues processed: 175 average time/residue: 0.5108 time to fit residues: 99.8845 Evaluate side-chains 167 residues out of total 1663 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 961 ASP Chi-restraints excluded: chain A residue 1430 LEU Chi-restraints excluded: chain A residue 1486 THR Chi-restraints excluded: chain A residue 1541 SER Chi-restraints excluded: chain A residue 1591 THR Chi-restraints excluded: chain A residue 1669 GLU Chi-restraints excluded: chain A residue 1672 MET Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1713 VAL Chi-restraints excluded: chain A residue 1792 ASN Chi-restraints excluded: chain A residue 1995 ASP Chi-restraints excluded: chain A residue 2355 GLU Chi-restraints excluded: chain A residue 2423 VAL Chi-restraints excluded: chain A residue 2507 GLN Chi-restraints excluded: chain A residue 2534 VAL Chi-restraints excluded: chain A residue 2648 THR Chi-restraints excluded: chain A residue 2701 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 118 optimal weight: 0.9980 chunk 46 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 162 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1419 ASN A1427 ASN A1668 HIS A1725 HIS A2087 ASN A2403 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.145197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.100433 restraints weight = 20938.357| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 2.46 r_work: 0.3121 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8965 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15661 Z= 0.158 Angle : 0.649 12.805 21266 Z= 0.330 Chirality : 0.046 0.270 2373 Planarity : 0.004 0.057 2737 Dihedral : 4.787 30.813 2106 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.56 % Allowed : 16.90 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.19), residues: 1894 helix: 1.36 (0.53), residues: 105 sheet: 0.82 (0.20), residues: 635 loop : -0.82 (0.18), residues: 1154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1371 TYR 0.015 0.001 TYR A2025 PHE 0.012 0.001 PHE A 974 TRP 0.018 0.001 TRP A 990 HIS 0.007 0.001 HIS A1668 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (15635) covalent geometry : angle 0.64200 / 0.33 (21199) SS BOND : bond 0.00191 / 0.11 ( 11) SS BOND : angle 0.77730 / 0.47 ( 22) hydrogen bonds : bond 0.03871 / 2.62 ( 476) hydrogen bonds : angle 5.12409 / 3.62 ( 1401) link_BETA1-4 : bond 0.00336 / 0.16 ( 4) link_BETA1-4 : angle 1.15605 / 0.70 ( 12) link_NAG-ASN : bond 0.00191 / 0.10 ( 11) link_NAG-ASN : angle 2.38430 / 1.50 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5365.47 seconds wall clock time: 92 minutes 1.77 seconds (5521.77 seconds total)