Starting phenix.real_space_refine on Fri Feb 6 23:28:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g42_51022/02_2026/9g42_51022.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g42_51022/02_2026/9g42_51022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g42_51022/02_2026/9g42_51022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g42_51022/02_2026/9g42_51022.map" model { file = "/net/cci-nas-00/data/ceres_data/9g42_51022/02_2026/9g42_51022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g42_51022/02_2026/9g42_51022.cif" } resolution = 2.82 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= 0.003 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 17374 2.51 5 N 4732 2.21 5 O 5348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27562 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 13616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1722, 13616 Classifications: {'peptide': 1722} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1657} Chain breaks: 2 Chain: "B" Number of atoms: 13616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1722, 13616 Classifications: {'peptide': 1722} Link IDs: {'PCIS': 1, 'PTRANS': 63, 'TRANS': 1657} Chain breaks: 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.89, per 1000 atoms: 0.21 Number of scatterers: 27562 At special positions: 0 Unit cell: (152.72, 163.51, 147.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5348 8.00 N 4732 7.00 C 17374 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A1216 " - pdb=" SG CYS A1219 " distance=2.03 Simple disulfide: pdb=" SG CYS A1320 " - pdb=" SG CYS A1328 " distance=2.03 Simple disulfide: pdb=" SG CYS A1387 " - pdb=" SG CYS A1440 " distance=2.03 Simple disulfide: pdb=" SG CYS A1504 " - pdb=" SG CYS A1512 " distance=2.03 Simple disulfide: pdb=" SG CYS A1506 " - pdb=" SG CYS A1514 " distance=2.03 Simple disulfide: pdb=" SG CYS B1216 " - pdb=" SG CYS B1219 " distance=2.03 Simple disulfide: pdb=" SG CYS B1320 " - pdb=" SG CYS B1328 " distance=2.03 Simple disulfide: pdb=" SG CYS B1387 " - pdb=" SG CYS B1440 " distance=2.03 Simple disulfide: pdb=" SG CYS B1504 " - pdb=" SG CYS B1512 " distance=2.03 Simple disulfide: pdb=" SG CYS B1506 " - pdb=" SG CYS B1514 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG A2801 " - " ASN A1757 " " NAG A2802 " - " ASN A1977 " " NAG A2803 " - " ASN A1696 " " NAG A2804 " - " ASN A2632 " " NAG A2805 " - " ASN A1791 " " NAG B2801 " - " ASN B1757 " " NAG B2802 " - " ASN B1977 " " NAG B2803 " - " ASN B1696 " " NAG B2804 " - " ASN B2632 " " NAG B2805 " - " ASN B1791 " " NAG C 1 " - " ASN A1600 " " NAG D 1 " - " ASN A2321 " " NAG E 1 " - " ASN A1876 " " NAG F 1 " - " ASN B1600 " " NAG G 1 " - " ASN B2321 " " NAG H 1 " - " ASN B1876 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 1.2 seconds 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6364 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 34 sheets defined 8.4% alpha, 52.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 1065 through 1067 No H-bonds generated for 'chain 'A' and resid 1065 through 1067' Processing helix chain 'A' and resid 1394 through 1396 No H-bonds generated for 'chain 'A' and resid 1394 through 1396' Processing helix chain 'A' and resid 1437 through 1441 removed outlier: 3.537A pdb=" N CYS A1440 " --> pdb=" O PRO A1437 " (cutoff:3.500A) Processing helix chain 'A' and resid 2394 through 2398 Processing helix chain 'A' and resid 2425 through 2427 No H-bonds generated for 'chain 'A' and resid 2425 through 2427' Processing helix chain 'A' and resid 2428 through 2433 removed outlier: 4.417A pdb=" N GLY A2433 " --> pdb=" O TRP A2429 " (cutoff:3.500A) Processing helix chain 'A' and resid 2455 through 2459 Processing helix chain 'A' and resid 2462 through 2470 Processing helix chain 'A' and resid 2473 through 2478 removed outlier: 4.253A pdb=" N ILE A2477 " --> pdb=" O GLN A2473 " (cutoff:3.500A) Processing helix chain 'A' and resid 2492 through 2501 Processing helix chain 'A' and resid 2508 through 2522 Processing helix chain 'A' and resid 2574 through 2585 Processing helix chain 'A' and resid 2611 through 2619 Processing helix chain 'A' and resid 2670 through 2700 removed outlier: 3.534A pdb=" N ARG A2686 " --> pdb=" O GLN A2682 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N THR A2690 " --> pdb=" O ARG A2686 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A2691 " --> pdb=" O ALA A2687 " (cutoff:3.500A) Processing helix chain 'A' and resid 2710 through 2721 Processing helix chain 'A' and resid 2737 through 2742 removed outlier: 3.636A pdb=" N ALA A2741 " --> pdb=" O PRO A2738 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ASP A2742 " --> pdb=" O GLU A2739 " (cutoff:3.500A) Processing helix chain 'A' and resid 2743 through 2745 No H-bonds generated for 'chain 'A' and resid 2743 through 2745' Processing helix chain 'B' and resid 1065 through 1067 No H-bonds generated for 'chain 'B' and resid 1065 through 1067' Processing helix chain 'B' and resid 1394 through 1396 No H-bonds generated for 'chain 'B' and resid 1394 through 1396' Processing helix chain 'B' and resid 1437 through 1441 removed outlier: 3.537A pdb=" N CYS B1440 " --> pdb=" O PRO B1437 " (cutoff:3.500A) Processing helix chain 'B' and resid 2394 through 2398 Processing helix chain 'B' and resid 2428 through 2433 removed outlier: 4.580A pdb=" N GLY B2433 " --> pdb=" O TRP B2429 " (cutoff:3.500A) Processing helix chain 'B' and resid 2444 through 2448 Processing helix chain 'B' and resid 2455 through 2459 Processing helix chain 'B' and resid 2462 through 2470 Processing helix chain 'B' and resid 2473 through 2478 removed outlier: 4.188A pdb=" N ILE B2477 " --> pdb=" O GLN B2473 " (cutoff:3.500A) Processing helix chain 'B' and resid 2492 through 2501 Processing helix chain 'B' and resid 2508 through 2522 Processing helix chain 'B' and resid 2574 through 2585 Processing helix chain 'B' and resid 2611 through 2619 Processing helix chain 'B' and resid 2670 through 2700 removed outlier: 3.796A pdb=" N THR B2690 " --> pdb=" O ARG B2686 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA B2691 " --> pdb=" O ALA B2687 " (cutoff:3.500A) Processing helix chain 'B' and resid 2710 through 2721 Processing helix chain 'B' and resid 2737 through 2742 removed outlier: 3.545A pdb=" N ALA B2741 " --> pdb=" O PRO B2738 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ASP B2742 " --> pdb=" O GLU B2739 " (cutoff:3.500A) Processing helix chain 'B' and resid 2743 through 2745 No H-bonds generated for 'chain 'B' and resid 2743 through 2745' Processing sheet with id=AA1, first strand: chain 'A' and resid 1021 through 1024 removed outlier: 3.625A pdb=" N ILE A1021 " --> pdb=" O THR A1077 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A1077 " --> pdb=" O ILE A1021 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1040 through 1041 Processing sheet with id=AA3, first strand: chain 'A' and resid 1099 through 1105 Processing sheet with id=AA4, first strand: chain 'A' and resid 1177 through 1179 Processing sheet with id=AA5, first strand: chain 'A' and resid 1520 through 1521 removed outlier: 3.933A pdb=" N ALA A1520 " --> pdb=" O ILE A1202 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N THR A1203 " --> pdb=" O ALA A1553 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA A1553 " --> pdb=" O THR A1203 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE A1551 " --> pdb=" O ILE A1205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1221 through 1222 removed outlier: 3.596A pdb=" N ILE A1262 " --> pdb=" O ILE A1250 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A1250 " --> pdb=" O ILE A1262 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ALA A1233 " --> pdb=" O GLY A1245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1273 through 1277 removed outlier: 4.802A pdb=" N LEU A1284 " --> pdb=" O VAL A1297 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE A1294 " --> pdb=" O VAL A1313 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1342 through 1347 removed outlier: 4.999A pdb=" N GLY A1344 " --> pdb=" O VAL A1356 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A1356 " --> pdb=" O GLY A1344 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE A1361 " --> pdb=" O LEU A1373 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1391 through 1392 removed outlier: 6.250A pdb=" N ILE A1432 " --> pdb=" O ARG A1423 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ARG A1423 " --> pdb=" O ILE A1432 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER A1412 " --> pdb=" O ASN A1407 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ASP A1403 " --> pdb=" O LEU A1416 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1461 through 1466 removed outlier: 5.359A pdb=" N ALA A1461 " --> pdb=" O THR A1477 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N THR A1477 " --> pdb=" O ALA A1461 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ALA A1463 " --> pdb=" O THR A1475 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A1485 " --> pdb=" O LEU A1497 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1567 through 1571 removed outlier: 8.119A pdb=" N GLN A1587 " --> pdb=" O ASN A1600 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN A1600 " --> pdb=" O GLN A1587 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A1589 " --> pdb=" O LEU A1598 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A1610 " --> pdb=" O ILE A1622 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A1621 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A1633 " --> pdb=" O LYS A1621 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG A1623 " --> pdb=" O ARG A1631 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG A1631 " --> pdb=" O LEU A1643 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A1652 " --> pdb=" O MET A1664 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA A1674 " --> pdb=" O TYR A1686 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A1696 " --> pdb=" O ASP A1687 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR A1695 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A1759 " --> pdb=" O CYS A1755 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1818 " --> pdb=" O GLU A1810 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A1812 " --> pdb=" O VAL A1816 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A1816 " --> pdb=" O ILE A1812 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1831 " --> pdb=" O LEU A1823 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A1825 " --> pdb=" O ASN A1829 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASN A1829 " --> pdb=" O VAL A1825 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE A1864 " --> pdb=" O VAL A1877 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A1876 " --> pdb=" O LEU A1888 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU A1888 " --> pdb=" O ASN A1876 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A1878 " --> pdb=" O ALA A1886 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A1886 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A1894 " --> pdb=" O PHE A1910 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE A1910 " --> pdb=" O SER A1894 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A1896 " --> pdb=" O ARG A1908 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG A1908 " --> pdb=" O ARG A1896 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A1898 " --> pdb=" O VAL A1906 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL A1906 " --> pdb=" O TYR A1918 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N HIS A1946 " --> pdb=" O MET A1958 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A1981 " --> pdb=" O THR A1993 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR A1993 " --> pdb=" O ILE A1981 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP A1983 " --> pdb=" O LEU A1991 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU A1991 " --> pdb=" O TYR A2004 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A2013 " --> pdb=" O PHE A2024 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS A2034 " --> pdb=" O TYR A2049 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER A2044 " --> pdb=" O PHE A2063 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A2063 " --> pdb=" O SER A2044 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A2046 " --> pdb=" O TYR A2061 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR A2061 " --> pdb=" O THR A2046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG A2048 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A2059 " --> pdb=" O ARG A2048 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A2050 " --> pdb=" O ASP A2057 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N LEU A2055 " --> pdb=" O TYR A2077 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TYR A2077 " --> pdb=" O LEU A2055 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP A2057 " --> pdb=" O TYR A2075 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG A2072 " --> pdb=" O PRO A2089 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A2074 " --> pdb=" O ILE A2087 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A2087 " --> pdb=" O ASP A2074 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR A2076 " --> pdb=" O ALA A2085 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1567 through 1571 removed outlier: 8.119A pdb=" N GLN A1587 " --> pdb=" O ASN A1600 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASN A1600 " --> pdb=" O GLN A1587 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR A1589 " --> pdb=" O LEU A1598 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR A1610 " --> pdb=" O ILE A1622 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS A1621 " --> pdb=" O LEU A1633 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N LEU A1633 " --> pdb=" O LYS A1621 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG A1623 " --> pdb=" O ARG A1631 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ARG A1631 " --> pdb=" O LEU A1643 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A1652 " --> pdb=" O MET A1664 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ALA A1674 " --> pdb=" O TYR A1686 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ASN A1696 " --> pdb=" O ASP A1687 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N THR A1695 " --> pdb=" O LEU A1707 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N THR A1759 " --> pdb=" O CYS A1755 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A1818 " --> pdb=" O GLU A1810 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE A1812 " --> pdb=" O VAL A1816 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL A1816 " --> pdb=" O ILE A1812 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A1831 " --> pdb=" O LEU A1823 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL A1825 " --> pdb=" O ASN A1829 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N ASN A1829 " --> pdb=" O VAL A1825 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N PHE A1864 " --> pdb=" O VAL A1877 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN A1876 " --> pdb=" O LEU A1888 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LEU A1888 " --> pdb=" O ASN A1876 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N SER A1878 " --> pdb=" O ALA A1886 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N ALA A1886 " --> pdb=" O THR A1897 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER A1894 " --> pdb=" O PHE A1910 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N PHE A1910 " --> pdb=" O SER A1894 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG A1896 " --> pdb=" O ARG A1908 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG A1908 " --> pdb=" O ARG A1896 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ASP A1898 " --> pdb=" O VAL A1906 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N VAL A1906 " --> pdb=" O TYR A1918 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N HIS A1946 " --> pdb=" O MET A1958 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE A1981 " --> pdb=" O THR A1993 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR A1993 " --> pdb=" O ILE A1981 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ASP A1983 " --> pdb=" O LEU A1991 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N LEU A1991 " --> pdb=" O TYR A2004 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N SER A2013 " --> pdb=" O PHE A2024 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS A2034 " --> pdb=" O TYR A2049 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N SER A2044 " --> pdb=" O PHE A2063 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N PHE A2063 " --> pdb=" O SER A2044 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N THR A2046 " --> pdb=" O TYR A2061 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N TYR A2061 " --> pdb=" O THR A2046 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ARG A2048 " --> pdb=" O GLN A2059 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N GLN A2059 " --> pdb=" O ARG A2048 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARG A2050 " --> pdb=" O ASP A2057 " (cutoff:3.500A) removed outlier: 11.898A pdb=" N LEU A2055 " --> pdb=" O TYR A2077 " (cutoff:3.500A) removed outlier: 8.759A pdb=" N TYR A2077 " --> pdb=" O LEU A2055 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ASP A2057 " --> pdb=" O TYR A2075 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG A2072 " --> pdb=" O PRO A2089 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP A2074 " --> pdb=" O ILE A2087 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A2087 " --> pdb=" O ASP A2074 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N THR A2076 " --> pdb=" O ALA A2085 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA A2085 " --> pdb=" O TYR A2101 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LEU A2100 " --> pdb=" O PHE A2113 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE A2113 " --> pdb=" O LEU A2100 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ARG A2102 " --> pdb=" O GLU A2111 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU A2111 " --> pdb=" O VAL A2118 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS A2145 " --> pdb=" O VAL A2161 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N MET A2151 " --> pdb=" O LEU A2155 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N LEU A2155 " --> pdb=" O MET A2151 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE A2170 " --> pdb=" O TYR A2187 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL A2200 " --> pdb=" O PRO A2204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2209 through 2210 removed outlier: 5.215A pdb=" N HIS A2217 " --> pdb=" O LEU A2230 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N LEU A2241 " --> pdb=" O PRO A2229 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ARG A2231 " --> pdb=" O THR A2239 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR A2239 " --> pdb=" O TYR A2246 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS A2255 " --> pdb=" O PHE A2262 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR A2271 " --> pdb=" O TYR A2284 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N SER A2281 " --> pdb=" O THR A2297 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N THR A2297 " --> pdb=" O SER A2281 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLN A2283 " --> pdb=" O TYR A2295 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N TYR A2295 " --> pdb=" O GLN A2283 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ARG A2285 " --> pdb=" O ALA A2293 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ALA A2293 " --> pdb=" O TYR A2305 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N PHE A2339 " --> pdb=" O VAL A2351 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A2350 " --> pdb=" O VAL A2362 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A2362 " --> pdb=" O TYR A2350 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA A2352 " --> pdb=" O LEU A2360 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU A2360 " --> pdb=" O LEU A2373 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN A2372 " --> pdb=" O ASP A2384 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP A2384 " --> pdb=" O GLN A2372 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN A2374 " --> pdb=" O TYR A2382 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 2399 through 2401 removed outlier: 3.770A pdb=" N LEU A2406 " --> pdb=" O ASP A2401 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2556 through 2561 removed outlier: 3.672A pdb=" N ALA A2587 " --> pdb=" O VAL A2565 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2556 through 2561 removed outlier: 3.672A pdb=" N ALA A2587 " --> pdb=" O VAL A2565 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR A2650 " --> pdb=" O TYR A2665 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY A2623 " --> pdb=" O VAL A2635 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2726 through 2730 Processing sheet with id=AB9, first strand: chain 'B' and resid 1021 through 1024 Processing sheet with id=AC1, first strand: chain 'B' and resid 1040 through 1041 Processing sheet with id=AC2, first strand: chain 'B' and resid 1099 through 1105 removed outlier: 3.655A pdb=" N VAL B1094 " --> pdb=" O PHE B1101 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1177 through 1179 Processing sheet with id=AC4, first strand: chain 'B' and resid 1520 through 1521 removed outlier: 3.892A pdb=" N ALA B1520 " --> pdb=" O ILE B1202 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B1203 " --> pdb=" O ALA B1553 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1553 " --> pdb=" O THR B1203 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ILE B1551 " --> pdb=" O ILE B1205 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 1221 through 1222 removed outlier: 3.594A pdb=" N ILE B1262 " --> pdb=" O ILE B1250 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE B1250 " --> pdb=" O ILE B1262 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B1233 " --> pdb=" O GLY B1245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1273 through 1277 removed outlier: 4.780A pdb=" N LEU B1284 " --> pdb=" O VAL B1297 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG B1296 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N VAL B1312 " --> pdb=" O ARG B1296 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1342 through 1347 removed outlier: 5.007A pdb=" N GLY B1344 " --> pdb=" O VAL B1356 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL B1356 " --> pdb=" O GLY B1344 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE B1361 " --> pdb=" O LEU B1373 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1391 through 1392 removed outlier: 6.187A pdb=" N ILE B1432 " --> pdb=" O ARG B1423 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ARG B1423 " --> pdb=" O ILE B1432 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER B1412 " --> pdb=" O ASN B1407 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP B1403 " --> pdb=" O LEU B1416 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1461 through 1466 removed outlier: 5.366A pdb=" N ALA B1461 " --> pdb=" O THR B1477 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR B1477 " --> pdb=" O ALA B1461 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ALA B1463 " --> pdb=" O THR B1475 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU B1485 " --> pdb=" O LEU B1497 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1567 through 1571 removed outlier: 8.076A pdb=" N GLN B1587 " --> pdb=" O ASN B1600 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN B1600 " --> pdb=" O GLN B1587 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B1589 " --> pdb=" O LEU B1598 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR B1610 " --> pdb=" O ILE B1622 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B1621 " --> pdb=" O LEU B1633 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B1633 " --> pdb=" O LYS B1621 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG B1623 " --> pdb=" O ARG B1631 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG B1631 " --> pdb=" O LEU B1643 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS B1652 " --> pdb=" O MET B1664 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B1667 " --> pdb=" O LEU B1673 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B1673 " --> pdb=" O ASP B1667 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N LEU B1672 " --> pdb=" O TYR B1688 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N TYR B1688 " --> pdb=" O LEU B1672 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA B1674 " --> pdb=" O TYR B1686 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B1685 " --> pdb=" O VAL B1697 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B1697 " --> pdb=" O PHE B1685 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP B1687 " --> pdb=" O THR B1695 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR B1695 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER B1802 " --> pdb=" O VAL B1825 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B1825 " --> pdb=" O SER B1802 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU B1804 " --> pdb=" O LEU B1823 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B1823 " --> pdb=" O GLU B1804 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B1806 " --> pdb=" O ARG B1821 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG B1821 " --> pdb=" O ARG B1806 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B1808 " --> pdb=" O PHE B1819 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE B1819 " --> pdb=" O ARG B1808 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU B1810 " --> pdb=" O THR B1817 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B1825 " --> pdb=" O ASN B1829 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN B1829 " --> pdb=" O VAL B1825 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE B1864 " --> pdb=" O VAL B1877 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN B1876 " --> pdb=" O LEU B1888 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU B1888 " --> pdb=" O ASN B1876 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER B1878 " --> pdb=" O ALA B1886 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA B1886 " --> pdb=" O THR B1897 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER B1894 " --> pdb=" O PHE B1910 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B1910 " --> pdb=" O SER B1894 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B1896 " --> pdb=" O ARG B1908 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG B1908 " --> pdb=" O ARG B1896 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B1898 " --> pdb=" O VAL B1906 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL B1906 " --> pdb=" O TYR B1918 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS B1946 " --> pdb=" O MET B1958 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B1981 " --> pdb=" O THR B1993 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B1993 " --> pdb=" O ILE B1981 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B1983 " --> pdb=" O LEU B1991 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B1991 " --> pdb=" O TYR B2004 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER B2013 " --> pdb=" O PHE B2024 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B2034 " --> pdb=" O TYR B2049 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER B2044 " --> pdb=" O PHE B2063 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B2063 " --> pdb=" O SER B2044 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B2046 " --> pdb=" O TYR B2061 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR B2061 " --> pdb=" O THR B2046 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B2048 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN B2059 " --> pdb=" O ARG B2048 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG B2050 " --> pdb=" O ASP B2057 " (cutoff:3.500A) removed outlier: 11.864A pdb=" N LEU B2055 " --> pdb=" O TYR B2077 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N TYR B2077 " --> pdb=" O LEU B2055 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP B2057 " --> pdb=" O TYR B2075 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG B2072 " --> pdb=" O PRO B2089 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B2074 " --> pdb=" O ILE B2087 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B2087 " --> pdb=" O ASP B2074 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B2076 " --> pdb=" O ALA B2085 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1567 through 1571 removed outlier: 8.076A pdb=" N GLN B1587 " --> pdb=" O ASN B1600 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASN B1600 " --> pdb=" O GLN B1587 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR B1589 " --> pdb=" O LEU B1598 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N THR B1610 " --> pdb=" O ILE B1622 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LYS B1621 " --> pdb=" O LEU B1633 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N LEU B1633 " --> pdb=" O LYS B1621 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N ARG B1623 " --> pdb=" O ARG B1631 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG B1631 " --> pdb=" O LEU B1643 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LYS B1652 " --> pdb=" O MET B1664 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ASP B1667 " --> pdb=" O LEU B1673 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU B1673 " --> pdb=" O ASP B1667 " (cutoff:3.500A) removed outlier: 10.265A pdb=" N LEU B1672 " --> pdb=" O TYR B1688 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N TYR B1688 " --> pdb=" O LEU B1672 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ALA B1674 " --> pdb=" O TYR B1686 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N PHE B1685 " --> pdb=" O VAL B1697 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B1697 " --> pdb=" O PHE B1685 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP B1687 " --> pdb=" O THR B1695 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N THR B1695 " --> pdb=" O LEU B1707 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N SER B1802 " --> pdb=" O VAL B1825 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL B1825 " --> pdb=" O SER B1802 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU B1804 " --> pdb=" O LEU B1823 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B1823 " --> pdb=" O GLU B1804 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B1806 " --> pdb=" O ARG B1821 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ARG B1821 " --> pdb=" O ARG B1806 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ARG B1808 " --> pdb=" O PHE B1819 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N PHE B1819 " --> pdb=" O ARG B1808 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU B1810 " --> pdb=" O THR B1817 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL B1825 " --> pdb=" O ASN B1829 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ASN B1829 " --> pdb=" O VAL B1825 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N PHE B1864 " --> pdb=" O VAL B1877 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN B1876 " --> pdb=" O LEU B1888 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU B1888 " --> pdb=" O ASN B1876 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N SER B1878 " --> pdb=" O ALA B1886 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N ALA B1886 " --> pdb=" O THR B1897 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N SER B1894 " --> pdb=" O PHE B1910 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B1910 " --> pdb=" O SER B1894 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B1896 " --> pdb=" O ARG B1908 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG B1908 " --> pdb=" O ARG B1896 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ASP B1898 " --> pdb=" O VAL B1906 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N VAL B1906 " --> pdb=" O TYR B1918 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N HIS B1946 " --> pdb=" O MET B1958 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE B1981 " --> pdb=" O THR B1993 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR B1993 " --> pdb=" O ILE B1981 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ASP B1983 " --> pdb=" O LEU B1991 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N LEU B1991 " --> pdb=" O TYR B2004 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N SER B2013 " --> pdb=" O PHE B2024 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS B2034 " --> pdb=" O TYR B2049 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N SER B2044 " --> pdb=" O PHE B2063 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N PHE B2063 " --> pdb=" O SER B2044 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR B2046 " --> pdb=" O TYR B2061 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N TYR B2061 " --> pdb=" O THR B2046 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ARG B2048 " --> pdb=" O GLN B2059 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N GLN B2059 " --> pdb=" O ARG B2048 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ARG B2050 " --> pdb=" O ASP B2057 " (cutoff:3.500A) removed outlier: 11.864A pdb=" N LEU B2055 " --> pdb=" O TYR B2077 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N TYR B2077 " --> pdb=" O LEU B2055 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASP B2057 " --> pdb=" O TYR B2075 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ARG B2072 " --> pdb=" O PRO B2089 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ASP B2074 " --> pdb=" O ILE B2087 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ILE B2087 " --> pdb=" O ASP B2074 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B2076 " --> pdb=" O ALA B2085 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N ALA B2085 " --> pdb=" O TYR B2101 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B2100 " --> pdb=" O PHE B2113 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE B2113 " --> pdb=" O LEU B2100 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG B2102 " --> pdb=" O GLU B2111 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLU B2111 " --> pdb=" O VAL B2118 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N LYS B2145 " --> pdb=" O VAL B2161 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N MET B2151 " --> pdb=" O LEU B2155 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N LEU B2155 " --> pdb=" O MET B2151 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ILE B2170 " --> pdb=" O TYR B2187 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B2200 " --> pdb=" O PRO B2204 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 2209 through 2210 removed outlier: 5.322A pdb=" N HIS B2217 " --> pdb=" O LEU B2230 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N LEU B2241 " --> pdb=" O PRO B2229 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG B2231 " --> pdb=" O THR B2239 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR B2239 " --> pdb=" O TYR B2246 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N CYS B2255 " --> pdb=" O PHE B2262 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N SER B2281 " --> pdb=" O THR B2297 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N THR B2297 " --> pdb=" O SER B2281 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N GLN B2283 " --> pdb=" O TYR B2295 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N TYR B2295 " --> pdb=" O GLN B2283 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ARG B2285 " --> pdb=" O ALA B2293 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA B2293 " --> pdb=" O TYR B2305 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE B2339 " --> pdb=" O VAL B2351 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B2350 " --> pdb=" O VAL B2362 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N VAL B2362 " --> pdb=" O TYR B2350 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B2352 " --> pdb=" O LEU B2360 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N LEU B2360 " --> pdb=" O LEU B2373 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN B2372 " --> pdb=" O ASP B2384 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ASP B2384 " --> pdb=" O GLN B2372 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLN B2374 " --> pdb=" O TYR B2382 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 2399 through 2401 removed outlier: 3.779A pdb=" N LEU B2406 " --> pdb=" O ASP B2401 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 2556 through 2561 removed outlier: 3.786A pdb=" N ALA B2587 " --> pdb=" O VAL B2565 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 2556 through 2561 removed outlier: 3.786A pdb=" N ALA B2587 " --> pdb=" O VAL B2565 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N THR B2650 " --> pdb=" O TYR B2665 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY B2623 " --> pdb=" O VAL B2635 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2727 through 2730 1436 hydrogen bonds defined for protein. 3825 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: 10.63 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9042 1.34 - 1.46: 6581 1.46 - 1.58: 12337 1.58 - 1.70: 0 1.70 - 1.82: 184 Bond restraints: 28144 Sorted by residual: bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.83e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.80e+00 bond pdb=" C1 NAG B2803 " pdb=" O5 NAG B2803 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.58e+00 ... (remaining 28139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 37693 2.64 - 5.29: 426 5.29 - 7.93: 34 7.93 - 10.58: 14 10.58 - 13.22: 3 Bond angle restraints: 38170 Sorted by residual: angle pdb=" CA TYR A1249 " pdb=" CB TYR A1249 " pdb=" CG TYR A1249 " ideal model delta sigma weight residual 113.90 122.47 -8.57 1.80e+00 3.09e-01 2.26e+01 angle pdb=" CA TYR B1249 " pdb=" CB TYR B1249 " pdb=" CG TYR B1249 " ideal model delta sigma weight residual 113.90 122.44 -8.54 1.80e+00 3.09e-01 2.25e+01 angle pdb=" CA GLN B1198 " pdb=" CB GLN B1198 " pdb=" CG GLN B1198 " ideal model delta sigma weight residual 114.10 123.51 -9.41 2.00e+00 2.50e-01 2.21e+01 angle pdb=" CA GLN A1198 " pdb=" CB GLN A1198 " pdb=" CG GLN A1198 " ideal model delta sigma weight residual 114.10 123.33 -9.23 2.00e+00 2.50e-01 2.13e+01 angle pdb=" CG1 ILE B1549 " pdb=" CB ILE B1549 " pdb=" CG2 ILE B1549 " ideal model delta sigma weight residual 110.70 97.48 13.22 3.00e+00 1.11e-01 1.94e+01 ... (remaining 38165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.90: 15405 20.90 - 41.79: 1330 41.79 - 62.69: 295 62.69 - 83.59: 71 83.59 - 104.49: 19 Dihedral angle restraints: 17120 sinusoidal: 7122 harmonic: 9998 Sorted by residual: dihedral pdb=" CB CYS A1504 " pdb=" SG CYS A1504 " pdb=" SG CYS A1512 " pdb=" CB CYS A1512 " ideal model delta sinusoidal sigma weight residual -86.00 -163.19 77.19 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS B1504 " pdb=" SG CYS B1504 " pdb=" SG CYS B1512 " pdb=" CB CYS B1512 " ideal model delta sinusoidal sigma weight residual -86.00 -163.15 77.15 1 1.00e+01 1.00e-02 7.46e+01 dihedral pdb=" CD ARG A1017 " pdb=" NE ARG A1017 " pdb=" CZ ARG A1017 " pdb=" NH1 ARG A1017 " ideal model delta sinusoidal sigma weight residual 0.00 63.95 -63.95 1 1.00e+01 1.00e-02 5.38e+01 ... (remaining 17117 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 4189 0.128 - 0.256: 100 0.256 - 0.383: 3 0.383 - 0.511: 3 0.511 - 0.639: 1 Chirality restraints: 4296 Sorted by residual: chirality pdb=" C1 NAG B2803 " pdb=" ND2 ASN B1696 " pdb=" C2 NAG B2803 " pdb=" O5 NAG B2803 " both_signs ideal model delta sigma weight residual False -2.40 -1.76 -0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.45 0.05 2.00e-02 2.50e+03 6.37e+00 chirality pdb=" CB ILE B1549 " pdb=" CA ILE B1549 " pdb=" CG1 ILE B1549 " pdb=" CG2 ILE B1549 " both_signs ideal model delta sigma weight residual False 2.64 3.04 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 4293 not shown) Planarity restraints: 4924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1017 " 0.855 9.50e-02 1.11e+02 3.84e-01 9.93e+01 pdb=" NE ARG A1017 " -0.070 2.00e-02 2.50e+03 pdb=" CZ ARG A1017 " 0.045 2.00e-02 2.50e+03 pdb=" NH1 ARG A1017 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A1017 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1017 " -0.815 9.50e-02 1.11e+02 3.67e-01 9.26e+01 pdb=" NE ARG B1017 " 0.070 2.00e-02 2.50e+03 pdb=" CZ ARG B1017 " -0.049 2.00e-02 2.50e+03 pdb=" NH1 ARG B1017 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B1017 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B2483 " -0.448 9.50e-02 1.11e+02 2.02e-01 3.14e+01 pdb=" NE ARG B2483 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG B2483 " -0.039 2.00e-02 2.50e+03 pdb=" NH1 ARG B2483 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG B2483 " -0.001 2.00e-02 2.50e+03 ... (remaining 4921 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1711 2.74 - 3.28: 23827 3.28 - 3.82: 44993 3.82 - 4.36: 54680 4.36 - 4.90: 96293 Nonbonded interactions: 221504 Sorted by model distance: nonbonded pdb=" OH TYR B1249 " pdb=" OG SER B1261 " model vdw 2.204 3.040 nonbonded pdb=" OH TYR A1249 " pdb=" OG SER A1261 " model vdw 2.207 3.040 nonbonded pdb=" OE1 GLU B2347 " pdb=" OH TYR B2349 " model vdw 2.288 3.040 nonbonded pdb=" O SER A1931 " pdb=" OG SER A1931 " model vdw 2.290 3.040 nonbonded pdb=" O SER B1931 " pdb=" OG SER B1931 " model vdw 2.296 3.040 ... (remaining 221499 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 30.070 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:6.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 : 0.004 0.063 28178 Z= 0.180 Angle : 0.754 19.259 38262 Z= 0.395 Chirality : 0.055 0.639 4296 Planarity : 0.011 0.384 4908 Dihedral : 16.697 104.485 10726 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.90 % Allowed : 19.90 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: -0.13 (0.14), residues: 3432 helix: -1.28 (0.30), residues: 212 sheet: 0.94 (0.16), residues: 1158 loop : -0.56 (0.14), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.058 0.002 ARG B1017 TYR 0.051 0.002 TYR B1249 PHE 0.046 0.002 PHE B1247 TRP 0.018 0.001 TRP B1682 HIS 0.017 0.002 HIS A1946 Details of bonding type rmsd covalent geometry : bond 0.00385 (28144) covalent geometry : angle 0.72926 (38170) SS BOND : bond 0.00220 ( 10) SS BOND : angle 1.79291 ( 20) hydrogen bonds : bond 0.20157 ( 1046) hydrogen bonds : angle 7.69704 ( 3825) link_BETA1-4 : bond 0.01247 ( 8) link_BETA1-4 : angle 1.57637 ( 24) link_NAG-ASN : bond 0.00681 ( 16) link_NAG-ASN : angle 5.26213 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 785 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1078 MET cc_start: 0.7100 (mtm) cc_final: 0.6874 (mtp) REVERT: A 1134 VAL cc_start: 0.8148 (t) cc_final: 0.7749 (p) REVERT: A 1166 ASN cc_start: 0.8211 (t0) cc_final: 0.7966 (t0) REVERT: A 1173 ASP cc_start: 0.7996 (t0) cc_final: 0.7656 (t0) REVERT: A 1660 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 1895 GLU cc_start: 0.7781 (tp30) cc_final: 0.7551 (tt0) REVERT: A 1953 VAL cc_start: 0.8517 (OUTLIER) cc_final: 0.8304 (t) REVERT: A 2093 GLU cc_start: 0.7551 (mp0) cc_final: 0.7192 (pp20) REVERT: A 2331 TYR cc_start: 0.8671 (m-80) cc_final: 0.8053 (m-80) REVERT: A 2455 ASP cc_start: 0.7618 (t0) cc_final: 0.7337 (t0) REVERT: A 2579 LYS cc_start: 0.8678 (mttt) cc_final: 0.8381 (mttp) REVERT: A 2592 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7978 (mtmm) REVERT: A 2614 ASP cc_start: 0.8031 (m-30) cc_final: 0.7637 (m-30) REVERT: A 2636 SER cc_start: 0.7923 (p) cc_final: 0.7693 (p) REVERT: A 2653 GLU cc_start: 0.7406 (tt0) cc_final: 0.7148 (pt0) REVERT: A 2665 TYR cc_start: 0.8506 (m-80) cc_final: 0.7973 (m-80) REVERT: A 2675 GLU cc_start: 0.8284 (tp30) cc_final: 0.7917 (tp30) REVERT: B 1114 THR cc_start: 0.9193 (OUTLIER) cc_final: 0.8960 (t) REVERT: B 1118 ASP cc_start: 0.7866 (p0) cc_final: 0.7634 (p0) REVERT: B 1136 SER cc_start: 0.8347 (p) cc_final: 0.8124 (p) REVERT: B 1152 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7352 (mmtt) REVERT: B 1173 ASP cc_start: 0.7914 (t0) cc_final: 0.7634 (t0) REVERT: B 1274 TYR cc_start: 0.6334 (m-80) cc_final: 0.6005 (m-80) REVERT: B 1540 THR cc_start: 0.8068 (p) cc_final: 0.7864 (t) REVERT: B 1639 GLN cc_start: 0.7699 (tp40) cc_final: 0.7232 (mp10) REVERT: B 1652 LYS cc_start: 0.8312 (tptt) cc_final: 0.8099 (ttpp) REVERT: B 1845 TYR cc_start: 0.8619 (p90) cc_final: 0.8402 (p90) REVERT: B 1917 SER cc_start: 0.8581 (m) cc_final: 0.8336 (t) REVERT: B 1966 TYR cc_start: 0.8693 (p90) cc_final: 0.8434 (p90) REVERT: B 2093 GLU cc_start: 0.7470 (mp0) cc_final: 0.7261 (pp20) REVERT: B 2331 TYR cc_start: 0.8679 (m-80) cc_final: 0.8153 (m-80) REVERT: B 2455 ASP cc_start: 0.7512 (t0) cc_final: 0.7261 (t0) REVERT: B 2579 LYS cc_start: 0.8648 (mttt) cc_final: 0.8376 (mttm) REVERT: B 2582 SER cc_start: 0.8760 (t) cc_final: 0.8474 (m) REVERT: B 2592 LYS cc_start: 0.8192 (mtmm) cc_final: 0.7963 (mtmm) REVERT: B 2614 ASP cc_start: 0.7858 (m-30) cc_final: 0.7380 (m-30) REVERT: B 2665 TYR cc_start: 0.8635 (m-80) cc_final: 0.7974 (m-80) REVERT: B 2701 ASP cc_start: 0.7973 (m-30) cc_final: 0.7676 (m-30) outliers start: 27 outliers final: 5 residues processed: 801 average time/residue: 0.6805 time to fit residues: 630.2347 Evaluate side-chains 634 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 627 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1696 ASN Chi-restraints excluded: chain A residue 1953 VAL Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain B residue 1114 THR Chi-restraints excluded: chain B residue 1510 VAL Chi-restraints excluded: chain B residue 1987 ASP Chi-restraints excluded: chain B residue 2112 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1220 ASN A1508 ASN A1618 ASN A1747 GLN A1773 HIS A1932 GLN A1946 HIS A2078 HIS A2162 GLN A2217 HIS ** A2447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2473 GLN A2511 GLN A2651 ASN B1166 ASN B1220 ASN B1508 ASN B1773 HIS B1946 HIS B2037 ASN B2137 HIS B2217 HIS B2448 ASN B2473 GLN B2511 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.141017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.108384 restraints weight = 40134.991| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 2.20 r_work: 0.3300 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 28178 Z= 0.184 Angle : 0.612 14.529 38262 Z= 0.316 Chirality : 0.048 0.388 4296 Planarity : 0.005 0.071 4908 Dihedral : 6.898 59.790 4345 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.71 % Allowed : 22.27 % Favored : 74.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.23 (0.15), residues: 3432 helix: 0.29 (0.34), residues: 226 sheet: 1.13 (0.16), residues: 1102 loop : -0.39 (0.14), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1849 TYR 0.029 0.002 TYR B1249 PHE 0.022 0.002 PHE A1772 TRP 0.015 0.001 TRP A2544 HIS 0.010 0.001 HIS B1773 Details of bonding type rmsd covalent geometry : bond 0.00417 (28144) covalent geometry : angle 0.58823 (38170) SS BOND : bond 0.00158 ( 10) SS BOND : angle 0.93356 ( 20) hydrogen bonds : bond 0.04146 ( 1046) hydrogen bonds : angle 5.27607 ( 3825) link_BETA1-4 : bond 0.00348 ( 8) link_BETA1-4 : angle 2.02412 ( 24) link_NAG-ASN : bond 0.00639 ( 16) link_NAG-ASN : angle 4.54334 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 659 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1096 VAL cc_start: 0.8072 (t) cc_final: 0.7692 (p) REVERT: A 1134 VAL cc_start: 0.8351 (t) cc_final: 0.8002 (p) REVERT: A 1135 VAL cc_start: 0.8030 (p) cc_final: 0.7829 (m) REVERT: A 1173 ASP cc_start: 0.8009 (t0) cc_final: 0.7686 (t0) REVERT: A 1391 MET cc_start: 0.6690 (OUTLIER) cc_final: 0.6355 (mpp) REVERT: A 1409 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6525 (ptm) REVERT: A 1424 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.5822 (pp) REVERT: A 1474 ILE cc_start: 0.8149 (mt) cc_final: 0.7820 (pt) REVERT: A 1556 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8274 (mmmm) REVERT: A 1660 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7411 (mm-30) REVERT: A 1806 ARG cc_start: 0.8476 (mtt180) cc_final: 0.8262 (mtt180) REVERT: A 1807 LEU cc_start: 0.8929 (mm) cc_final: 0.8719 (mt) REVERT: A 1845 TYR cc_start: 0.8649 (p90) cc_final: 0.8388 (p90) REVERT: A 1850 LYS cc_start: 0.8777 (mttm) cc_final: 0.8573 (mttm) REVERT: A 1922 ASP cc_start: 0.7660 (t0) cc_final: 0.7455 (t0) REVERT: A 2132 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8452 (ptm) REVERT: A 2231 ARG cc_start: 0.8359 (ttm-80) cc_final: 0.8095 (mtm-85) REVERT: A 2331 TYR cc_start: 0.8624 (m-80) cc_final: 0.8337 (m-80) REVERT: A 2455 ASP cc_start: 0.7643 (t0) cc_final: 0.7399 (t0) REVERT: A 2543 HIS cc_start: 0.8054 (OUTLIER) cc_final: 0.7593 (t70) REVERT: A 2579 LYS cc_start: 0.8513 (mttt) cc_final: 0.8264 (mttp) REVERT: A 2588 TYR cc_start: 0.8521 (m-80) cc_final: 0.8221 (m-80) REVERT: A 2592 LYS cc_start: 0.8326 (mtmm) cc_final: 0.8117 (mtmm) REVERT: A 2614 ASP cc_start: 0.7996 (m-30) cc_final: 0.7561 (m-30) REVERT: A 2626 VAL cc_start: 0.8215 (t) cc_final: 0.8008 (m) REVERT: A 2665 TYR cc_start: 0.8627 (m-80) cc_final: 0.8073 (m-80) REVERT: A 2674 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7487 (tm-30) REVERT: A 2675 GLU cc_start: 0.8547 (tp30) cc_final: 0.8109 (tp30) REVERT: B 1135 VAL cc_start: 0.8096 (p) cc_final: 0.7787 (m) REVERT: B 1136 SER cc_start: 0.8334 (p) cc_final: 0.7635 (p) REVERT: B 1152 LYS cc_start: 0.7778 (mmtt) cc_final: 0.7321 (mmtt) REVERT: B 1163 ASP cc_start: 0.8257 (p0) cc_final: 0.8057 (p0) REVERT: B 1173 ASP cc_start: 0.7983 (t0) cc_final: 0.7710 (t0) REVERT: B 1206 MET cc_start: 0.4801 (mmm) cc_final: 0.4469 (mmm) REVERT: B 1274 TYR cc_start: 0.6083 (m-80) cc_final: 0.5806 (m-80) REVERT: B 1391 MET cc_start: 0.6338 (OUTLIER) cc_final: 0.5963 (mpp) REVERT: B 1607 ASN cc_start: 0.8435 (m-40) cc_final: 0.8185 (m-40) REVERT: B 1631 ARG cc_start: 0.8086 (mmm-85) cc_final: 0.7733 (mtm110) REVERT: B 1639 GLN cc_start: 0.7880 (tp40) cc_final: 0.7230 (mp10) REVERT: B 1642 THR cc_start: 0.8629 (OUTLIER) cc_final: 0.8319 (p) REVERT: B 1652 LYS cc_start: 0.8453 (tptt) cc_final: 0.8158 (mtpp) REVERT: B 1753 GLN cc_start: 0.8045 (tt0) cc_final: 0.7684 (mt0) REVERT: B 1762 VAL cc_start: 0.8691 (t) cc_final: 0.8386 (p) REVERT: B 1806 ARG cc_start: 0.8612 (mtt90) cc_final: 0.8244 (mtt180) REVERT: B 1917 SER cc_start: 0.8701 (m) cc_final: 0.8346 (p) REVERT: B 1950 MET cc_start: 0.8662 (mmt) cc_final: 0.8388 (mmt) REVERT: B 2173 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 2267 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8361 (mmtt) REVERT: B 2331 TYR cc_start: 0.8604 (m-80) cc_final: 0.8270 (m-80) REVERT: B 2579 LYS cc_start: 0.8542 (mttt) cc_final: 0.8262 (mttm) REVERT: B 2592 LYS cc_start: 0.8392 (mtmm) cc_final: 0.8171 (mtmm) REVERT: B 2614 ASP cc_start: 0.7928 (m-30) cc_final: 0.7494 (m-30) REVERT: B 2665 TYR cc_start: 0.8671 (m-80) cc_final: 0.7940 (m-80) REVERT: B 2667 LEU cc_start: 0.9016 (mp) cc_final: 0.8770 (mm) REVERT: B 2724 GLN cc_start: 0.7672 (mp10) cc_final: 0.7109 (mp10) outliers start: 111 outliers final: 35 residues processed: 708 average time/residue: 0.6960 time to fit residues: 568.9143 Evaluate side-chains 648 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 605 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1116 ILE Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1220 ASN Chi-restraints excluded: chain A residue 1391 MET Chi-restraints excluded: chain A residue 1409 MET Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1696 ASN Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2064 SER Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2244 VAL Chi-restraints excluded: chain A residue 2281 SER Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2525 GLU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1116 ILE Chi-restraints excluded: chain B residue 1131 SER Chi-restraints excluded: chain B residue 1220 ASN Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1474 ILE Chi-restraints excluded: chain B residue 1634 LEU Chi-restraints excluded: chain B residue 1642 THR Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1941 SER Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 1975 GLU Chi-restraints excluded: chain B residue 2064 SER Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2106 ILE Chi-restraints excluded: chain B residue 2112 HIS Chi-restraints excluded: chain B residue 2267 LYS Chi-restraints excluded: chain B residue 2536 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 98 optimal weight: 2.9990 chunk 255 optimal weight: 0.9980 chunk 188 optimal weight: 0.8980 chunk 317 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 248 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1186 HIS A1319 GLN A1773 HIS A1946 HIS A2217 HIS A2256 GLN ** A2447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2473 GLN B1166 ASN B1733 ASN B1773 HIS B1946 HIS B2137 HIS B2162 GLN B2217 HIS B2473 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.141764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108413 restraints weight = 39972.730| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.27 r_work: 0.3295 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 28178 Z= 0.133 Angle : 0.552 13.422 38262 Z= 0.286 Chirality : 0.046 0.376 4296 Planarity : 0.004 0.049 4908 Dihedral : 5.907 59.818 4338 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.28 % Allowed : 22.91 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.41 (0.15), residues: 3432 helix: 0.77 (0.36), residues: 226 sheet: 1.17 (0.15), residues: 1118 loop : -0.26 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2483 TYR 0.021 0.001 TYR A1249 PHE 0.013 0.001 PHE A1247 TRP 0.009 0.001 TRP B1682 HIS 0.006 0.001 HIS B2217 Details of bonding type rmsd covalent geometry : bond 0.00299 (28144) covalent geometry : angle 0.53077 (38170) SS BOND : bond 0.00369 ( 10) SS BOND : angle 0.68318 ( 20) hydrogen bonds : bond 0.03947 ( 1046) hydrogen bonds : angle 4.97122 ( 3825) link_BETA1-4 : bond 0.00533 ( 8) link_BETA1-4 : angle 1.80285 ( 24) link_NAG-ASN : bond 0.00502 ( 16) link_NAG-ASN : angle 4.07682 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 616 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1059 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8434 (mttm) REVERT: A 1096 VAL cc_start: 0.8147 (t) cc_final: 0.7764 (p) REVERT: A 1134 VAL cc_start: 0.8421 (t) cc_final: 0.8111 (p) REVERT: A 1135 VAL cc_start: 0.8120 (p) cc_final: 0.7877 (m) REVERT: A 1173 ASP cc_start: 0.8017 (t0) cc_final: 0.7684 (t0) REVERT: A 1391 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6109 (mpp) REVERT: A 1409 MET cc_start: 0.6769 (OUTLIER) cc_final: 0.6407 (ptm) REVERT: A 1424 ILE cc_start: 0.6669 (OUTLIER) cc_final: 0.5867 (pp) REVERT: A 1474 ILE cc_start: 0.8167 (mt) cc_final: 0.7870 (pt) REVERT: A 1579 VAL cc_start: 0.9057 (t) cc_final: 0.8838 (m) REVERT: A 1629 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.8160 (ttp) REVERT: A 1660 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7384 (mm-30) REVERT: A 1711 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8381 (mtm) REVERT: A 1807 LEU cc_start: 0.8922 (mm) cc_final: 0.8705 (mt) REVERT: A 1845 TYR cc_start: 0.8663 (p90) cc_final: 0.8428 (p90) REVERT: A 1850 LYS cc_start: 0.8771 (mttm) cc_final: 0.8560 (mttp) REVERT: A 1870 SER cc_start: 0.8826 (p) cc_final: 0.8308 (t) REVERT: A 1922 ASP cc_start: 0.7746 (t0) cc_final: 0.7539 (t0) REVERT: A 2132 MET cc_start: 0.8752 (OUTLIER) cc_final: 0.8438 (ptm) REVERT: A 2231 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8051 (mtm-85) REVERT: A 2240 ARG cc_start: 0.8458 (mtp-110) cc_final: 0.8082 (mtp-110) REVERT: A 2331 TYR cc_start: 0.8676 (m-80) cc_final: 0.8271 (m-80) REVERT: A 2341 MET cc_start: 0.8815 (mtm) cc_final: 0.8479 (mtp) REVERT: A 2455 ASP cc_start: 0.7664 (t0) cc_final: 0.7424 (t0) REVERT: A 2543 HIS cc_start: 0.7975 (OUTLIER) cc_final: 0.7507 (t70) REVERT: A 2579 LYS cc_start: 0.8468 (mttt) cc_final: 0.8171 (mttp) REVERT: A 2588 TYR cc_start: 0.8542 (m-80) cc_final: 0.8308 (m-80) REVERT: A 2592 LYS cc_start: 0.8295 (mtmm) cc_final: 0.8068 (mtmm) REVERT: A 2614 ASP cc_start: 0.8120 (m-30) cc_final: 0.7660 (m-30) REVERT: A 2626 VAL cc_start: 0.8234 (t) cc_final: 0.8017 (m) REVERT: A 2665 TYR cc_start: 0.8559 (m-80) cc_final: 0.7933 (m-80) REVERT: A 2674 GLU cc_start: 0.7911 (tm-30) cc_final: 0.7539 (tm-30) REVERT: A 2675 GLU cc_start: 0.8474 (tp30) cc_final: 0.8049 (tp30) REVERT: A 2700 ARG cc_start: 0.7865 (mtp180) cc_final: 0.7522 (ttp-170) REVERT: B 1078 MET cc_start: 0.8049 (ptp) cc_final: 0.7779 (ptp) REVERT: B 1103 LYS cc_start: 0.7648 (ttmm) cc_final: 0.7416 (ttmm) REVERT: B 1136 SER cc_start: 0.8308 (p) cc_final: 0.7371 (p) REVERT: B 1152 LYS cc_start: 0.7773 (mmtt) cc_final: 0.7381 (mmtt) REVERT: B 1163 ASP cc_start: 0.8231 (OUTLIER) cc_final: 0.8027 (p0) REVERT: B 1173 ASP cc_start: 0.7966 (t0) cc_final: 0.7692 (t0) REVERT: B 1206 MET cc_start: 0.4815 (mmm) cc_final: 0.4447 (mmm) REVERT: B 1274 TYR cc_start: 0.6105 (m-80) cc_final: 0.5801 (m-80) REVERT: B 1391 MET cc_start: 0.6335 (OUTLIER) cc_final: 0.5649 (mpp) REVERT: B 1485 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.7064 (pt) REVERT: B 1607 ASN cc_start: 0.8496 (m-40) cc_final: 0.8245 (m-40) REVERT: B 1631 ARG cc_start: 0.8102 (mmm-85) cc_final: 0.7704 (mtm110) REVERT: B 1639 GLN cc_start: 0.7896 (tp40) cc_final: 0.7247 (mp10) REVERT: B 1642 THR cc_start: 0.8657 (m) cc_final: 0.8378 (p) REVERT: B 1652 LYS cc_start: 0.8457 (tptt) cc_final: 0.8165 (mtpp) REVERT: B 1753 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7648 (mt0) REVERT: B 1762 VAL cc_start: 0.8713 (t) cc_final: 0.8442 (p) REVERT: B 1806 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8239 (mtt90) REVERT: B 1845 TYR cc_start: 0.8674 (p90) cc_final: 0.8383 (p90) REVERT: B 1917 SER cc_start: 0.8701 (m) cc_final: 0.8332 (p) REVERT: B 1950 MET cc_start: 0.8647 (mmt) cc_final: 0.8313 (mmt) REVERT: B 2058 LYS cc_start: 0.8817 (ttpp) cc_final: 0.8567 (ttpt) REVERT: B 2231 ARG cc_start: 0.8405 (ttm-80) cc_final: 0.8100 (mtm-85) REVERT: B 2331 TYR cc_start: 0.8640 (m-80) cc_final: 0.8285 (m-80) REVERT: B 2483 ARG cc_start: 0.7976 (mtp-110) cc_final: 0.7702 (mtp85) REVERT: B 2543 HIS cc_start: 0.7984 (OUTLIER) cc_final: 0.7568 (t70) REVERT: B 2579 LYS cc_start: 0.8489 (mttt) cc_final: 0.8192 (mttm) REVERT: B 2592 LYS cc_start: 0.8367 (mtmm) cc_final: 0.8145 (mtmm) REVERT: B 2614 ASP cc_start: 0.7990 (m-30) cc_final: 0.7569 (m-30) REVERT: B 2665 TYR cc_start: 0.8647 (m-80) cc_final: 0.7846 (m-80) REVERT: B 2667 LEU cc_start: 0.9023 (mp) cc_final: 0.8819 (mm) REVERT: B 2674 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 2724 GLN cc_start: 0.7690 (mp10) cc_final: 0.7255 (mp10) REVERT: B 2736 GLN cc_start: 0.8217 (OUTLIER) cc_final: 0.7899 (mp-120) outliers start: 98 outliers final: 40 residues processed: 654 average time/residue: 0.7090 time to fit residues: 534.3309 Evaluate side-chains 639 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 585 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1059 LYS Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1111 LEU Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1391 MET Chi-restraints excluded: chain A residue 1409 MET Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1696 ASN Chi-restraints excluded: chain A residue 1711 MET Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1811 GLN Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 2019 SER Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2133 THR Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2657 SER Chi-restraints excluded: chain B residue 1111 LEU Chi-restraints excluded: chain B residue 1130 LEU Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1474 ILE Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1687 ASP Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1753 GLN Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2106 ILE Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2718 LEU Chi-restraints excluded: chain B residue 2736 GLN Chi-restraints excluded: chain B residue 2739 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 326 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 307 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 200 optimal weight: 5.9990 chunk 327 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 197 optimal weight: 0.2980 chunk 194 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1632 HIS A1773 HIS A1946 HIS A2217 HIS ** A2447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2473 GLN B1192 ASN B1753 GLN B1773 HIS B1946 HIS ** B2112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2217 HIS B2473 GLN B2753 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106033 restraints weight = 39727.195| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.21 r_work: 0.3267 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 28178 Z= 0.224 Angle : 0.595 12.473 38262 Z= 0.308 Chirality : 0.048 0.356 4296 Planarity : 0.004 0.058 4908 Dihedral : 5.527 53.540 4336 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.55 % Allowed : 22.74 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.14), residues: 3432 helix: 0.81 (0.35), residues: 226 sheet: 1.06 (0.15), residues: 1132 loop : -0.27 (0.14), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A2062 TYR 0.021 0.002 TYR A1249 PHE 0.015 0.002 PHE A1995 TRP 0.010 0.001 TRP B1682 HIS 0.008 0.001 HIS B2112 Details of bonding type rmsd covalent geometry : bond 0.00514 (28144) covalent geometry : angle 0.57548 (38170) SS BOND : bond 0.00136 ( 10) SS BOND : angle 0.52236 ( 20) hydrogen bonds : bond 0.04165 ( 1046) hydrogen bonds : angle 4.98436 ( 3825) link_BETA1-4 : bond 0.00364 ( 8) link_BETA1-4 : angle 1.77487 ( 24) link_NAG-ASN : bond 0.00602 ( 16) link_NAG-ASN : angle 4.17424 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 611 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1134 VAL cc_start: 0.8593 (t) cc_final: 0.8358 (p) REVERT: A 1135 VAL cc_start: 0.8388 (p) cc_final: 0.8104 (m) REVERT: A 1173 ASP cc_start: 0.7961 (t0) cc_final: 0.7621 (t0) REVERT: A 1391 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6168 (mpp) REVERT: A 1424 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.5982 (pp) REVERT: A 1526 ILE cc_start: 0.8217 (mt) cc_final: 0.7855 (mp) REVERT: A 1579 VAL cc_start: 0.9062 (t) cc_final: 0.8817 (m) REVERT: A 1629 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8309 (ttp) REVERT: A 1635 MET cc_start: 0.8646 (mmt) cc_final: 0.8419 (mmm) REVERT: A 1660 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7415 (mm-30) REVERT: A 1667 ASP cc_start: 0.8045 (t0) cc_final: 0.7800 (t0) REVERT: A 1807 LEU cc_start: 0.8962 (mm) cc_final: 0.8735 (mt) REVERT: A 1845 TYR cc_start: 0.8600 (p90) cc_final: 0.8389 (p90) REVERT: A 1850 LYS cc_start: 0.8846 (mttm) cc_final: 0.8645 (mttp) REVERT: A 1906 VAL cc_start: 0.8767 (OUTLIER) cc_final: 0.8528 (t) REVERT: A 1922 ASP cc_start: 0.7673 (t0) cc_final: 0.7465 (t0) REVERT: A 1985 SER cc_start: 0.8550 (t) cc_final: 0.8260 (p) REVERT: A 2132 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8467 (ptm) REVERT: A 2231 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8150 (mtm-85) REVERT: A 2331 TYR cc_start: 0.8676 (m-80) cc_final: 0.8353 (m-80) REVERT: A 2455 ASP cc_start: 0.7620 (t0) cc_final: 0.7390 (t0) REVERT: A 2543 HIS cc_start: 0.7987 (OUTLIER) cc_final: 0.7417 (t70) REVERT: A 2579 LYS cc_start: 0.8515 (mttt) cc_final: 0.8210 (mttp) REVERT: A 2588 TYR cc_start: 0.8533 (m-80) cc_final: 0.8332 (m-80) REVERT: A 2592 LYS cc_start: 0.8328 (mtmm) cc_final: 0.8097 (mtmm) REVERT: A 2614 ASP cc_start: 0.8172 (m-30) cc_final: 0.7719 (m-30) REVERT: A 2626 VAL cc_start: 0.8269 (t) cc_final: 0.8058 (m) REVERT: A 2665 TYR cc_start: 0.8623 (m-80) cc_final: 0.7966 (m-80) REVERT: A 2674 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7459 (tm-30) REVERT: A 2681 ASP cc_start: 0.8050 (t70) cc_final: 0.7740 (t0) REVERT: A 2700 ARG cc_start: 0.7916 (mtp180) cc_final: 0.7562 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7428 (mmt-90) cc_final: 0.7142 (mmt-90) REVERT: B 1080 GLN cc_start: 0.7589 (mp10) cc_final: 0.7329 (mp10) REVERT: B 1152 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7277 (mmmm) REVERT: B 1163 ASP cc_start: 0.8279 (OUTLIER) cc_final: 0.8063 (p0) REVERT: B 1173 ASP cc_start: 0.7997 (t0) cc_final: 0.7704 (t0) REVERT: B 1274 TYR cc_start: 0.6108 (m-80) cc_final: 0.5705 (m-80) REVERT: B 1391 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.6118 (mpp) REVERT: B 1485 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7097 (pt) REVERT: B 1607 ASN cc_start: 0.8519 (m-40) cc_final: 0.8297 (m-40) REVERT: B 1631 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7699 (mtm110) REVERT: B 1639 GLN cc_start: 0.7920 (tp40) cc_final: 0.7321 (mp10) REVERT: B 1642 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8331 (p) REVERT: B 1652 LYS cc_start: 0.8484 (tptt) cc_final: 0.8173 (mtpp) REVERT: B 1667 ASP cc_start: 0.8021 (t0) cc_final: 0.7797 (t0) REVERT: B 1762 VAL cc_start: 0.8740 (t) cc_final: 0.8466 (p) REVERT: B 1806 ARG cc_start: 0.8630 (mtt180) cc_final: 0.8272 (mtt180) REVERT: B 1819 PHE cc_start: 0.8907 (t80) cc_final: 0.8679 (t80) REVERT: B 1845 TYR cc_start: 0.8612 (p90) cc_final: 0.8287 (p90) REVERT: B 1917 SER cc_start: 0.8667 (m) cc_final: 0.8346 (p) REVERT: B 1950 MET cc_start: 0.8661 (mmt) cc_final: 0.8372 (mmt) REVERT: B 2058 LYS cc_start: 0.8767 (ttpp) cc_final: 0.8521 (ttpt) REVERT: B 2093 GLU cc_start: 0.7896 (mp0) cc_final: 0.7376 (pp20) REVERT: B 2231 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8196 (mtm-85) REVERT: B 2331 TYR cc_start: 0.8659 (m-80) cc_final: 0.8102 (m-80) REVERT: B 2483 ARG cc_start: 0.7938 (mtp-110) cc_final: 0.7492 (mtp85) REVERT: B 2579 LYS cc_start: 0.8532 (mttt) cc_final: 0.8159 (mttm) REVERT: B 2582 SER cc_start: 0.8732 (p) cc_final: 0.8532 (p) REVERT: B 2592 LYS cc_start: 0.8375 (mtmm) cc_final: 0.8157 (mtmm) REVERT: B 2614 ASP cc_start: 0.8057 (m-30) cc_final: 0.7631 (m-30) REVERT: B 2665 TYR cc_start: 0.8702 (m-80) cc_final: 0.7937 (m-80) REVERT: B 2674 GLU cc_start: 0.7792 (tm-30) cc_final: 0.7415 (tm-30) REVERT: B 2724 GLN cc_start: 0.7655 (mp10) cc_final: 0.7234 (mp10) REVERT: B 2753 ASN cc_start: 0.8230 (m110) cc_final: 0.7802 (OUTLIER) outliers start: 106 outliers final: 46 residues processed: 656 average time/residue: 0.7233 time to fit residues: 546.8642 Evaluate side-chains 639 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 584 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1391 MET Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1647 THR Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1753 GLN Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1906 VAL Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2133 THR Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2462 ASP Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2657 SER Chi-restraints excluded: chain B residue 1130 LEU Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1494 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1555 SER Chi-restraints excluded: chain B residue 1583 ASP Chi-restraints excluded: chain B residue 1642 THR Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1915 VAL Chi-restraints excluded: chain B residue 1942 SER Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 1975 GLU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2128 THR Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2434 LYS Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 210 optimal weight: 20.0000 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 60 optimal weight: 0.7980 chunk 332 optimal weight: 2.9990 chunk 309 optimal weight: 0.9980 chunk 205 optimal weight: 9.9990 chunk 137 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1309 ASN A1773 HIS A1946 HIS A2217 HIS A2447 ASN A2473 GLN A2736 GLN B1309 ASN ** B1801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1946 HIS B2137 HIS B2217 HIS B2473 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.138648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106197 restraints weight = 39631.873| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.21 r_work: 0.3268 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28178 Z= 0.190 Angle : 0.572 9.548 38262 Z= 0.296 Chirality : 0.047 0.336 4296 Planarity : 0.004 0.059 4908 Dihedral : 5.225 52.345 4334 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.41 % Allowed : 23.88 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.42 (0.14), residues: 3432 helix: 0.93 (0.36), residues: 226 sheet: 1.11 (0.15), residues: 1158 loop : -0.26 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1153 TYR 0.019 0.002 TYR A1249 PHE 0.012 0.002 PHE B1355 TRP 0.010 0.001 TRP B1682 HIS 0.006 0.001 HIS B2217 Details of bonding type rmsd covalent geometry : bond 0.00434 (28144) covalent geometry : angle 0.55727 (38170) SS BOND : bond 0.00105 ( 10) SS BOND : angle 0.43972 ( 20) hydrogen bonds : bond 0.03884 ( 1046) hydrogen bonds : angle 4.89825 ( 3825) link_BETA1-4 : bond 0.00387 ( 8) link_BETA1-4 : angle 1.52051 ( 24) link_NAG-ASN : bond 0.00472 ( 16) link_NAG-ASN : angle 3.53055 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 607 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1079 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7776 (p) REVERT: A 1134 VAL cc_start: 0.8586 (t) cc_final: 0.8351 (p) REVERT: A 1135 VAL cc_start: 0.8455 (p) cc_final: 0.8162 (m) REVERT: A 1173 ASP cc_start: 0.7970 (t0) cc_final: 0.7641 (t0) REVERT: A 1391 MET cc_start: 0.6967 (OUTLIER) cc_final: 0.6541 (mpp) REVERT: A 1424 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6083 (pp) REVERT: A 1488 VAL cc_start: 0.8082 (t) cc_final: 0.7771 (m) REVERT: A 1526 ILE cc_start: 0.8221 (mt) cc_final: 0.7911 (mp) REVERT: A 1579 VAL cc_start: 0.9061 (t) cc_final: 0.8817 (m) REVERT: A 1607 ASN cc_start: 0.8530 (m-40) cc_final: 0.8312 (m-40) REVERT: A 1629 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.8355 (ttp) REVERT: A 1635 MET cc_start: 0.8613 (mmt) cc_final: 0.8405 (mmm) REVERT: A 1660 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7419 (mm-30) REVERT: A 1695 THR cc_start: 0.8622 (m) cc_final: 0.8421 (p) REVERT: A 1789 ARG cc_start: 0.8252 (mtp180) cc_final: 0.8034 (mtp180) REVERT: A 1807 LEU cc_start: 0.8947 (mm) cc_final: 0.8729 (mt) REVERT: A 1809 LYS cc_start: 0.7104 (mttt) cc_final: 0.6780 (mttt) REVERT: A 1848 HIS cc_start: 0.8477 (m-70) cc_final: 0.8192 (m-70) REVERT: A 1870 SER cc_start: 0.8830 (OUTLIER) cc_final: 0.8361 (t) REVERT: A 1922 ASP cc_start: 0.7662 (t0) cc_final: 0.7456 (t0) REVERT: A 1985 SER cc_start: 0.8561 (t) cc_final: 0.8322 (p) REVERT: A 2132 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8423 (ptm) REVERT: A 2154 SER cc_start: 0.8953 (OUTLIER) cc_final: 0.8717 (t) REVERT: A 2228 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8322 (ttm) REVERT: A 2331 TYR cc_start: 0.8699 (m-80) cc_final: 0.8337 (m-80) REVERT: A 2341 MET cc_start: 0.8881 (mtm) cc_final: 0.8600 (mtp) REVERT: A 2455 ASP cc_start: 0.7634 (t0) cc_final: 0.7404 (t0) REVERT: A 2543 HIS cc_start: 0.7978 (OUTLIER) cc_final: 0.7474 (t70) REVERT: A 2579 LYS cc_start: 0.8485 (mttt) cc_final: 0.8178 (mttp) REVERT: A 2592 LYS cc_start: 0.8317 (mtmm) cc_final: 0.8085 (mtmm) REVERT: A 2614 ASP cc_start: 0.8260 (m-30) cc_final: 0.7824 (m-30) REVERT: A 2626 VAL cc_start: 0.8281 (t) cc_final: 0.8064 (m) REVERT: A 2660 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8316 (tp) REVERT: A 2665 TYR cc_start: 0.8633 (m-80) cc_final: 0.8045 (m-80) REVERT: A 2674 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 2700 ARG cc_start: 0.7919 (mtp180) cc_final: 0.7559 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7527 (mmt-90) cc_final: 0.7235 (mmt-90) REVERT: B 1080 GLN cc_start: 0.7696 (mp10) cc_final: 0.7460 (mp10) REVERT: B 1110 ASN cc_start: 0.8696 (m110) cc_final: 0.8467 (m-40) REVERT: B 1152 LYS cc_start: 0.7744 (mmtt) cc_final: 0.7344 (mmmm) REVERT: B 1163 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.8071 (p0) REVERT: B 1173 ASP cc_start: 0.8004 (t0) cc_final: 0.7723 (t0) REVERT: B 1274 TYR cc_start: 0.6130 (m-80) cc_final: 0.5722 (m-80) REVERT: B 1391 MET cc_start: 0.6594 (OUTLIER) cc_final: 0.6177 (mpp) REVERT: B 1485 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.7118 (pt) REVERT: B 1555 SER cc_start: 0.8592 (OUTLIER) cc_final: 0.8387 (m) REVERT: B 1607 ASN cc_start: 0.8539 (m-40) cc_final: 0.8334 (t0) REVERT: B 1639 GLN cc_start: 0.7911 (tp40) cc_final: 0.7315 (mp10) REVERT: B 1642 THR cc_start: 0.8627 (m) cc_final: 0.8318 (p) REVERT: B 1652 LYS cc_start: 0.8530 (tptt) cc_final: 0.8221 (mtpp) REVERT: B 1806 ARG cc_start: 0.8604 (mtt180) cc_final: 0.8228 (mtt180) REVERT: B 1845 TYR cc_start: 0.8625 (p90) cc_final: 0.8352 (p90) REVERT: B 1917 SER cc_start: 0.8682 (m) cc_final: 0.8366 (p) REVERT: B 1922 ASP cc_start: 0.7608 (t0) cc_final: 0.7357 (t0) REVERT: B 1950 MET cc_start: 0.8669 (mmt) cc_final: 0.8335 (mmt) REVERT: B 2058 LYS cc_start: 0.8751 (ttpp) cc_final: 0.8503 (ttpt) REVERT: B 2093 GLU cc_start: 0.7810 (mp0) cc_final: 0.7362 (pp20) REVERT: B 2211 ASP cc_start: 0.7962 (t0) cc_final: 0.7673 (t70) REVERT: B 2231 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8193 (mtm-85) REVERT: B 2331 TYR cc_start: 0.8651 (m-80) cc_final: 0.8080 (m-80) REVERT: B 2483 ARG cc_start: 0.7932 (mtp-110) cc_final: 0.7513 (mtp85) REVERT: B 2543 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7509 (t70) REVERT: B 2579 LYS cc_start: 0.8506 (mttt) cc_final: 0.8138 (mttm) REVERT: B 2592 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8173 (mtmm) REVERT: B 2614 ASP cc_start: 0.8112 (m-30) cc_final: 0.7708 (m-30) REVERT: B 2665 TYR cc_start: 0.8706 (m-80) cc_final: 0.7951 (m-80) REVERT: B 2674 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7350 (tm-30) REVERT: B 2724 GLN cc_start: 0.7647 (mp10) cc_final: 0.7201 (mp10) REVERT: B 2753 ASN cc_start: 0.8176 (m110) cc_final: 0.7671 (OUTLIER) outliers start: 102 outliers final: 50 residues processed: 655 average time/residue: 0.6558 time to fit residues: 497.5785 Evaluate side-chains 646 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 582 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1079 THR Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1391 MET Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1696 ASN Chi-restraints excluded: chain A residue 1719 ILE Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1811 GLN Chi-restraints excluded: chain A residue 1870 SER Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2133 THR Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2228 MET Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2547 THR Chi-restraints excluded: chain A residue 2557 MET Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2606 VAL Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain B residue 1091 HIS Chi-restraints excluded: chain B residue 1130 LEU Chi-restraints excluded: chain B residue 1136 SER Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1555 SER Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2106 ILE Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2128 THR Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2662 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 155 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 2.9990 chunk 318 optimal weight: 0.8980 chunk 303 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 281 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 ASN A1773 HIS A1946 HIS A2217 HIS A2302 HIS A2473 GLN A2736 GLN B1102 GLN ** B1801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1946 HIS B2137 HIS B2217 HIS B2473 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.139244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.106874 restraints weight = 39641.738| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.21 r_work: 0.3278 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28178 Z= 0.140 Angle : 0.548 9.397 38262 Z= 0.284 Chirality : 0.046 0.337 4296 Planarity : 0.004 0.046 4908 Dihedral : 5.021 52.165 4334 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.28 % Allowed : 24.28 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.50 (0.15), residues: 3432 helix: 1.07 (0.36), residues: 226 sheet: 1.13 (0.15), residues: 1158 loop : -0.19 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1849 TYR 0.018 0.001 TYR B1249 PHE 0.011 0.001 PHE B2558 TRP 0.011 0.001 TRP B1682 HIS 0.007 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00322 (28144) covalent geometry : angle 0.53414 (38170) SS BOND : bond 0.00077 ( 10) SS BOND : angle 1.42555 ( 20) hydrogen bonds : bond 0.03583 ( 1046) hydrogen bonds : angle 4.79048 ( 3825) link_BETA1-4 : bond 0.00431 ( 8) link_BETA1-4 : angle 1.41898 ( 24) link_NAG-ASN : bond 0.00405 ( 16) link_NAG-ASN : angle 3.29779 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 598 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1080 GLN cc_start: 0.7639 (mp10) cc_final: 0.7396 (mp10) REVERT: A 1096 VAL cc_start: 0.8425 (t) cc_final: 0.8053 (p) REVERT: A 1134 VAL cc_start: 0.8569 (t) cc_final: 0.8334 (p) REVERT: A 1135 VAL cc_start: 0.8506 (p) cc_final: 0.8190 (m) REVERT: A 1173 ASP cc_start: 0.7950 (t0) cc_final: 0.7595 (t0) REVERT: A 1206 MET cc_start: 0.5342 (mmm) cc_final: 0.5062 (mmm) REVERT: A 1391 MET cc_start: 0.7020 (pmm) cc_final: 0.6619 (mpp) REVERT: A 1424 ILE cc_start: 0.6824 (OUTLIER) cc_final: 0.6066 (pp) REVERT: A 1488 VAL cc_start: 0.8071 (t) cc_final: 0.7762 (m) REVERT: A 1526 ILE cc_start: 0.8212 (mt) cc_final: 0.7925 (mp) REVERT: A 1579 VAL cc_start: 0.9047 (t) cc_final: 0.8833 (m) REVERT: A 1607 ASN cc_start: 0.8523 (m-40) cc_final: 0.8316 (m-40) REVERT: A 1629 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: A 1660 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7399 (mm-30) REVERT: A 1807 LEU cc_start: 0.8939 (mm) cc_final: 0.8716 (mt) REVERT: A 1848 HIS cc_start: 0.8400 (m-70) cc_final: 0.8147 (m-70) REVERT: A 1870 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8366 (t) REVERT: A 1896 ARG cc_start: 0.8326 (mtm-85) cc_final: 0.8119 (mtt90) REVERT: A 1922 ASP cc_start: 0.7691 (t0) cc_final: 0.7471 (t0) REVERT: A 1985 SER cc_start: 0.8587 (t) cc_final: 0.8351 (p) REVERT: A 2132 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8354 (ptm) REVERT: A 2154 SER cc_start: 0.8935 (OUTLIER) cc_final: 0.8706 (t) REVERT: A 2228 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8252 (ttm) REVERT: A 2331 TYR cc_start: 0.8689 (m-80) cc_final: 0.8235 (m-80) REVERT: A 2341 MET cc_start: 0.8872 (mtm) cc_final: 0.8576 (mtp) REVERT: A 2455 ASP cc_start: 0.7634 (t0) cc_final: 0.7403 (t0) REVERT: A 2543 HIS cc_start: 0.7952 (OUTLIER) cc_final: 0.7485 (t70) REVERT: A 2567 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8124 (t) REVERT: A 2579 LYS cc_start: 0.8481 (mttt) cc_final: 0.8217 (mttp) REVERT: A 2592 LYS cc_start: 0.8320 (mtmm) cc_final: 0.8095 (mtmm) REVERT: A 2614 ASP cc_start: 0.8238 (m-30) cc_final: 0.7770 (m-30) REVERT: A 2626 VAL cc_start: 0.8270 (t) cc_final: 0.8053 (m) REVERT: A 2660 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8301 (tp) REVERT: A 2665 TYR cc_start: 0.8628 (m-80) cc_final: 0.7969 (m-80) REVERT: A 2674 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7365 (tm-30) REVERT: A 2700 ARG cc_start: 0.7944 (mtp180) cc_final: 0.7591 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7529 (mmt-90) cc_final: 0.7231 (mmt-90) REVERT: B 1080 GLN cc_start: 0.7704 (mp10) cc_final: 0.7455 (mp10) REVERT: B 1110 ASN cc_start: 0.8731 (m110) cc_final: 0.8484 (m-40) REVERT: B 1152 LYS cc_start: 0.7691 (mmtt) cc_final: 0.7432 (mmmm) REVERT: B 1163 ASP cc_start: 0.8300 (OUTLIER) cc_final: 0.8089 (p0) REVERT: B 1173 ASP cc_start: 0.7975 (t0) cc_final: 0.7688 (t0) REVERT: B 1274 TYR cc_start: 0.6123 (m-80) cc_final: 0.5717 (m-80) REVERT: B 1391 MET cc_start: 0.6638 (pmm) cc_final: 0.6185 (mpp) REVERT: B 1485 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7126 (pt) REVERT: B 1639 GLN cc_start: 0.7914 (tp40) cc_final: 0.7294 (mp10) REVERT: B 1642 THR cc_start: 0.8611 (m) cc_final: 0.8312 (p) REVERT: B 1652 LYS cc_start: 0.8515 (tptt) cc_final: 0.8182 (mtpp) REVERT: B 1806 ARG cc_start: 0.8595 (mtt180) cc_final: 0.8210 (mtt180) REVERT: B 1845 TYR cc_start: 0.8622 (p90) cc_final: 0.8333 (p90) REVERT: B 1917 SER cc_start: 0.8658 (m) cc_final: 0.8351 (p) REVERT: B 1922 ASP cc_start: 0.7665 (t0) cc_final: 0.7400 (t0) REVERT: B 1950 MET cc_start: 0.8656 (mmt) cc_final: 0.8294 (mmt) REVERT: B 2331 TYR cc_start: 0.8650 (m-80) cc_final: 0.8295 (m-80) REVERT: B 2483 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7512 (mtp85) REVERT: B 2543 HIS cc_start: 0.7897 (OUTLIER) cc_final: 0.7452 (t70) REVERT: B 2579 LYS cc_start: 0.8421 (mttt) cc_final: 0.8162 (mttm) REVERT: B 2592 LYS cc_start: 0.8395 (mtmm) cc_final: 0.8187 (mtmm) REVERT: B 2614 ASP cc_start: 0.8081 (m-30) cc_final: 0.7588 (m-30) REVERT: B 2665 TYR cc_start: 0.8706 (m-80) cc_final: 0.7966 (m-80) REVERT: B 2674 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7290 (tm-30) REVERT: B 2724 GLN cc_start: 0.7639 (mp10) cc_final: 0.7218 (mp10) REVERT: B 2753 ASN cc_start: 0.8174 (m110) cc_final: 0.7672 (OUTLIER) outliers start: 98 outliers final: 53 residues processed: 645 average time/residue: 0.6942 time to fit residues: 517.3461 Evaluate side-chains 639 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 575 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1629 MET Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1719 ILE Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1753 GLN Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1870 SER Chi-restraints excluded: chain A residue 1943 ASP Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2133 THR Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2228 MET Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2601 ASP Chi-restraints excluded: chain A residue 2606 VAL Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain A residue 2670 ASP Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1494 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1807 LEU Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2106 ILE Chi-restraints excluded: chain B residue 2122 ASP Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2547 THR Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2662 SER Chi-restraints excluded: chain B residue 2718 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 97 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 283 optimal weight: 0.9980 chunk 288 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 319 optimal weight: 4.9990 chunk 332 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1756 ASN A1773 HIS A1946 HIS A2217 HIS A2473 GLN A2736 GLN B1801 ASN B1946 HIS B2217 HIS B2473 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105604 restraints weight = 39576.632| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.18 r_work: 0.3258 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 28178 Z= 0.216 Angle : 0.593 10.252 38262 Z= 0.307 Chirality : 0.047 0.320 4296 Planarity : 0.004 0.075 4908 Dihedral : 5.181 53.249 4334 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.65 % Allowed : 24.11 % Favored : 72.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.42 (0.14), residues: 3432 helix: 0.99 (0.35), residues: 226 sheet: 1.02 (0.15), residues: 1168 loop : -0.21 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A2578 TYR 0.019 0.002 TYR B1249 PHE 0.018 0.002 PHE B2558 TRP 0.014 0.001 TRP B1682 HIS 0.007 0.001 HIS A2311 Details of bonding type rmsd covalent geometry : bond 0.00499 (28144) covalent geometry : angle 0.57873 (38170) SS BOND : bond 0.00119 ( 10) SS BOND : angle 1.22097 ( 20) hydrogen bonds : bond 0.03960 ( 1046) hydrogen bonds : angle 4.88862 ( 3825) link_BETA1-4 : bond 0.00409 ( 8) link_BETA1-4 : angle 1.50164 ( 24) link_NAG-ASN : bond 0.00518 ( 16) link_NAG-ASN : angle 3.52637 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 598 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1080 GLN cc_start: 0.7792 (mp10) cc_final: 0.7554 (mp10) REVERT: A 1103 LYS cc_start: 0.7965 (tttt) cc_final: 0.7719 (mttt) REVERT: A 1134 VAL cc_start: 0.8616 (t) cc_final: 0.8395 (p) REVERT: A 1135 VAL cc_start: 0.8578 (p) cc_final: 0.8232 (m) REVERT: A 1173 ASP cc_start: 0.7987 (t0) cc_final: 0.7655 (t0) REVERT: A 1206 MET cc_start: 0.5202 (mmm) cc_final: 0.4920 (mmm) REVERT: A 1391 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6621 (mpp) REVERT: A 1424 ILE cc_start: 0.6935 (OUTLIER) cc_final: 0.6181 (pp) REVERT: A 1488 VAL cc_start: 0.8132 (t) cc_final: 0.7835 (m) REVERT: A 1526 ILE cc_start: 0.8244 (mt) cc_final: 0.7967 (mp) REVERT: A 1579 VAL cc_start: 0.9042 (t) cc_final: 0.8797 (m) REVERT: A 1607 ASN cc_start: 0.8558 (m-40) cc_final: 0.8339 (m-40) REVERT: A 1660 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 1772 PHE cc_start: 0.7278 (p90) cc_final: 0.7009 (p90) REVERT: A 1807 LEU cc_start: 0.8969 (mm) cc_final: 0.8741 (mt) REVERT: A 1809 LYS cc_start: 0.7121 (mttt) cc_final: 0.6698 (mttt) REVERT: A 1848 HIS cc_start: 0.8525 (m-70) cc_final: 0.8205 (m-70) REVERT: A 1870 SER cc_start: 0.8795 (p) cc_final: 0.8346 (t) REVERT: A 1922 ASP cc_start: 0.7677 (t0) cc_final: 0.7441 (t0) REVERT: A 1985 SER cc_start: 0.8617 (t) cc_final: 0.8391 (p) REVERT: A 2102 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8218 (ttt-90) REVERT: A 2111 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7829 (mt-10) REVERT: A 2132 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8411 (ptm) REVERT: A 2154 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8722 (t) REVERT: A 2228 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8268 (ttm) REVERT: A 2331 TYR cc_start: 0.8692 (m-80) cc_final: 0.8307 (m-80) REVERT: A 2341 MET cc_start: 0.8871 (mtm) cc_final: 0.8580 (mtp) REVERT: A 2543 HIS cc_start: 0.7916 (OUTLIER) cc_final: 0.7306 (t70) REVERT: A 2579 LYS cc_start: 0.8495 (mttt) cc_final: 0.8193 (mttp) REVERT: A 2592 LYS cc_start: 0.8325 (mtmm) cc_final: 0.8096 (mtmm) REVERT: A 2614 ASP cc_start: 0.8255 (m-30) cc_final: 0.7844 (m-30) REVERT: A 2626 VAL cc_start: 0.8293 (t) cc_final: 0.8079 (m) REVERT: A 2660 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8326 (tp) REVERT: A 2665 TYR cc_start: 0.8660 (m-80) cc_final: 0.8073 (m-80) REVERT: A 2674 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 2681 ASP cc_start: 0.8081 (t70) cc_final: 0.7770 (t0) REVERT: A 2700 ARG cc_start: 0.7996 (mtp180) cc_final: 0.7640 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7529 (mmt-90) cc_final: 0.7253 (mmt-90) REVERT: B 1080 GLN cc_start: 0.7767 (mp10) cc_final: 0.7550 (mp10) REVERT: B 1110 ASN cc_start: 0.8745 (m110) cc_final: 0.8495 (m-40) REVERT: B 1152 LYS cc_start: 0.7866 (mmtt) cc_final: 0.7455 (mmmm) REVERT: B 1163 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8078 (p0) REVERT: B 1173 ASP cc_start: 0.7985 (t0) cc_final: 0.7581 (t0) REVERT: B 1274 TYR cc_start: 0.6142 (m-80) cc_final: 0.5697 (m-80) REVERT: B 1391 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6242 (mpp) REVERT: B 1485 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7119 (pt) REVERT: B 1543 ILE cc_start: 0.6779 (OUTLIER) cc_final: 0.6347 (tt) REVERT: B 1560 VAL cc_start: 0.8624 (p) cc_final: 0.8366 (m) REVERT: B 1631 ARG cc_start: 0.8241 (mtp85) cc_final: 0.7586 (mtm110) REVERT: B 1639 GLN cc_start: 0.7975 (tp40) cc_final: 0.7381 (mp10) REVERT: B 1642 THR cc_start: 0.8602 (m) cc_final: 0.8368 (p) REVERT: B 1652 LYS cc_start: 0.8540 (tptt) cc_final: 0.8204 (mtpp) REVERT: B 1754 LEU cc_start: 0.8346 (mm) cc_final: 0.8127 (mt) REVERT: B 1845 TYR cc_start: 0.8617 (p90) cc_final: 0.8302 (p90) REVERT: B 1917 SER cc_start: 0.8671 (m) cc_final: 0.8365 (p) REVERT: B 1922 ASP cc_start: 0.7611 (t0) cc_final: 0.7347 (t0) REVERT: B 1950 MET cc_start: 0.8695 (mmt) cc_final: 0.8401 (mmt) REVERT: B 2058 LYS cc_start: 0.8756 (ttpp) cc_final: 0.8494 (ttpt) REVERT: B 2211 ASP cc_start: 0.7901 (t0) cc_final: 0.7615 (t70) REVERT: B 2331 TYR cc_start: 0.8695 (m-80) cc_final: 0.8341 (m-80) REVERT: B 2483 ARG cc_start: 0.7930 (mtp-110) cc_final: 0.7503 (mtp85) REVERT: B 2543 HIS cc_start: 0.7960 (OUTLIER) cc_final: 0.7462 (t70) REVERT: B 2579 LYS cc_start: 0.8435 (mttt) cc_final: 0.8176 (mttm) REVERT: B 2592 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8192 (mtmm) REVERT: B 2614 ASP cc_start: 0.8124 (m-30) cc_final: 0.7722 (m-30) REVERT: B 2665 TYR cc_start: 0.8727 (m-80) cc_final: 0.7985 (m-80) REVERT: B 2674 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7267 (tm-30) REVERT: B 2724 GLN cc_start: 0.7617 (mp10) cc_final: 0.7185 (mp10) REVERT: B 2745 SER cc_start: 0.8676 (p) cc_final: 0.8394 (t) outliers start: 109 outliers final: 62 residues processed: 653 average time/residue: 0.7305 time to fit residues: 554.2833 Evaluate side-chains 655 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 580 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1076 ILE Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1091 HIS Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1391 MET Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1719 ILE Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1753 GLN Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2102 ARG Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2228 MET Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2606 VAL Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain B residue 1136 SER Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1494 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1543 ILE Chi-restraints excluded: chain B residue 1583 ASP Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1807 LEU Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2106 ILE Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2122 ASP Chi-restraints excluded: chain B residue 2128 THR Chi-restraints excluded: chain B residue 2228 MET Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2434 LYS Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2547 THR Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2662 SER Chi-restraints excluded: chain B residue 2718 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 332 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 165 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 291 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1773 HIS A1946 HIS A2217 HIS A2396 HIS A2473 GLN A2736 GLN B1587 GLN ** B1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1801 ASN B1946 HIS B2217 HIS B2473 GLN B2753 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.105717 restraints weight = 39774.723| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.17 r_work: 0.3259 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28178 Z= 0.200 Angle : 0.586 10.298 38262 Z= 0.303 Chirality : 0.047 0.320 4296 Planarity : 0.004 0.063 4908 Dihedral : 5.149 54.142 4334 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.94 % Allowed : 25.28 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.41 (0.14), residues: 3432 helix: 1.03 (0.35), residues: 226 sheet: 1.00 (0.15), residues: 1168 loop : -0.22 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B2240 TYR 0.018 0.002 TYR A1521 PHE 0.014 0.002 PHE B2558 TRP 0.014 0.001 TRP B1682 HIS 0.007 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00462 (28144) covalent geometry : angle 0.57255 (38170) SS BOND : bond 0.00103 ( 10) SS BOND : angle 1.10205 ( 20) hydrogen bonds : bond 0.03839 ( 1046) hydrogen bonds : angle 4.86673 ( 3825) link_BETA1-4 : bond 0.00405 ( 8) link_BETA1-4 : angle 1.49129 ( 24) link_NAG-ASN : bond 0.00462 ( 16) link_NAG-ASN : angle 3.42713 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 591 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1080 GLN cc_start: 0.7850 (mp10) cc_final: 0.7648 (mp10) REVERT: A 1103 LYS cc_start: 0.7986 (tttt) cc_final: 0.7781 (mttt) REVERT: A 1134 VAL cc_start: 0.8618 (t) cc_final: 0.8395 (p) REVERT: A 1173 ASP cc_start: 0.7989 (t0) cc_final: 0.7659 (t0) REVERT: A 1206 MET cc_start: 0.5248 (mmm) cc_final: 0.4971 (mmm) REVERT: A 1391 MET cc_start: 0.7206 (pmm) cc_final: 0.6947 (mpp) REVERT: A 1424 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6200 (pp) REVERT: A 1488 VAL cc_start: 0.8171 (t) cc_final: 0.7865 (m) REVERT: A 1526 ILE cc_start: 0.8236 (mt) cc_final: 0.7953 (mp) REVERT: A 1535 VAL cc_start: 0.8482 (t) cc_final: 0.8029 (m) REVERT: A 1579 VAL cc_start: 0.9038 (t) cc_final: 0.8800 (m) REVERT: A 1607 ASN cc_start: 0.8551 (m-40) cc_final: 0.8314 (m-40) REVERT: A 1635 MET cc_start: 0.8618 (mmt) cc_final: 0.8396 (mmm) REVERT: A 1660 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7408 (mm-30) REVERT: A 1772 PHE cc_start: 0.7192 (p90) cc_final: 0.6894 (p90) REVERT: A 1789 ARG cc_start: 0.8261 (mtp180) cc_final: 0.8027 (mtp180) REVERT: A 1806 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8209 (mtt180) REVERT: A 1807 LEU cc_start: 0.8974 (mm) cc_final: 0.8746 (mt) REVERT: A 1848 HIS cc_start: 0.8524 (m-70) cc_final: 0.8241 (m-70) REVERT: A 1870 SER cc_start: 0.8811 (p) cc_final: 0.8367 (t) REVERT: A 1922 ASP cc_start: 0.7695 (t0) cc_final: 0.7447 (t0) REVERT: A 1985 SER cc_start: 0.8576 (t) cc_final: 0.8325 (p) REVERT: A 2102 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.8208 (ttt-90) REVERT: A 2111 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7855 (mt-10) REVERT: A 2132 MET cc_start: 0.8748 (OUTLIER) cc_final: 0.8394 (ptm) REVERT: A 2154 SER cc_start: 0.8934 (OUTLIER) cc_final: 0.8702 (t) REVERT: A 2228 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8257 (ttm) REVERT: A 2331 TYR cc_start: 0.8694 (m-80) cc_final: 0.8304 (m-80) REVERT: A 2341 MET cc_start: 0.8874 (mtm) cc_final: 0.8585 (mtp) REVERT: A 2455 ASP cc_start: 0.7767 (m-30) cc_final: 0.7495 (m-30) REVERT: A 2543 HIS cc_start: 0.7903 (OUTLIER) cc_final: 0.7350 (t70) REVERT: A 2579 LYS cc_start: 0.8495 (mttt) cc_final: 0.8274 (mttp) REVERT: A 2592 LYS cc_start: 0.8348 (mtmm) cc_final: 0.8115 (mtmm) REVERT: A 2614 ASP cc_start: 0.8268 (m-30) cc_final: 0.7853 (m-30) REVERT: A 2626 VAL cc_start: 0.8276 (t) cc_final: 0.8068 (m) REVERT: A 2660 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 2665 TYR cc_start: 0.8646 (m-80) cc_final: 0.8047 (m-80) REVERT: A 2674 GLU cc_start: 0.7883 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 2681 ASP cc_start: 0.8060 (t70) cc_final: 0.7750 (t0) REVERT: A 2700 ARG cc_start: 0.7977 (mtp180) cc_final: 0.7632 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7216 (mmt-90) REVERT: B 1080 GLN cc_start: 0.7820 (mp10) cc_final: 0.7590 (mp10) REVERT: B 1110 ASN cc_start: 0.8735 (m110) cc_final: 0.8500 (m-40) REVERT: B 1151 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7353 (tm-30) REVERT: B 1152 LYS cc_start: 0.7868 (mmtt) cc_final: 0.7525 (mmmm) REVERT: B 1163 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8087 (p0) REVERT: B 1173 ASP cc_start: 0.7987 (t0) cc_final: 0.7584 (t0) REVERT: B 1274 TYR cc_start: 0.6134 (m-80) cc_final: 0.5711 (m-80) REVERT: B 1391 MET cc_start: 0.6807 (pmm) cc_final: 0.6313 (mpp) REVERT: B 1409 MET cc_start: 0.7434 (ptp) cc_final: 0.6998 (ptp) REVERT: B 1485 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7136 (pt) REVERT: B 1543 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6403 (tt) REVERT: B 1560 VAL cc_start: 0.8649 (p) cc_final: 0.8389 (m) REVERT: B 1631 ARG cc_start: 0.8262 (mtp85) cc_final: 0.7590 (mtm110) REVERT: B 1639 GLN cc_start: 0.7954 (tp40) cc_final: 0.7350 (mp10) REVERT: B 1642 THR cc_start: 0.8577 (m) cc_final: 0.8274 (p) REVERT: B 1652 LYS cc_start: 0.8538 (tptt) cc_final: 0.8196 (mtpp) REVERT: B 1754 LEU cc_start: 0.8333 (mm) cc_final: 0.8112 (mt) REVERT: B 1806 ARG cc_start: 0.8709 (mtm-85) cc_final: 0.8160 (mtt180) REVERT: B 1845 TYR cc_start: 0.8610 (p90) cc_final: 0.8288 (p90) REVERT: B 1914 LYS cc_start: 0.8811 (mttm) cc_final: 0.8527 (mtpp) REVERT: B 1917 SER cc_start: 0.8668 (m) cc_final: 0.8366 (p) REVERT: B 1922 ASP cc_start: 0.7652 (t0) cc_final: 0.7378 (t0) REVERT: B 1950 MET cc_start: 0.8689 (mmt) cc_final: 0.8351 (mmt) REVERT: B 2058 LYS cc_start: 0.8743 (ttpp) cc_final: 0.8475 (ttpt) REVERT: B 2211 ASP cc_start: 0.7964 (t0) cc_final: 0.7676 (t70) REVERT: B 2331 TYR cc_start: 0.8677 (m-80) cc_final: 0.8318 (m-80) REVERT: B 2483 ARG cc_start: 0.7914 (mtp-110) cc_final: 0.7402 (mtp180) REVERT: B 2543 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7436 (t70) REVERT: B 2579 LYS cc_start: 0.8414 (mttt) cc_final: 0.8151 (mttm) REVERT: B 2592 LYS cc_start: 0.8429 (mtmm) cc_final: 0.8218 (mtmm) REVERT: B 2614 ASP cc_start: 0.8097 (m-30) cc_final: 0.7705 (m-30) REVERT: B 2665 TYR cc_start: 0.8719 (m-80) cc_final: 0.7964 (m-80) REVERT: B 2674 GLU cc_start: 0.7738 (tm-30) cc_final: 0.7322 (tm-30) REVERT: B 2724 GLN cc_start: 0.7608 (mp10) cc_final: 0.7197 (mp10) REVERT: B 2745 SER cc_start: 0.8679 (p) cc_final: 0.8397 (t) REVERT: B 2753 ASN cc_start: 0.8193 (m110) cc_final: 0.7801 (p0) outliers start: 88 outliers final: 58 residues processed: 637 average time/residue: 0.7071 time to fit residues: 519.6420 Evaluate side-chains 650 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 581 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1130 LEU Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1637 ASP Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1719 ILE Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1753 GLN Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2102 ARG Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2228 MET Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2606 VAL Chi-restraints excluded: chain A residue 2636 SER Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain B residue 1136 SER Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1494 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1543 ILE Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1710 GLU Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1753 GLN Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2122 ASP Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2547 THR Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2662 SER Chi-restraints excluded: chain B residue 2700 ARG Chi-restraints excluded: chain B residue 2718 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 74 optimal weight: 0.9980 chunk 309 optimal weight: 2.9990 chunk 323 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 279 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1733 ASN A1773 HIS A1946 HIS A2217 HIS A2473 GLN A2736 GLN ** B1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1946 HIS B2217 HIS B2473 GLN B2736 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105980 restraints weight = 39716.644| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.12 r_work: 0.3265 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 28178 Z= 0.194 Angle : 0.589 11.271 38262 Z= 0.304 Chirality : 0.047 0.316 4296 Planarity : 0.004 0.048 4908 Dihedral : 5.128 54.787 4334 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.88 % Allowed : 25.48 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.39 (0.14), residues: 3432 helix: 1.06 (0.35), residues: 226 sheet: 0.98 (0.15), residues: 1170 loop : -0.23 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG B2240 TYR 0.020 0.002 TYR A1521 PHE 0.016 0.002 PHE B1772 TRP 0.014 0.001 TRP B1682 HIS 0.008 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00450 (28144) covalent geometry : angle 0.57530 (38170) SS BOND : bond 0.00102 ( 10) SS BOND : angle 1.04119 ( 20) hydrogen bonds : bond 0.03821 ( 1046) hydrogen bonds : angle 4.85897 ( 3825) link_BETA1-4 : bond 0.00389 ( 8) link_BETA1-4 : angle 1.47138 ( 24) link_NAG-ASN : bond 0.00464 ( 16) link_NAG-ASN : angle 3.39142 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 593 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1080 GLN cc_start: 0.7958 (mp10) cc_final: 0.7747 (mp10) REVERT: A 1103 LYS cc_start: 0.7973 (tttt) cc_final: 0.7735 (ttpp) REVERT: A 1134 VAL cc_start: 0.8626 (t) cc_final: 0.8417 (p) REVERT: A 1173 ASP cc_start: 0.7977 (t0) cc_final: 0.7682 (t0) REVERT: A 1206 MET cc_start: 0.5182 (mmm) cc_final: 0.4907 (mmm) REVERT: A 1391 MET cc_start: 0.7258 (OUTLIER) cc_final: 0.7046 (mpp) REVERT: A 1424 ILE cc_start: 0.6979 (OUTLIER) cc_final: 0.6280 (pp) REVERT: A 1488 VAL cc_start: 0.8196 (t) cc_final: 0.7890 (m) REVERT: A 1526 ILE cc_start: 0.8249 (mt) cc_final: 0.7966 (mp) REVERT: A 1535 VAL cc_start: 0.8525 (t) cc_final: 0.8099 (m) REVERT: A 1560 VAL cc_start: 0.8683 (p) cc_final: 0.8428 (m) REVERT: A 1579 VAL cc_start: 0.9041 (t) cc_final: 0.8807 (m) REVERT: A 1607 ASN cc_start: 0.8552 (m-40) cc_final: 0.8321 (m-40) REVERT: A 1635 MET cc_start: 0.8606 (mmt) cc_final: 0.8386 (mmm) REVERT: A 1660 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 1772 PHE cc_start: 0.7262 (p90) cc_final: 0.6959 (p90) REVERT: A 1806 ARG cc_start: 0.8565 (mtm-85) cc_final: 0.8203 (mtt180) REVERT: A 1807 LEU cc_start: 0.8975 (mm) cc_final: 0.8744 (mt) REVERT: A 1870 SER cc_start: 0.8804 (p) cc_final: 0.8357 (t) REVERT: A 1922 ASP cc_start: 0.7658 (t0) cc_final: 0.7416 (t0) REVERT: A 1985 SER cc_start: 0.8642 (t) cc_final: 0.8406 (p) REVERT: A 2102 ARG cc_start: 0.8510 (OUTLIER) cc_final: 0.8205 (ttt-90) REVERT: A 2111 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7856 (mt-10) REVERT: A 2132 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8331 (ptm) REVERT: A 2154 SER cc_start: 0.8949 (OUTLIER) cc_final: 0.8708 (t) REVERT: A 2219 LEU cc_start: 0.8639 (pt) cc_final: 0.8388 (pp) REVERT: A 2228 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8272 (ttm) REVERT: A 2331 TYR cc_start: 0.8692 (m-80) cc_final: 0.8308 (m-80) REVERT: A 2341 MET cc_start: 0.8876 (mtm) cc_final: 0.8581 (mtp) REVERT: A 2455 ASP cc_start: 0.7770 (m-30) cc_final: 0.7510 (m-30) REVERT: A 2543 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7286 (t70) REVERT: A 2578 ARG cc_start: 0.8281 (mtt-85) cc_final: 0.8060 (mtt180) REVERT: A 2579 LYS cc_start: 0.8505 (mttt) cc_final: 0.8201 (mttp) REVERT: A 2592 LYS cc_start: 0.8337 (mtmm) cc_final: 0.8113 (mtmm) REVERT: A 2614 ASP cc_start: 0.8336 (m-30) cc_final: 0.7906 (m-30) REVERT: A 2626 VAL cc_start: 0.8278 (t) cc_final: 0.7995 (p) REVERT: A 2660 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8292 (tp) REVERT: A 2665 TYR cc_start: 0.8667 (m-80) cc_final: 0.8077 (m-80) REVERT: A 2674 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 2681 ASP cc_start: 0.8063 (t70) cc_final: 0.7752 (t0) REVERT: A 2700 ARG cc_start: 0.7961 (mtp180) cc_final: 0.7627 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7500 (mmt-90) cc_final: 0.7264 (mmt-90) REVERT: B 1080 GLN cc_start: 0.7830 (mp10) cc_final: 0.7617 (mp10) REVERT: B 1110 ASN cc_start: 0.8723 (m110) cc_final: 0.8509 (m-40) REVERT: B 1151 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7355 (tm-30) REVERT: B 1152 LYS cc_start: 0.7882 (mmtt) cc_final: 0.7521 (mmmm) REVERT: B 1163 ASP cc_start: 0.8333 (OUTLIER) cc_final: 0.8057 (p0) REVERT: B 1173 ASP cc_start: 0.7983 (t0) cc_final: 0.7586 (t0) REVERT: B 1274 TYR cc_start: 0.6133 (m-80) cc_final: 0.5716 (m-80) REVERT: B 1391 MET cc_start: 0.6759 (OUTLIER) cc_final: 0.6163 (mpp) REVERT: B 1409 MET cc_start: 0.7445 (ptp) cc_final: 0.7083 (ptp) REVERT: B 1485 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7148 (pt) REVERT: B 1543 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6488 (tt) REVERT: B 1560 VAL cc_start: 0.8645 (p) cc_final: 0.8395 (m) REVERT: B 1631 ARG cc_start: 0.8249 (mtp85) cc_final: 0.7631 (mtm110) REVERT: B 1639 GLN cc_start: 0.7905 (tp40) cc_final: 0.7291 (mp10) REVERT: B 1652 LYS cc_start: 0.8543 (tptt) cc_final: 0.8205 (mtpp) REVERT: B 1754 LEU cc_start: 0.8353 (mm) cc_final: 0.8119 (mt) REVERT: B 1805 TRP cc_start: 0.9014 (m100) cc_final: 0.8635 (m100) REVERT: B 1806 ARG cc_start: 0.8699 (mtm-85) cc_final: 0.8155 (mtt180) REVERT: B 1845 TYR cc_start: 0.8617 (p90) cc_final: 0.8303 (p90) REVERT: B 1914 LYS cc_start: 0.8814 (mttm) cc_final: 0.8537 (mtpp) REVERT: B 1917 SER cc_start: 0.8672 (m) cc_final: 0.8378 (p) REVERT: B 1922 ASP cc_start: 0.7612 (t0) cc_final: 0.7336 (t0) REVERT: B 1950 MET cc_start: 0.8693 (mmt) cc_final: 0.8364 (mmt) REVERT: B 2058 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8473 (ttpt) REVERT: B 2219 LEU cc_start: 0.8480 (pt) cc_final: 0.8230 (pp) REVERT: B 2331 TYR cc_start: 0.8685 (m-80) cc_final: 0.8347 (m-80) REVERT: B 2483 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7432 (mtp180) REVERT: B 2543 HIS cc_start: 0.7940 (OUTLIER) cc_final: 0.7444 (t70) REVERT: B 2578 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7873 (mtt180) REVERT: B 2579 LYS cc_start: 0.8426 (mttt) cc_final: 0.8167 (mttm) REVERT: B 2614 ASP cc_start: 0.8109 (m-30) cc_final: 0.7722 (m-30) REVERT: B 2665 TYR cc_start: 0.8715 (m-80) cc_final: 0.7963 (m-80) REVERT: B 2674 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7298 (tm-30) REVERT: B 2724 GLN cc_start: 0.7603 (mp10) cc_final: 0.7175 (mp10) REVERT: B 2745 SER cc_start: 0.8678 (p) cc_final: 0.8395 (t) REVERT: B 2753 ASN cc_start: 0.8189 (m110) cc_final: 0.7682 (OUTLIER) outliers start: 86 outliers final: 57 residues processed: 639 average time/residue: 0.7085 time to fit residues: 522.9179 Evaluate side-chains 648 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 579 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1078 MET Chi-restraints excluded: chain A residue 1144 CYS Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1391 MET Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1677 SER Chi-restraints excluded: chain A residue 1719 ILE Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1921 LEU Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2102 ARG Chi-restraints excluded: chain A residue 2106 ILE Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2228 MET Chi-restraints excluded: chain A residue 2368 LEU Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2606 VAL Chi-restraints excluded: chain A residue 2660 LEU Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1391 MET Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1494 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1543 ILE Chi-restraints excluded: chain B residue 1677 SER Chi-restraints excluded: chain B residue 1728 VAL Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1753 GLN Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2122 ASP Chi-restraints excluded: chain B residue 2128 THR Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2368 LEU Chi-restraints excluded: chain B residue 2434 LYS Chi-restraints excluded: chain B residue 2450 LEU Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2547 THR Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2662 SER Chi-restraints excluded: chain B residue 2700 ARG Chi-restraints excluded: chain B residue 2718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 11 optimal weight: 0.3980 chunk 54 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 330 optimal weight: 2.9990 chunk 202 optimal weight: 9.9990 chunk 318 optimal weight: 0.5980 chunk 82 optimal weight: 0.0070 chunk 9 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1773 HIS A1946 HIS ** A2141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 HIS A2473 GLN A2736 GLN ** B1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1946 HIS B2137 HIS B2217 HIS B2473 GLN B2736 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.138918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.106824 restraints weight = 39778.775| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.22 r_work: 0.3277 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28178 Z= 0.132 Angle : 0.560 11.609 38262 Z= 0.290 Chirality : 0.046 0.320 4296 Planarity : 0.004 0.055 4908 Dihedral : 4.935 59.051 4334 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.31 % Allowed : 26.19 % Favored : 71.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3432 helix: 1.24 (0.36), residues: 226 sheet: 1.02 (0.15), residues: 1168 loop : -0.18 (0.14), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG B2240 TYR 0.018 0.001 TYR A1521 PHE 0.017 0.001 PHE B1772 TRP 0.012 0.001 TRP B1682 HIS 0.009 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00304 (28144) covalent geometry : angle 0.54721 (38170) SS BOND : bond 0.00088 ( 10) SS BOND : angle 0.98863 ( 20) hydrogen bonds : bond 0.03483 ( 1046) hydrogen bonds : angle 4.72696 ( 3825) link_BETA1-4 : bond 0.00521 ( 8) link_BETA1-4 : angle 1.36878 ( 24) link_NAG-ASN : bond 0.00349 ( 16) link_NAG-ASN : angle 3.18255 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6864 Ramachandran restraints generated. 3432 Oldfield, 0 Emsley, 3432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 667 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 598 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1103 LYS cc_start: 0.7888 (tttt) cc_final: 0.7673 (ttpp) REVERT: A 1110 ASN cc_start: 0.8662 (m110) cc_final: 0.8354 (m-40) REVERT: A 1134 VAL cc_start: 0.8624 (t) cc_final: 0.8395 (p) REVERT: A 1173 ASP cc_start: 0.7977 (t0) cc_final: 0.7649 (t0) REVERT: A 1206 MET cc_start: 0.5180 (mmm) cc_final: 0.4913 (mmm) REVERT: A 1424 ILE cc_start: 0.6919 (OUTLIER) cc_final: 0.6214 (pp) REVERT: A 1488 VAL cc_start: 0.8148 (t) cc_final: 0.7853 (m) REVERT: A 1526 ILE cc_start: 0.8205 (mt) cc_final: 0.7919 (mp) REVERT: A 1535 VAL cc_start: 0.8496 (t) cc_final: 0.8052 (m) REVERT: A 1560 VAL cc_start: 0.8707 (p) cc_final: 0.8447 (m) REVERT: A 1660 GLU cc_start: 0.7695 (mm-30) cc_final: 0.7412 (mm-30) REVERT: A 1772 PHE cc_start: 0.7244 (p90) cc_final: 0.6897 (p90) REVERT: A 1806 ARG cc_start: 0.8556 (mtm-85) cc_final: 0.8162 (mtt180) REVERT: A 1848 HIS cc_start: 0.8298 (m-70) cc_final: 0.8048 (m-70) REVERT: A 1870 SER cc_start: 0.8807 (p) cc_final: 0.8393 (t) REVERT: A 1922 ASP cc_start: 0.7654 (t0) cc_final: 0.7415 (t0) REVERT: A 1985 SER cc_start: 0.8628 (t) cc_final: 0.8404 (p) REVERT: A 2102 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.8286 (ttt-90) REVERT: A 2111 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7851 (mt-10) REVERT: A 2132 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8310 (ptm) REVERT: A 2154 SER cc_start: 0.8930 (OUTLIER) cc_final: 0.8695 (t) REVERT: A 2219 LEU cc_start: 0.8620 (pt) cc_final: 0.8381 (pp) REVERT: A 2228 MET cc_start: 0.8492 (ttp) cc_final: 0.8234 (ttm) REVERT: A 2331 TYR cc_start: 0.8674 (m-80) cc_final: 0.8225 (m-80) REVERT: A 2341 MET cc_start: 0.8867 (mtm) cc_final: 0.8546 (mtp) REVERT: A 2455 ASP cc_start: 0.7731 (m-30) cc_final: 0.7481 (m-30) REVERT: A 2543 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7277 (t70) REVERT: A 2567 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8158 (t) REVERT: A 2578 ARG cc_start: 0.8257 (mtt-85) cc_final: 0.8034 (mtt180) REVERT: A 2579 LYS cc_start: 0.8469 (mttt) cc_final: 0.8196 (mttp) REVERT: A 2592 LYS cc_start: 0.8330 (mtmm) cc_final: 0.8111 (mtmm) REVERT: A 2614 ASP cc_start: 0.8307 (m-30) cc_final: 0.7875 (m-30) REVERT: A 2626 VAL cc_start: 0.8276 (t) cc_final: 0.7973 (p) REVERT: A 2665 TYR cc_start: 0.8640 (m-80) cc_final: 0.8041 (m-80) REVERT: A 2674 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7325 (tm-30) REVERT: A 2684 ARG cc_start: 0.8610 (ttt-90) cc_final: 0.8268 (ttt-90) REVERT: A 2700 ARG cc_start: 0.7922 (mtp180) cc_final: 0.7590 (ttp-170) REVERT: A 2722 ARG cc_start: 0.7491 (mmt-90) cc_final: 0.7223 (mmt-90) REVERT: B 1034 SER cc_start: 0.8477 (t) cc_final: 0.8265 (p) REVERT: B 1080 GLN cc_start: 0.7855 (mp10) cc_final: 0.7625 (mp10) REVERT: B 1103 LYS cc_start: 0.7819 (OUTLIER) cc_final: 0.7576 (ttmm) REVERT: B 1151 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7330 (tp30) REVERT: B 1152 LYS cc_start: 0.7853 (mmtt) cc_final: 0.7433 (mmmm) REVERT: B 1163 ASP cc_start: 0.8328 (OUTLIER) cc_final: 0.8049 (p0) REVERT: B 1173 ASP cc_start: 0.7978 (t0) cc_final: 0.7696 (t0) REVERT: B 1274 TYR cc_start: 0.6073 (m-80) cc_final: 0.5684 (m-80) REVERT: B 1391 MET cc_start: 0.6730 (pmm) cc_final: 0.6161 (mpp) REVERT: B 1409 MET cc_start: 0.7438 (ptp) cc_final: 0.7181 (ptp) REVERT: B 1485 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7099 (pt) REVERT: B 1543 ILE cc_start: 0.6865 (OUTLIER) cc_final: 0.6477 (tt) REVERT: B 1560 VAL cc_start: 0.8645 (p) cc_final: 0.8389 (m) REVERT: B 1631 ARG cc_start: 0.8175 (mtp85) cc_final: 0.7528 (mtm110) REVERT: B 1639 GLN cc_start: 0.7897 (tp40) cc_final: 0.7277 (mp10) REVERT: B 1642 THR cc_start: 0.8585 (m) cc_final: 0.8253 (p) REVERT: B 1652 LYS cc_start: 0.8537 (tptt) cc_final: 0.8223 (mtpp) REVERT: B 1754 LEU cc_start: 0.8317 (mm) cc_final: 0.8082 (mt) REVERT: B 1805 TRP cc_start: 0.9011 (m100) cc_final: 0.8588 (m100) REVERT: B 1806 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8329 (mtm-85) REVERT: B 1845 TYR cc_start: 0.8635 (p90) cc_final: 0.8282 (p90) REVERT: B 1914 LYS cc_start: 0.8812 (mttm) cc_final: 0.8550 (mtpp) REVERT: B 1917 SER cc_start: 0.8667 (m) cc_final: 0.8356 (p) REVERT: B 1922 ASP cc_start: 0.7608 (t0) cc_final: 0.7331 (t0) REVERT: B 1950 MET cc_start: 0.8675 (mmt) cc_final: 0.8314 (mmt) REVERT: B 2058 LYS cc_start: 0.8714 (ttpp) cc_final: 0.8457 (ttpt) REVERT: B 2219 LEU cc_start: 0.8450 (pt) cc_final: 0.8228 (pp) REVERT: B 2240 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7960 (mtp-110) REVERT: B 2331 TYR cc_start: 0.8688 (m-80) cc_final: 0.8368 (m-80) REVERT: B 2483 ARG cc_start: 0.7924 (mtp-110) cc_final: 0.7501 (mtp85) REVERT: B 2543 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7437 (t70) REVERT: B 2579 LYS cc_start: 0.8396 (mttt) cc_final: 0.8145 (mttm) REVERT: B 2614 ASP cc_start: 0.8105 (m-30) cc_final: 0.7670 (m-30) REVERT: B 2665 TYR cc_start: 0.8687 (m-80) cc_final: 0.7916 (m-80) REVERT: B 2674 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7170 (tm-30) REVERT: B 2724 GLN cc_start: 0.7591 (mp10) cc_final: 0.7194 (mp10) REVERT: B 2753 ASN cc_start: 0.8198 (m110) cc_final: 0.7725 (OUTLIER) outliers start: 69 outliers final: 45 residues processed: 635 average time/residue: 0.6845 time to fit residues: 503.7721 Evaluate side-chains 637 residues out of total 2990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 582 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1201 ILE Chi-restraints excluded: chain A residue 1424 ILE Chi-restraints excluded: chain A residue 1475 THR Chi-restraints excluded: chain A residue 1494 ILE Chi-restraints excluded: chain A residue 1540 THR Chi-restraints excluded: chain A residue 1652 LYS Chi-restraints excluded: chain A residue 1719 ILE Chi-restraints excluded: chain A residue 1730 VAL Chi-restraints excluded: chain A residue 1753 GLN Chi-restraints excluded: chain A residue 1796 MET Chi-restraints excluded: chain A residue 1815 LYS Chi-restraints excluded: chain A residue 1957 SER Chi-restraints excluded: chain A residue 1959 SER Chi-restraints excluded: chain A residue 1987 ASP Chi-restraints excluded: chain A residue 2081 SER Chi-restraints excluded: chain A residue 2102 ARG Chi-restraints excluded: chain A residue 2110 VAL Chi-restraints excluded: chain A residue 2128 THR Chi-restraints excluded: chain A residue 2132 MET Chi-restraints excluded: chain A residue 2154 SER Chi-restraints excluded: chain A residue 2536 SER Chi-restraints excluded: chain A residue 2543 HIS Chi-restraints excluded: chain A residue 2567 THR Chi-restraints excluded: chain A residue 2606 VAL Chi-restraints excluded: chain B residue 1103 LYS Chi-restraints excluded: chain B residue 1163 ASP Chi-restraints excluded: chain B residue 1177 THR Chi-restraints excluded: chain B residue 1201 ILE Chi-restraints excluded: chain B residue 1349 LYS Chi-restraints excluded: chain B residue 1485 LEU Chi-restraints excluded: chain B residue 1494 ILE Chi-restraints excluded: chain B residue 1526 ILE Chi-restraints excluded: chain B residue 1540 THR Chi-restraints excluded: chain B residue 1543 ILE Chi-restraints excluded: chain B residue 1730 VAL Chi-restraints excluded: chain B residue 1753 GLN Chi-restraints excluded: chain B residue 1796 MET Chi-restraints excluded: chain B residue 1816 VAL Chi-restraints excluded: chain B residue 1839 ILE Chi-restraints excluded: chain B residue 1870 SER Chi-restraints excluded: chain B residue 1921 LEU Chi-restraints excluded: chain B residue 1959 SER Chi-restraints excluded: chain B residue 2093 GLU Chi-restraints excluded: chain B residue 2098 VAL Chi-restraints excluded: chain B residue 2110 VAL Chi-restraints excluded: chain B residue 2122 ASP Chi-restraints excluded: chain B residue 2234 LEU Chi-restraints excluded: chain B residue 2334 LEU Chi-restraints excluded: chain B residue 2536 SER Chi-restraints excluded: chain B residue 2543 HIS Chi-restraints excluded: chain B residue 2606 VAL Chi-restraints excluded: chain B residue 2622 ILE Chi-restraints excluded: chain B residue 2636 SER Chi-restraints excluded: chain B residue 2662 SER Chi-restraints excluded: chain B residue 2718 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 344 random chunks: chunk 111 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 316 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 254 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 308 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1587 GLN A1733 ASN A1756 ASN A1773 HIS A1946 HIS ** A2141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2217 HIS A2473 GLN A2736 GLN ** B1607 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1946 HIS ** B2141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2217 HIS B2283 GLN B2302 HIS B2473 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.137527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.105597 restraints weight = 39654.141| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.16 r_work: 0.3256 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 28178 Z= 0.235 Angle : 0.606 11.564 38262 Z= 0.313 Chirality : 0.048 0.304 4296 Planarity : 0.004 0.052 4908 Dihedral : 5.084 59.481 4334 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.58 % Allowed : 26.02 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % 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: 0.40 (0.14), residues: 3432 helix: 1.15 (0.35), residues: 226 sheet: 0.98 (0.15), residues: 1170 loop : -0.23 (0.14), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A2240 TYR 0.024 0.002 TYR B1521 PHE 0.017 0.002 PHE B1772 TRP 0.015 0.001 TRP B1682 HIS 0.009 0.001 HIS A1773 Details of bonding type rmsd covalent geometry : bond 0.00543 (28144) covalent geometry : angle 0.59315 (38170) SS BOND : bond 0.00109 ( 10) SS BOND : angle 1.04701 ( 20) hydrogen bonds : bond 0.03909 ( 1046) hydrogen bonds : angle 4.81032 ( 3825) link_BETA1-4 : bond 0.00362 ( 8) link_BETA1-4 : angle 1.42687 ( 24) link_NAG-ASN : bond 0.00497 ( 16) link_NAG-ASN : angle 3.42894 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13212.15 seconds wall clock time: 224 minutes 51.03 seconds (13491.03 seconds total)