Starting phenix.real_space_refine on Sat Aug 23 10:48:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0t_18803/08_2025/8r0t_18803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0t_18803/08_2025/8r0t_18803.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0t_18803/08_2025/8r0t_18803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0t_18803/08_2025/8r0t_18803.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0t_18803/08_2025/8r0t_18803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0t_18803/08_2025/8r0t_18803.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 134 5.16 5 C 7115 2.51 5 N 1978 2.21 5 O 2230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11461 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 110 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 11} Chain: "B" Number of atoms: 2946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 2946 Classifications: {'peptide': 399} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 32, 'TRANS': 366} Chain: "C" Number of atoms: 6854 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 927, 6845 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 65, 'TRANS': 861} Conformer: "B" Number of residues, atoms: 927, 6845 Classifications: {'peptide': 927} Link IDs: {'PTRANS': 65, 'TRANS': 861} bond proxies already assigned to first conformer: 7007 Chain: "F" Number of atoms: 1449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1449 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CA': 2, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 15 Unusual residues: {' CA': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AGLU C2012 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU C2012 " occ=0.50 Time building chain proxies: 3.31, per 1000 atoms: 0.29 Number of scatterers: 11461 At special positions: 0 Unit cell: (86, 114.38, 131.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 134 16.00 O 2230 8.00 N 1978 7.00 C 7115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=56, symmetry=0 Simple disulfide: pdb=" SG CYS B1275 " - pdb=" SG CYS B1433 " distance=2.03 Simple disulfide: pdb=" SG CYS B1284 " - pdb=" SG CYS B1392 " distance=2.03 Simple disulfide: pdb=" SG CYS B1437 " - pdb=" SG CYS B1441 " distance=2.03 Simple disulfide: pdb=" SG CYS B1458 " - pdb=" SG CYS B1485 " distance=2.03 Simple disulfide: pdb=" SG CYS B1472 " - pdb=" SG CYS B1510 " distance=2.03 Simple disulfide: pdb=" SG CYS B1500 " - pdb=" SG CYS B1526 " distance=2.03 Simple disulfide: pdb=" SG CYS B1530 " - pdb=" SG CYS B1567 " distance=2.03 Simple disulfide: pdb=" SG CYS B1539 " - pdb=" SG CYS B1563 " distance=2.03 Simple disulfide: pdb=" SG CYS B1543 " - pdb=" SG CYS B1559 " distance=2.03 Simple disulfide: pdb=" SG CYS B1547 " - pdb=" SG CYS B1587 " distance=2.03 Simple disulfide: pdb=" SG CYS B1569 " - pdb=" SG CYS B1580 " distance=2.03 Simple disulfide: pdb=" SG CYS B1589 " - pdb=" SG CYS B1614 " distance=2.03 Simple disulfide: pdb=" SG CYS B1608 " - pdb=" SG CYS B1634 " distance=2.02 Simple disulfide: pdb=" SG CYS B1612 " - pdb=" SG CYS B1623 " distance=2.03 Simple disulfide: pdb=" SG CYS B1628 " - pdb=" SG CYS B1644 " distance=2.03 Simple disulfide: pdb=" SG CYS B1652 " - pdb=" SG CYS C1791 " distance=2.04 Simple disulfide: pdb=" SG CYS C1674 " - pdb=" SG CYS C1820 " distance=2.03 Simple disulfide: pdb=" SG CYS C1682 " - pdb=" SG CYS C1788 " distance=2.03 Simple disulfide: pdb=" SG CYS C1823 " - pdb=" SG CYS C1828 " distance=2.03 Simple disulfide: pdb=" SG CYS C1832 " - pdb=" SG CYS C1877 " distance=2.03 Simple disulfide: pdb=" SG CYS C1846 " - pdb=" SG CYS C1872 " distance=2.03 Simple disulfide: pdb=" SG CYS C1859 " - pdb=" SG CYS C1897 " distance=2.03 Simple disulfide: pdb=" SG CYS C1887 " - pdb=" SG CYS C1913 " distance=2.03 Simple disulfide: pdb=" SG CYS C1917 " - pdb=" SG CYS C1951 " distance=2.03 Simple disulfide: pdb=" SG CYS C1926 " - pdb=" SG CYS C1947 " distance=2.03 Simple disulfide: pdb=" SG CYS C1930 " - pdb=" SG CYS C1943 " distance=2.03 Simple disulfide: pdb=" SG CYS C1934 " - pdb=" SG CYS C1970 " distance=2.03 Simple disulfide: pdb=" SG CYS C1953 " - pdb=" SG CYS C1964 " distance=2.03 Simple disulfide: pdb=" SG CYS C1972 " - pdb=" SG CYS C1997 " distance=2.03 Simple disulfide: pdb=" SG CYS C1991 " - pdb=" SG CYS C2017 " distance=2.03 Simple disulfide: pdb=" SG CYS C1995 " - pdb=" SG CYS C2005 " distance=2.03 Simple disulfide: pdb=" SG CYS C2011 " - pdb=" SG CYS C2026 " distance=2.03 Simple disulfide: pdb=" SG CYS C2034 " - pdb=" SG CYS C2164 " distance=2.03 Simple disulfide: pdb=" SG CYS C2056 " - pdb=" SG CYS C2202 " distance=2.03 Simple disulfide: pdb=" SG CYS C2064 " - pdb=" SG CYS C2161 " distance=2.03 Simple disulfide: pdb=" SG CYS C2206 " - pdb=" SG CYS C2211 " distance=2.03 Simple disulfide: pdb=" SG CYS C2214 " - pdb=" SG CYS C2259 " distance=2.04 Simple disulfide: pdb=" SG CYS C2228 " - pdb=" SG CYS C2254 " distance=2.02 Simple disulfide: pdb=" SG CYS C2241 " - pdb=" SG CYS C2279 " distance=2.03 Simple disulfide: pdb=" SG CYS C2269 " - pdb=" SG CYS C2295 " distance=2.03 Simple disulfide: pdb=" SG CYS C2299 " - pdb=" SG CYS C2333 " distance=2.03 Simple disulfide: pdb=" SG CYS C2308 " - pdb=" SG CYS C2329 " distance=2.03 Simple disulfide: pdb=" SG CYS C2312 " - pdb=" SG CYS C2325 " distance=2.03 Simple disulfide: pdb=" SG CYS C2316 " - pdb=" SG CYS C2352 " distance=2.03 Simple disulfide: pdb=" SG CYS C2335 " - pdb=" SG CYS C2346 " distance=2.03 Simple disulfide: pdb=" SG CYS C2354 " - pdb=" SG CYS C2378 " distance=2.03 Simple disulfide: pdb=" SG CYS C2372 " - pdb=" SG CYS C2397 " distance=2.03 Simple disulfide: pdb=" SG CYS C2376 " - pdb=" SG CYS C2386 " distance=2.03 Simple disulfide: pdb=" SG CYS C2391 " - pdb=" SG CYS C2406 " distance=2.03 Simple disulfide: pdb=" SG CYS C2413 " - pdb=" SG CYS C2550 " distance=2.03 Simple disulfide: pdb=" SG CYS C2443 " - pdb=" SG CYS C2547 " distance=2.03 Simple disulfide: pdb=" SG CYS C2462 " - pdb=" SG CYS F2581 " distance=2.03 Simple disulfide: pdb=" SG CYS C2581 " - pdb=" SG CYS F2462 " distance=2.03 Simple disulfide: pdb=" SG CYS F2391 " - pdb=" SG CYS F2406 " distance=2.03 Simple disulfide: pdb=" SG CYS F2413 " - pdb=" SG CYS F2550 " distance=2.03 Simple disulfide: pdb=" SG CYS F2443 " - pdb=" SG CYS F2547 " 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 NAG-ASN " NAG A1301 " - " ASN A1250 " " NAG B1701 " - " ASN B1410 " " NAG C2601 " - " ASN C2364 " " NAG C2602 " - " ASN C2420 " " NAG C2603 " - " ASN C1693 " " NAG C2604 " - " ASN C2170 " " NAG F2601 " - " ASN F2420 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 690.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2726 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 27 sheets defined 13.0% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'B' and resid 1416 through 1418 No H-bonds generated for 'chain 'B' and resid 1416 through 1418' Processing helix chain 'B' and resid 1419 through 1424 Processing helix chain 'B' and resid 1446 through 1453 removed outlier: 4.172A pdb=" N GLU B1450 " --> pdb=" O GLU B1446 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B1451 " --> pdb=" O ASP B1447 " (cutoff:3.500A) Processing helix chain 'B' and resid 1471 through 1476 removed outlier: 4.206A pdb=" N HIS B1475 " --> pdb=" O SER B1471 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B1476 " --> pdb=" O CYS B1472 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1471 through 1476' Processing helix chain 'B' and resid 1478 through 1491 removed outlier: 3.533A pdb=" N LYS B1483 " --> pdb=" O GLU B1479 " (cutoff:3.500A) Processing helix chain 'B' and resid 1495 through 1513 removed outlier: 4.211A pdb=" N LEU B1499 " --> pdb=" O SER B1495 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B1506 " --> pdb=" O ALA B1502 " (cutoff:3.500A) Processing helix chain 'B' and resid 1520 through 1525 Processing helix chain 'B' and resid 1556 through 1560 removed outlier: 3.812A pdb=" N ASP B1560 " --> pdb=" O THR B1557 " (cutoff:3.500A) Processing helix chain 'C' and resid 1838 through 1842 removed outlier: 3.847A pdb=" N GLY C1842 " --> pdb=" O PRO C1839 " (cutoff:3.500A) Processing helix chain 'C' and resid 1856 through 1863 removed outlier: 3.750A pdb=" N SER C1861 " --> pdb=" O ALA C1857 " (cutoff:3.500A) Processing helix chain 'C' and resid 1865 through 1879 removed outlier: 4.159A pdb=" N GLU C1870 " --> pdb=" O THR C1866 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N ALA C1871 " --> pdb=" O GLN C1867 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N CYS C1872 " --> pdb=" O TYR C1868 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU C1873 " --> pdb=" O PHE C1869 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU C1874 " --> pdb=" O GLU C1870 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP C1875 " --> pdb=" O ALA C1871 " (cutoff:3.500A) Processing helix chain 'C' and resid 1882 through 1900 Proline residue: C1888 - end of helix removed outlier: 3.593A pdb=" N ALA C1891 " --> pdb=" O CYS C1887 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA C1896 " --> pdb=" O THR C1892 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA C1900 " --> pdb=" O ALA C1896 " (cutoff:3.500A) Processing helix chain 'C' and resid 1988 through 1992 removed outlier: 3.610A pdb=" N CYS C1991 " --> pdb=" O GLY C1988 " (cutoff:3.500A) Processing helix chain 'C' and resid 2185 through 2193 Processing helix chain 'C' and resid 2213 through 2221 removed outlier: 3.726A pdb=" N GLU C2217 " --> pdb=" O VAL C2213 " (cutoff:3.500A) Processing helix chain 'C' and resid 2225 through 2233 removed outlier: 3.701A pdb=" N ASP C2233 " --> pdb=" O GLY C2229 " (cutoff:3.500A) Processing helix chain 'C' and resid 2247 through 2256 removed outlier: 3.919A pdb=" N ARG C2252 " --> pdb=" O LEU C2248 " (cutoff:3.500A) Processing helix chain 'C' and resid 2267 through 2279 removed outlier: 4.893A pdb=" N ALA C2273 " --> pdb=" O CYS C2269 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ALA C2274 " --> pdb=" O ARG C2270 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N TYR C2275 " --> pdb=" O SER C2271 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THR C2276 " --> pdb=" O LEU C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2322 through 2328 removed outlier: 4.003A pdb=" N THR C2326 " --> pdb=" O THR C2323 " (cutoff:3.500A) Processing helix chain 'C' and resid 2369 through 2371 No H-bonds generated for 'chain 'C' and resid 2369 through 2371' Processing helix chain 'C' and resid 2462 through 2466 removed outlier: 3.625A pdb=" N ASP C2466 " --> pdb=" O HIS C2463 " (cutoff:3.500A) Processing helix chain 'C' and resid 2556 through 2561 removed outlier: 4.290A pdb=" N ASP C2560 " --> pdb=" O ASP C2556 " (cutoff:3.500A) Processing helix chain 'F' and resid 2462 through 2466 removed outlier: 3.907A pdb=" N ASN F2465 " --> pdb=" O CYS F2462 " (cutoff:3.500A) Processing helix chain 'F' and resid 2490 through 2494 Processing sheet with id=AA1, first strand: chain 'B' and resid 1268 through 1269 Processing sheet with id=AA2, first strand: chain 'B' and resid 1277 through 1281 removed outlier: 6.548A pdb=" N VAL B1297 " --> pdb=" O LEU B1279 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY B1281 " --> pdb=" O PHE B1295 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE B1295 " --> pdb=" O GLY B1281 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B1314 " --> pdb=" O LYS B1300 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLU B1302 " --> pdb=" O VAL B1312 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL B1312 " --> pdb=" O GLU B1302 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 1345 through 1346 Processing sheet with id=AA4, first strand: chain 'B' and resid 1535 through 1540 removed outlier: 3.898A pdb=" N GLU B1537 " --> pdb=" O GLY B1566 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B1566 " --> pdb=" O GLU B1537 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N CYS B1539 " --> pdb=" O VAL B1564 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B1564 " --> pdb=" O CYS B1539 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 1574 through 1576 Processing sheet with id=AA6, first strand: chain 'B' and resid 1602 through 1603 removed outlier: 3.522A pdb=" N SER B1620 " --> pdb=" O GLY B1615 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1632 through 1633 Processing sheet with id=AA8, first strand: chain 'B' and resid 1652 through 1655 removed outlier: 3.578A pdb=" N CYS B1652 " --> pdb=" O LEU C1777 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 1659 through 1661 Processing sheet with id=AB1, first strand: chain 'C' and resid 1675 through 1679 removed outlier: 7.028A pdb=" N VAL C1694 " --> pdb=" O LEU C1678 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER C1711 " --> pdb=" O ALA C1697 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N GLU C1699 " --> pdb=" O THR C1709 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N THR C1709 " --> pdb=" O GLU C1699 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 1921 through 1927 removed outlier: 3.941A pdb=" N CYS C1926 " --> pdb=" O ARG C1948 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG C1948 " --> pdb=" O CYS C1926 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 1956 through 1959 removed outlier: 5.072A pdb=" N PHE C1957 " --> pdb=" O CYS C1964 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N CYS C1964 " --> pdb=" O PHE C1957 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C1959 " --> pdb=" O ASP C1962 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 1996 through 1997 Processing sheet with id=AB5, first strand: chain 'C' and resid 2016 through 2020 Processing sheet with id=AB6, first strand: chain 'C' and resid 2062 through 2063 Processing sheet with id=AB7, first strand: chain 'C' and resid 2073 through 2077 Processing sheet with id=AB8, first strand: chain 'C' and resid 2121 through 2124 Processing sheet with id=AB9, first strand: chain 'C' and resid 2303 through 2306 Processing sheet with id=AC1, first strand: chain 'C' and resid 2341 through 2342 Processing sheet with id=AC2, first strand: chain 'C' and resid 2373 through 2375 removed outlier: 5.999A pdb=" N ALA C2389 " --> pdb=" O GLU C2374 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 2411 through 2414 removed outlier: 3.635A pdb=" N LEU C2517 " --> pdb=" O ARG C2509 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG C2509 " --> pdb=" O LEU C2517 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N HIS C2519 " --> pdb=" O SER C2507 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL C2508 " --> pdb=" O ALA C2500 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 2435 through 2438 removed outlier: 3.538A pdb=" N ASP C2458 " --> pdb=" O LYS C2471 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 2482 through 2483 removed outlier: 4.164A pdb=" N ALA C2489 " --> pdb=" O VAL C2496 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 2398 through 2400 removed outlier: 4.347A pdb=" N GLU F2398 " --> pdb=" O GLU F2405 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 2411 through 2415 removed outlier: 4.285A pdb=" N LEU F2534 " --> pdb=" O ILE F2415 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ASP F2535 " --> pdb=" O TRP F2527 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N TRP F2527 " --> pdb=" O ASP F2535 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 2421 through 2422 removed outlier: 3.677A pdb=" N ASN F2429 " --> pdb=" O LEU F2421 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 2436 through 2438 removed outlier: 3.777A pdb=" N ALA F2457 " --> pdb=" O TYR F2437 " (cutoff:3.500A) 241 hydrogen bonds defined for protein. 567 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.71 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3554 1.33 - 1.46: 2284 1.46 - 1.58: 5761 1.58 - 1.70: 3 1.70 - 1.82: 150 Bond restraints: 11752 Sorted by residual: bond pdb=" N PRO C2569 " pdb=" CD PRO C2569 " ideal model delta sigma weight residual 1.473 1.586 -0.113 1.40e-02 5.10e+03 6.54e+01 bond pdb=" N PRO C1741 " pdb=" CD PRO C1741 " ideal model delta sigma weight residual 1.473 1.573 -0.100 1.40e-02 5.10e+03 5.06e+01 bond pdb=" N PRO C2451 " pdb=" CD PRO C2451 " ideal model delta sigma weight residual 1.473 1.388 0.085 1.40e-02 5.10e+03 3.67e+01 bond pdb=" CA ARG C2252 " pdb=" C ARG C2252 " ideal model delta sigma weight residual 1.522 1.596 -0.073 1.37e-02 5.33e+03 2.85e+01 bond pdb=" CA GLN C2557 " pdb=" C GLN C2557 " ideal model delta sigma weight residual 1.524 1.590 -0.065 1.28e-02 6.10e+03 2.62e+01 ... (remaining 11747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 15791 3.70 - 7.40: 211 7.40 - 11.10: 32 11.10 - 14.80: 4 14.80 - 18.50: 1 Bond angle restraints: 16039 Sorted by residual: angle pdb=" N THR C2558 " pdb=" CA THR C2558 " pdb=" C THR C2558 " ideal model delta sigma weight residual 111.33 126.07 -14.74 1.21e+00 6.83e-01 1.48e+02 angle pdb=" N PRO C1935 " pdb=" CA PRO C1935 " pdb=" C PRO C1935 " ideal model delta sigma weight residual 110.50 92.00 18.50 1.57e+00 4.06e-01 1.39e+02 angle pdb=" N GLU C2571 " pdb=" CA GLU C2571 " pdb=" C GLU C2571 " ideal model delta sigma weight residual 111.28 101.27 10.01 1.09e+00 8.42e-01 8.43e+01 angle pdb=" N PRO C1741 " pdb=" CA PRO C1741 " pdb=" CB PRO C1741 " ideal model delta sigma weight residual 102.25 108.67 -6.42 7.00e-01 2.04e+00 8.42e+01 angle pdb=" CA PRO B1442 " pdb=" N PRO B1442 " pdb=" CD PRO B1442 " ideal model delta sigma weight residual 112.00 99.58 12.42 1.40e+00 5.10e-01 7.87e+01 ... (remaining 16034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.66: 6692 24.66 - 49.31: 392 49.31 - 73.97: 60 73.97 - 98.62: 15 98.62 - 123.28: 8 Dihedral angle restraints: 7167 sinusoidal: 2865 harmonic: 4302 Sorted by residual: dihedral pdb=" C PHE F2553 " pdb=" N PHE F2553 " pdb=" CA PHE F2553 " pdb=" CB PHE F2553 " ideal model delta harmonic sigma weight residual -122.60 -105.72 -16.88 0 2.50e+00 1.60e-01 4.56e+01 dihedral pdb=" CB CYS C1934 " pdb=" SG CYS C1934 " pdb=" SG CYS C1970 " pdb=" CB CYS C1970 " ideal model delta sinusoidal sigma weight residual 93.00 42.54 50.46 1 1.00e+01 1.00e-02 3.49e+01 dihedral pdb=" N PRO C2569 " pdb=" C PRO C2569 " pdb=" CA PRO C2569 " pdb=" CB PRO C2569 " ideal model delta harmonic sigma weight residual 115.10 128.77 -13.67 0 2.50e+00 1.60e-01 2.99e+01 ... (remaining 7164 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 1699 0.157 - 0.314: 52 0.314 - 0.472: 9 0.472 - 0.629: 2 0.629 - 0.786: 1 Chirality restraints: 1763 Sorted by residual: chirality pdb=" C1 NAG B1701 " pdb=" ND2 ASN B1410 " pdb=" C2 NAG B1701 " pdb=" O5 NAG B1701 " both_signs ideal model delta sigma weight residual False -2.40 -1.61 -0.79 2.00e-01 2.50e+01 1.55e+01 chirality pdb=" CA PRO C2569 " pdb=" N PRO C2569 " pdb=" C PRO C2569 " pdb=" CB PRO C2569 " both_signs ideal model delta sigma weight residual False 2.72 2.20 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" C1 NAG F2601 " pdb=" ND2 ASN F2420 " pdb=" C2 NAG F2601 " pdb=" O5 NAG F2601 " both_signs ideal model delta sigma weight residual False -2.40 -1.88 -0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 1760 not shown) Planarity restraints: 2145 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1701 " 0.053 2.00e-02 2.50e+03 4.34e-02 2.35e+01 pdb=" C7 NAG B1701 " -0.013 2.00e-02 2.50e+03 pdb=" C8 NAG B1701 " 0.040 2.00e-02 2.50e+03 pdb=" N2 NAG B1701 " -0.069 2.00e-02 2.50e+03 pdb=" O7 NAG B1701 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS B1441 " 0.067 5.00e-02 4.00e+02 9.34e-02 1.40e+01 pdb=" N PRO B1442 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO B1442 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B1442 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F2571 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C GLU F2571 " 0.048 2.00e-02 2.50e+03 pdb=" O GLU F2571 " -0.018 2.00e-02 2.50e+03 pdb=" N LYS F2572 " -0.016 2.00e-02 2.50e+03 ... (remaining 2142 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 46 2.32 - 2.96: 6040 2.96 - 3.61: 17814 3.61 - 4.25: 26551 4.25 - 4.90: 41818 Nonbonded interactions: 92269 Sorted by model distance: nonbonded pdb=" OG1 THR B1282 " pdb=" CE2 TYR B1387 " model vdw 1.670 3.340 nonbonded pdb=" OD1 ASP F2577 " pdb=" N PHE F2578 " model vdw 2.024 3.120 nonbonded pdb=" O ASN B1401 " pdb="CA CA B1702 " model vdw 2.024 2.510 nonbonded pdb=" OD1 ASN B1397 " pdb="CA CA B1702 " model vdw 2.040 2.510 nonbonded pdb=" OD1 ASP B1405 " pdb="CA CA B1702 " model vdw 2.085 2.510 ... (remaining 92264 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5066 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 : 0.005 0.113 11815 Z= 0.369 Angle : 1.103 18.496 16172 Z= 0.711 Chirality : 0.073 0.786 1763 Planarity : 0.006 0.093 2138 Dihedral : 15.942 123.275 4273 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 27.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 6.85 % Allowed : 13.94 % Favored : 79.21 % Cbeta Deviations : 0.66 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.77 (0.20), residues: 1529 helix: -1.77 (0.41), residues: 146 sheet: -2.08 (0.34), residues: 196 loop : -1.96 (0.17), residues: 1187 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2252 TYR 0.010 0.001 TYR B1387 PHE 0.027 0.002 PHE F2553 TRP 0.017 0.001 TRP C2573 HIS 0.005 0.001 HIS C1659 Details of bonding type rmsd covalent geometry : bond 0.00543 (11752) covalent geometry : angle 1.08905 (16039) SS BOND : bond 0.00298 ( 56) SS BOND : angle 1.05246 ( 112) hydrogen bonds : bond 0.23110 ( 241) hydrogen bonds : angle 10.08588 ( 567) link_NAG-ASN : bond 0.01391 ( 7) link_NAG-ASN : angle 4.97829 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 205 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1388 HIS cc_start: 0.6794 (p90) cc_final: 0.6495 (p90) REVERT: B 1487 LEU cc_start: 0.7954 (tp) cc_final: 0.7634 (tt) REVERT: C 2524 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7178 (p) outliers start: 85 outliers final: 29 residues processed: 279 average time/residue: 0.0797 time to fit residues: 33.4144 Evaluate side-chains 157 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1547 CYS Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain C residue 1723 LEU Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1800 ASP Chi-restraints excluded: chain C residue 1846 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1980 VAL Chi-restraints excluded: chain C residue 2056 CYS Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2164 CYS Chi-restraints excluded: chain C residue 2220 GLN Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2346 CYS Chi-restraints excluded: chain C residue 2436 VAL Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2524 VAL Chi-restraints excluded: chain F residue 2406 CYS Chi-restraints excluded: chain F residue 2425 ASP Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2518 VAL Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 77 optimal weight: 0.0980 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 20.0000 overall best weight: 2.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1314 GLN ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1659 HIS C1704 GLN C1726 GLN C1799 ASN ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2041 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2313 GLN C2395 HIS ** C2473 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2520 GLN ** F2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.077800 restraints weight = 81187.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.080253 restraints weight = 53276.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.082133 restraints weight = 33240.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.082406 restraints weight = 24809.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.082544 restraints weight = 22869.130| |-----------------------------------------------------------------------------| r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3754 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3754 r_free = 0.3754 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3754 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11815 Z= 0.249 Angle : 0.922 12.350 16172 Z= 0.468 Chirality : 0.057 0.510 1763 Planarity : 0.006 0.070 2138 Dihedral : 12.072 106.175 1811 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 5.80 % Allowed : 19.74 % Favored : 74.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.96 (0.20), residues: 1529 helix: -2.26 (0.35), residues: 157 sheet: -1.94 (0.34), residues: 205 loop : -2.09 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C2290 TYR 0.032 0.003 TYR B1387 PHE 0.021 0.003 PHE C2175 TRP 0.027 0.003 TRP C2289 HIS 0.008 0.002 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00515 (11752) covalent geometry : angle 0.89272 (16039) SS BOND : bond 0.00704 ( 56) SS BOND : angle 2.10952 ( 112) hydrogen bonds : bond 0.04972 ( 241) hydrogen bonds : angle 8.91232 ( 567) link_NAG-ASN : bond 0.00764 ( 7) link_NAG-ASN : angle 4.77026 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 136 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1272 GLN cc_start: 0.6968 (mp10) cc_final: 0.6765 (mp10) REVERT: B 1360 LYS cc_start: 0.7323 (mmtm) cc_final: 0.7015 (mmtm) REVERT: B 1378 ARG cc_start: 0.7737 (ttp-170) cc_final: 0.7295 (ttp-170) REVERT: B 1398 MET cc_start: 0.8719 (tmm) cc_final: 0.7846 (ttm) REVERT: B 1487 LEU cc_start: 0.8558 (tp) cc_final: 0.8310 (tt) REVERT: C 1710 ARG cc_start: 0.7261 (mtp85) cc_final: 0.6959 (mtp-110) REVERT: C 2223 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: C 2368 MET cc_start: 0.5687 (ttm) cc_final: 0.5432 (ttp) REVERT: C 2415 ILE cc_start: 0.8084 (mm) cc_final: 0.7785 (mm) REVERT: C 2456 LEU cc_start: 0.8680 (mt) cc_final: 0.8269 (tp) REVERT: C 2571 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7582 (tm-30) REVERT: F 2466 ASP cc_start: 0.7466 (m-30) cc_final: 0.7176 (m-30) REVERT: F 2559 ASN cc_start: 0.6989 (OUTLIER) cc_final: 0.6741 (p0) outliers start: 72 outliers final: 42 residues processed: 202 average time/residue: 0.0893 time to fit residues: 26.6010 Evaluate side-chains 161 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1369 LEU Chi-restraints excluded: chain B residue 1381 VAL Chi-restraints excluded: chain B residue 1437 CYS Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1528 ILE Chi-restraints excluded: chain B residue 1535 HIS Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain C residue 1700 HIS Chi-restraints excluded: chain C residue 1752 ILE Chi-restraints excluded: chain C residue 1761 THR Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1941 VAL Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2052 LEU Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2223 GLU Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2259 CYS Chi-restraints excluded: chain C residue 2272 LEU Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2305 TYR Chi-restraints excluded: chain C residue 2436 VAL Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2520 GLN Chi-restraints excluded: chain C residue 2526 VAL Chi-restraints excluded: chain F residue 2395 HIS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2482 THR Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2518 VAL Chi-restraints excluded: chain F residue 2524 VAL Chi-restraints excluded: chain F residue 2559 ASN Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 148 optimal weight: 8.9990 chunk 97 optimal weight: 0.0170 chunk 96 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 22 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 68 optimal weight: 0.0010 chunk 41 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 127 optimal weight: 0.9980 overall best weight: 0.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1613 HIS ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2041 HIS ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2520 GLN C2557 GLN F2520 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.094645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.079351 restraints weight = 121136.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.082119 restraints weight = 64164.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.084554 restraints weight = 41541.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.085112 restraints weight = 27899.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.086740 restraints weight = 23720.527| |-----------------------------------------------------------------------------| r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3834 r_free = 0.3834 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6531 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11815 Z= 0.156 Angle : 0.837 13.455 16172 Z= 0.417 Chirality : 0.053 0.467 1763 Planarity : 0.006 0.065 2138 Dihedral : 10.956 106.039 1792 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.17 % Favored : 90.83 % Rotamer: Outliers : 4.67 % Allowed : 21.19 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.83 (0.20), residues: 1529 helix: -1.89 (0.37), residues: 157 sheet: -1.92 (0.34), residues: 209 loop : -2.02 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1948 TYR 0.033 0.002 TYR B1387 PHE 0.021 0.002 PHE C1668 TRP 0.035 0.002 TRP C2289 HIS 0.008 0.001 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00350 (11752) covalent geometry : angle 0.80219 (16039) SS BOND : bond 0.00414 ( 56) SS BOND : angle 2.43775 ( 112) hydrogen bonds : bond 0.04224 ( 241) hydrogen bonds : angle 8.04799 ( 567) link_NAG-ASN : bond 0.00836 ( 7) link_NAG-ASN : angle 4.06160 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 130 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1249 TYR cc_start: 0.7348 (p90) cc_final: 0.7122 (p90) REVERT: B 1272 GLN cc_start: 0.6944 (mp10) cc_final: 0.6607 (mp10) REVERT: B 1374 ASP cc_start: 0.6748 (t70) cc_final: 0.5674 (t70) REVERT: B 1378 ARG cc_start: 0.7704 (ttp-170) cc_final: 0.7245 (ttp-170) REVERT: B 1388 HIS cc_start: 0.7877 (p90) cc_final: 0.7535 (p90) REVERT: B 1398 MET cc_start: 0.8464 (tmm) cc_final: 0.7655 (ttm) REVERT: B 1487 LEU cc_start: 0.8488 (tp) cc_final: 0.8259 (tt) REVERT: C 2058 TYR cc_start: 0.7815 (m-10) cc_final: 0.7584 (m-10) REVERT: C 2322 LEU cc_start: 0.6356 (tp) cc_final: 0.6072 (tt) REVERT: C 2384 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7501 (tt) REVERT: C 2452 TRP cc_start: 0.7053 (t-100) cc_final: 0.6781 (t-100) REVERT: C 2456 LEU cc_start: 0.8502 (mt) cc_final: 0.8113 (tp) REVERT: C 2571 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7542 (tm-30) REVERT: C 2574 ARG cc_start: 0.6231 (ttt180) cc_final: 0.5367 (tpt-90) REVERT: F 2466 ASP cc_start: 0.7385 (m-30) cc_final: 0.7064 (m-30) REVERT: F 2545 MET cc_start: 0.8068 (mmp) cc_final: 0.7468 (mmm) outliers start: 58 outliers final: 38 residues processed: 174 average time/residue: 0.0812 time to fit residues: 21.2138 Evaluate side-chains 155 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 116 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1309 VAL Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1571 GLU Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1700 HIS Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1824 GLU Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1997 CYS Chi-restraints excluded: chain C residue 2003 VAL Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2259 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2436 VAL Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain F residue 2406 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2518 VAL Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 45 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 105 optimal weight: 0.0670 chunk 24 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1314 GLN ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2492 ASN ** F2552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.094525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079639 restraints weight = 94860.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.082789 restraints weight = 54008.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.084581 restraints weight = 32097.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.085041 restraints weight = 23599.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.085770 restraints weight = 21514.204| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6590 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11815 Z= 0.147 Angle : 0.790 11.766 16172 Z= 0.392 Chirality : 0.052 0.454 1763 Planarity : 0.005 0.062 2138 Dihedral : 10.543 104.427 1792 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 5.32 % Allowed : 21.03 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.77 (0.20), residues: 1529 helix: -1.67 (0.39), residues: 156 sheet: -1.91 (0.34), residues: 208 loop : -2.00 (0.17), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C2101 TYR 0.027 0.002 TYR B1311 PHE 0.024 0.002 PHE B1408 TRP 0.022 0.002 TRP C2289 HIS 0.007 0.001 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00332 (11752) covalent geometry : angle 0.76590 (16039) SS BOND : bond 0.00403 ( 56) SS BOND : angle 1.60513 ( 112) hydrogen bonds : bond 0.03743 ( 241) hydrogen bonds : angle 7.70348 ( 567) link_NAG-ASN : bond 0.00888 ( 7) link_NAG-ASN : angle 4.27456 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 127 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1261 TYR cc_start: 0.8180 (m-80) cc_final: 0.7848 (m-80) REVERT: B 1272 GLN cc_start: 0.6976 (mp10) cc_final: 0.6638 (mp10) REVERT: B 1283 LEU cc_start: 0.7718 (pt) cc_final: 0.7183 (mt) REVERT: B 1378 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7440 (mtm110) REVERT: B 1388 HIS cc_start: 0.7856 (p90) cc_final: 0.7560 (p90) REVERT: B 1398 MET cc_start: 0.8524 (tmm) cc_final: 0.7811 (ttm) REVERT: C 1723 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7685 (mt) REVERT: C 2136 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8508 (mmmm) REVERT: C 2361 MET cc_start: 0.8871 (mmm) cc_final: 0.8396 (mmm) REVERT: C 2384 LEU cc_start: 0.7952 (OUTLIER) cc_final: 0.7474 (tt) REVERT: C 2452 TRP cc_start: 0.7081 (t-100) cc_final: 0.6792 (t-100) REVERT: C 2456 LEU cc_start: 0.8494 (mt) cc_final: 0.8110 (tp) REVERT: C 2571 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7575 (tm-30) REVERT: F 2466 ASP cc_start: 0.7426 (m-30) cc_final: 0.7062 (m-30) REVERT: F 2537 MET cc_start: 0.7757 (mmm) cc_final: 0.6988 (mmm) outliers start: 66 outliers final: 45 residues processed: 184 average time/residue: 0.0782 time to fit residues: 21.7786 Evaluate side-chains 164 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 117 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1309 VAL Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1465 THR Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1571 GLU Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1700 HIS Chi-restraints excluded: chain C residue 1723 LEU Chi-restraints excluded: chain C residue 1761 THR Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1824 GLU Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 2003 VAL Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2148 ILE Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain F residue 2436 VAL Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2483 VAL Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2518 VAL Chi-restraints excluded: chain F residue 2524 VAL Chi-restraints excluded: chain F residue 2559 ASN Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 126 optimal weight: 4.9990 chunk 131 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.091686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.077098 restraints weight = 101889.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.080167 restraints weight = 56270.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.081880 restraints weight = 35086.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.082279 restraints weight = 25695.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.082639 restraints weight = 23177.143| |-----------------------------------------------------------------------------| r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11815 Z= 0.198 Angle : 0.851 12.036 16172 Z= 0.421 Chirality : 0.054 0.448 1763 Planarity : 0.006 0.063 2138 Dihedral : 10.343 105.703 1791 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 21.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.62 % Favored : 89.38 % Rotamer: Outliers : 6.20 % Allowed : 21.92 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.87 (0.20), residues: 1529 helix: -1.80 (0.38), residues: 158 sheet: -2.03 (0.33), residues: 218 loop : -2.04 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C2232 TYR 0.031 0.002 TYR B1311 PHE 0.021 0.003 PHE F2475 TRP 0.028 0.002 TRP C2289 HIS 0.008 0.001 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00436 (11752) covalent geometry : angle 0.82599 (16039) SS BOND : bond 0.00465 ( 56) SS BOND : angle 1.66034 ( 112) hydrogen bonds : bond 0.04324 ( 241) hydrogen bonds : angle 7.82762 ( 567) link_NAG-ASN : bond 0.00734 ( 7) link_NAG-ASN : angle 4.68501 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 124 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1272 GLN cc_start: 0.7072 (mp10) cc_final: 0.6679 (mp10) REVERT: B 1288 ASN cc_start: 0.7321 (m-40) cc_final: 0.7112 (m-40) REVERT: B 1290 GLU cc_start: 0.6314 (pm20) cc_final: 0.6112 (pm20) REVERT: B 1388 HIS cc_start: 0.8057 (p90) cc_final: 0.7786 (p90) REVERT: B 1398 MET cc_start: 0.8645 (tmm) cc_final: 0.7938 (ttm) REVERT: B 1417 ILE cc_start: 0.8644 (mp) cc_final: 0.8433 (mm) REVERT: C 2058 TYR cc_start: 0.8218 (m-10) cc_final: 0.8009 (m-10) REVERT: C 2322 LEU cc_start: 0.6626 (tt) cc_final: 0.5941 (mt) REVERT: C 2361 MET cc_start: 0.9046 (mmm) cc_final: 0.8165 (mmm) REVERT: C 2384 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7567 (tt) REVERT: C 2452 TRP cc_start: 0.7070 (t-100) cc_final: 0.6810 (t-100) REVERT: C 2456 LEU cc_start: 0.8586 (mt) cc_final: 0.8233 (tp) REVERT: C 2571 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7556 (tm-30) REVERT: F 2410 ARG cc_start: 0.7612 (mmp80) cc_final: 0.7375 (mmp80) REVERT: F 2466 ASP cc_start: 0.7471 (m-30) cc_final: 0.7085 (m-30) REVERT: F 2540 ASP cc_start: 0.8097 (t0) cc_final: 0.7502 (t0) REVERT: F 2559 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7138 (p0) outliers start: 77 outliers final: 52 residues processed: 187 average time/residue: 0.0888 time to fit residues: 24.7381 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 109 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1528 ILE Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1660 TYR Chi-restraints excluded: chain C residue 1723 LEU Chi-restraints excluded: chain C residue 1752 ILE Chi-restraints excluded: chain C residue 1757 VAL Chi-restraints excluded: chain C residue 1761 THR Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1802 LEU Chi-restraints excluded: chain C residue 1872 CYS Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 2003 VAL Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2305 TYR Chi-restraints excluded: chain C residue 2355 VAL Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2492 ASN Chi-restraints excluded: chain F residue 2395 HIS Chi-restraints excluded: chain F residue 2436 VAL Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2483 VAL Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2524 VAL Chi-restraints excluded: chain F residue 2559 ASN Chi-restraints excluded: chain F residue 2568 THR Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 142 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 0.0030 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.094382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.079153 restraints weight = 122334.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.082612 restraints weight = 64004.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.084299 restraints weight = 38280.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.084824 restraints weight = 27686.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.085613 restraints weight = 24260.352| |-----------------------------------------------------------------------------| r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11815 Z= 0.141 Angle : 0.809 12.537 16172 Z= 0.395 Chirality : 0.052 0.440 1763 Planarity : 0.006 0.070 2138 Dihedral : 9.996 106.083 1790 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.92 % Allowed : 23.29 % Favored : 71.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.78 (0.20), residues: 1529 helix: -1.64 (0.39), residues: 157 sheet: -1.78 (0.36), residues: 198 loop : -2.05 (0.17), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C2232 TYR 0.026 0.002 TYR B1311 PHE 0.027 0.002 PHE C2476 TRP 0.034 0.002 TRP A1256 HIS 0.007 0.001 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00317 (11752) covalent geometry : angle 0.78976 (16039) SS BOND : bond 0.00301 ( 56) SS BOND : angle 1.30986 ( 112) hydrogen bonds : bond 0.03724 ( 241) hydrogen bonds : angle 7.39896 ( 567) link_NAG-ASN : bond 0.00763 ( 7) link_NAG-ASN : angle 4.35063 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 125 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1272 GLN cc_start: 0.6979 (mp10) cc_final: 0.6609 (mp10) REVERT: B 1283 LEU cc_start: 0.7783 (pt) cc_final: 0.7477 (mm) REVERT: B 1290 GLU cc_start: 0.6253 (pm20) cc_final: 0.5993 (pm20) REVERT: B 1388 HIS cc_start: 0.7973 (p90) cc_final: 0.7577 (p90) REVERT: B 1398 MET cc_start: 0.8497 (tmm) cc_final: 0.7872 (ttm) REVERT: B 1408 PHE cc_start: 0.7253 (m-80) cc_final: 0.6992 (m-80) REVERT: C 1969 GLN cc_start: 0.7997 (OUTLIER) cc_final: 0.7648 (mp10) REVERT: C 2307 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.8770 (mp) REVERT: C 2322 LEU cc_start: 0.6678 (tt) cc_final: 0.6163 (mt) REVERT: C 2384 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7464 (tt) REVERT: C 2452 TRP cc_start: 0.6983 (t-100) cc_final: 0.6648 (t-100) REVERT: C 2456 LEU cc_start: 0.8479 (mt) cc_final: 0.8100 (tp) REVERT: C 2571 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7552 (tm-30) REVERT: F 2466 ASP cc_start: 0.7454 (m-30) cc_final: 0.7080 (m-30) REVERT: F 2516 MET cc_start: 0.7041 (tpp) cc_final: 0.6502 (tpp) REVERT: F 2540 ASP cc_start: 0.8146 (t0) cc_final: 0.7516 (t0) outliers start: 61 outliers final: 42 residues processed: 179 average time/residue: 0.0781 time to fit residues: 21.2768 Evaluate side-chains 156 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 111 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1571 GLU Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1660 TYR Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1969 GLN Chi-restraints excluded: chain C residue 2003 VAL Chi-restraints excluded: chain C residue 2023 VAL Chi-restraints excluded: chain C residue 2045 LEU Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2101 ARG Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2305 TYR Chi-restraints excluded: chain C residue 2307 ILE Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain F residue 2436 VAL Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2483 VAL Chi-restraints excluded: chain F residue 2568 THR Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 70 optimal weight: 0.5980 chunk 61 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 3 optimal weight: 8.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.094829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.079761 restraints weight = 109618.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.083231 restraints weight = 60319.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.085374 restraints weight = 35507.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.085787 restraints weight = 25170.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.086677 restraints weight = 21841.910| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3835 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3835 r_free = 0.3835 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3835 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11815 Z= 0.138 Angle : 0.799 11.294 16172 Z= 0.390 Chirality : 0.051 0.434 1763 Planarity : 0.005 0.067 2138 Dihedral : 9.819 103.597 1790 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 4.59 % Allowed : 24.34 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -2.73 (0.20), residues: 1529 helix: -1.52 (0.39), residues: 157 sheet: -1.65 (0.36), residues: 198 loop : -2.05 (0.18), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C2290 TYR 0.028 0.002 TYR B1311 PHE 0.025 0.002 PHE C2476 TRP 0.044 0.002 TRP A1256 HIS 0.010 0.001 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00318 (11752) covalent geometry : angle 0.77962 (16039) SS BOND : bond 0.00281 ( 56) SS BOND : angle 1.29284 ( 112) hydrogen bonds : bond 0.03586 ( 241) hydrogen bonds : angle 7.15211 ( 567) link_NAG-ASN : bond 0.00757 ( 7) link_NAG-ASN : angle 4.25467 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 122 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1283 LEU cc_start: 0.7721 (pt) cc_final: 0.7487 (mm) REVERT: B 1378 ARG cc_start: 0.7793 (ttp-170) cc_final: 0.7440 (ttp-170) REVERT: B 1388 HIS cc_start: 0.7902 (p90) cc_final: 0.7592 (p90) REVERT: B 1398 MET cc_start: 0.8493 (tmm) cc_final: 0.7993 (ttm) REVERT: C 1969 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.7740 (mp10) REVERT: C 2238 PHE cc_start: 0.7282 (m-80) cc_final: 0.6864 (m-10) REVERT: C 2307 ILE cc_start: 0.9318 (OUTLIER) cc_final: 0.8872 (mp) REVERT: C 2322 LEU cc_start: 0.6663 (tt) cc_final: 0.6182 (mt) REVERT: C 2384 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7480 (tt) REVERT: C 2452 TRP cc_start: 0.7037 (t-100) cc_final: 0.6741 (t-100) REVERT: C 2571 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7532 (tm-30) REVERT: F 2466 ASP cc_start: 0.7421 (m-30) cc_final: 0.7020 (m-30) REVERT: F 2540 ASP cc_start: 0.7948 (t0) cc_final: 0.7360 (t0) outliers start: 57 outliers final: 43 residues processed: 174 average time/residue: 0.0865 time to fit residues: 22.9101 Evaluate side-chains 153 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 107 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1490 CYS Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1660 TYR Chi-restraints excluded: chain C residue 1752 ILE Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1969 GLN Chi-restraints excluded: chain C residue 1970 CYS Chi-restraints excluded: chain C residue 2023 VAL Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2241 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2305 TYR Chi-restraints excluded: chain C residue 2307 ILE Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2492 ASN Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2474 ILE Chi-restraints excluded: chain F residue 2483 VAL Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2568 THR Chi-restraints excluded: chain F residue 2581 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1370 GLN ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1435 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1438 GLN ** C1732 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.088264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.074445 restraints weight = 86508.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.076847 restraints weight = 59924.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.077865 restraints weight = 37074.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.079194 restraints weight = 31088.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079382 restraints weight = 26141.144| |-----------------------------------------------------------------------------| r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.6355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11815 Z= 0.314 Angle : 0.968 11.216 16172 Z= 0.491 Chirality : 0.057 0.445 1763 Planarity : 0.007 0.108 2138 Dihedral : 10.502 108.315 1790 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 29.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 12.52 % Favored : 87.42 % Rotamer: Outliers : 5.00 % Allowed : 23.85 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -3.14 (0.20), residues: 1529 helix: -2.17 (0.37), residues: 151 sheet: -1.74 (0.34), residues: 212 loop : -2.33 (0.17), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C2290 TYR 0.040 0.003 TYR B1387 PHE 0.036 0.004 PHE C2476 TRP 0.052 0.004 TRP B1424 HIS 0.029 0.002 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00684 (11752) covalent geometry : angle 0.94553 (16039) SS BOND : bond 0.00634 ( 56) SS BOND : angle 1.82246 ( 112) hydrogen bonds : bond 0.05176 ( 241) hydrogen bonds : angle 8.20163 ( 567) link_NAG-ASN : bond 0.00739 ( 7) link_NAG-ASN : angle 4.63580 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 112 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1249 TYR cc_start: 0.7586 (p90) cc_final: 0.7368 (p90) REVERT: B 1378 ARG cc_start: 0.7758 (ttp-170) cc_final: 0.7358 (mtm110) REVERT: B 1388 HIS cc_start: 0.8109 (p90) cc_final: 0.7727 (p90) REVERT: B 1408 PHE cc_start: 0.7950 (m-80) cc_final: 0.7748 (m-80) REVERT: C 1880 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7394 (pp30) REVERT: C 1969 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.7901 (mt0) REVERT: C 2238 PHE cc_start: 0.7386 (m-80) cc_final: 0.7150 (m-10) REVERT: C 2307 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.8914 (mp) REVERT: C 2322 LEU cc_start: 0.7365 (tt) cc_final: 0.7021 (mt) REVERT: C 2384 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7653 (tt) REVERT: C 2571 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 2572 LYS cc_start: 0.7994 (mttt) cc_final: 0.7669 (mttt) REVERT: F 2466 ASP cc_start: 0.7515 (m-30) cc_final: 0.7112 (m-30) REVERT: F 2540 ASP cc_start: 0.7982 (t0) cc_final: 0.7467 (t0) outliers start: 62 outliers final: 48 residues processed: 168 average time/residue: 0.0744 time to fit residues: 19.0405 Evaluate side-chains 155 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 103 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1279 LEU Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1441 CYS Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1452 TYR Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1490 CYS Chi-restraints excluded: chain B residue 1528 ILE Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1660 TYR Chi-restraints excluded: chain C residue 1752 ILE Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1872 CYS Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1880 GLN Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1969 GLN Chi-restraints excluded: chain C residue 1970 CYS Chi-restraints excluded: chain C residue 2019 ILE Chi-restraints excluded: chain C residue 2045 LEU Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2215 LEU Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2307 ILE Chi-restraints excluded: chain C residue 2355 VAL Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2447 GLN Chi-restraints excluded: chain C residue 2492 ASN Chi-restraints excluded: chain C residue 2526 VAL Chi-restraints excluded: chain F residue 2436 VAL Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2524 VAL Chi-restraints excluded: chain F residue 2568 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 140 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 89 optimal weight: 0.2980 chunk 74 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1732 GLN ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.093563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.079635 restraints weight = 82207.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.082397 restraints weight = 53732.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084057 restraints weight = 33430.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084086 restraints weight = 25532.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.084430 restraints weight = 25454.407| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3783 r_free = 0.3783 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 moved from start: 0.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11815 Z= 0.150 Angle : 0.851 11.758 16172 Z= 0.417 Chirality : 0.054 0.419 1763 Planarity : 0.006 0.071 2138 Dihedral : 9.952 107.378 1788 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.44 % Favored : 90.56 % Rotamer: Outliers : 4.11 % Allowed : 25.62 % Favored : 70.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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 aren not related in a simple way. whole: -3.05 (0.20), residues: 1529 helix: -2.00 (0.38), residues: 151 sheet: -2.04 (0.34), residues: 208 loop : -2.20 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2454 TYR 0.024 0.002 TYR B1311 PHE 0.027 0.002 PHE F2476 TRP 0.045 0.003 TRP C2452 HIS 0.005 0.001 HIS C2147 Details of bonding type rmsd covalent geometry : bond 0.00337 (11752) covalent geometry : angle 0.83309 (16039) SS BOND : bond 0.00352 ( 56) SS BOND : angle 1.38143 ( 112) hydrogen bonds : bond 0.03671 ( 241) hydrogen bonds : angle 7.45778 ( 567) link_NAG-ASN : bond 0.00747 ( 7) link_NAG-ASN : angle 4.21872 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 120 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1261 TYR cc_start: 0.8129 (m-80) cc_final: 0.7892 (m-80) REVERT: B 1283 LEU cc_start: 0.7645 (pt) cc_final: 0.7025 (mt) REVERT: B 1388 HIS cc_start: 0.8033 (p90) cc_final: 0.7619 (p90) REVERT: B 1398 MET cc_start: 0.8487 (tmm) cc_final: 0.7729 (ttm) REVERT: C 1969 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: C 2141 LEU cc_start: 0.0202 (OUTLIER) cc_final: -0.0075 (tt) REVERT: C 2307 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9031 (mp) REVERT: C 2322 LEU cc_start: 0.7160 (tt) cc_final: 0.6873 (mt) REVERT: C 2384 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7457 (tt) REVERT: C 2571 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7787 (tm-30) REVERT: F 2466 ASP cc_start: 0.7515 (m-30) cc_final: 0.7164 (m-30) REVERT: F 2540 ASP cc_start: 0.7916 (t0) cc_final: 0.7466 (t0) REVERT: F 2557 GLN cc_start: 0.8819 (pm20) cc_final: 0.8449 (pp30) outliers start: 51 outliers final: 38 residues processed: 167 average time/residue: 0.0844 time to fit residues: 21.0383 Evaluate side-chains 149 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 107 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1441 CYS Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1490 CYS Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1660 TYR Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1969 GLN Chi-restraints excluded: chain C residue 1970 CYS Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2095 GLN Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2101 ARG Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2141 LEU Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2259 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2307 ILE Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain F residue 2436 VAL Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 101 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 16 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 86 optimal weight: 0.0470 chunk 111 optimal weight: 9.9990 chunk 67 optimal weight: 20.0000 chunk 30 optimal weight: 0.5980 overall best weight: 1.3284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1726 GLN ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.091801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.076989 restraints weight = 118850.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.080384 restraints weight = 63226.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082112 restraints weight = 37039.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.082617 restraints weight = 26629.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.084145 restraints weight = 23314.318| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3805 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3805 r_free = 0.3805 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.6701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11815 Z= 0.157 Angle : 0.849 11.365 16172 Z= 0.418 Chirality : 0.053 0.419 1763 Planarity : 0.006 0.089 2138 Dihedral : 9.823 106.222 1788 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.29 % Favored : 89.71 % Rotamer: Outliers : 3.55 % Allowed : 26.67 % Favored : 69.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -3.03 (0.20), residues: 1529 helix: -1.87 (0.38), residues: 151 sheet: -1.91 (0.34), residues: 209 loop : -2.22 (0.17), residues: 1169 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F2510 TYR 0.028 0.002 TYR B1311 PHE 0.028 0.002 PHE B1408 TRP 0.045 0.003 TRP C2289 HIS 0.004 0.001 HIS F2395 Details of bonding type rmsd covalent geometry : bond 0.00358 (11752) covalent geometry : angle 0.83066 (16039) SS BOND : bond 0.00343 ( 56) SS BOND : angle 1.41310 ( 112) hydrogen bonds : bond 0.03750 ( 241) hydrogen bonds : angle 7.43524 ( 567) link_NAG-ASN : bond 0.00710 ( 7) link_NAG-ASN : angle 4.21334 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3058 Ramachandran restraints generated. 1529 Oldfield, 0 Emsley, 1529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 113 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1261 TYR cc_start: 0.8154 (m-80) cc_final: 0.7865 (m-80) REVERT: B 1283 LEU cc_start: 0.7616 (pt) cc_final: 0.7019 (mt) REVERT: B 1388 HIS cc_start: 0.7920 (p90) cc_final: 0.7497 (p90) REVERT: B 1398 MET cc_start: 0.8423 (tmm) cc_final: 0.7635 (ttm) REVERT: C 1969 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7537 (mp10) REVERT: C 2307 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9029 (mp) REVERT: C 2322 LEU cc_start: 0.7110 (tt) cc_final: 0.6857 (mt) REVERT: C 2384 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7407 (tt) REVERT: C 2467 LYS cc_start: 0.8626 (ptmt) cc_final: 0.8329 (tttp) REVERT: C 2571 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7726 (tm-30) REVERT: F 2466 ASP cc_start: 0.7447 (m-30) cc_final: 0.7091 (m-30) outliers start: 44 outliers final: 39 residues processed: 151 average time/residue: 0.0865 time to fit residues: 19.2212 Evaluate side-chains 153 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 111 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1274 THR Chi-restraints excluded: chain B residue 1282 THR Chi-restraints excluded: chain B residue 1309 VAL Chi-restraints excluded: chain B residue 1334 VAL Chi-restraints excluded: chain B residue 1441 CYS Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1486 VAL Chi-restraints excluded: chain B residue 1490 CYS Chi-restraints excluded: chain B residue 1569 CYS Chi-restraints excluded: chain B residue 1580 CYS Chi-restraints excluded: chain B residue 1589 CYS Chi-restraints excluded: chain B residue 1614 CYS Chi-restraints excluded: chain C residue 1660 TYR Chi-restraints excluded: chain C residue 1723 LEU Chi-restraints excluded: chain C residue 1752 ILE Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1877 CYS Chi-restraints excluded: chain C residue 1897 CYS Chi-restraints excluded: chain C residue 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU Chi-restraints excluded: chain C residue 1965 VAL Chi-restraints excluded: chain C residue 1969 GLN Chi-restraints excluded: chain C residue 1970 CYS Chi-restraints excluded: chain C residue 2064 CYS Chi-restraints excluded: chain C residue 2097 VAL Chi-restraints excluded: chain C residue 2101 ARG Chi-restraints excluded: chain C residue 2123 VAL Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2224 LYS Chi-restraints excluded: chain C residue 2259 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2307 ILE Chi-restraints excluded: chain C residue 2384 LEU Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain F residue 2436 VAL Chi-restraints excluded: chain F residue 2443 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2568 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 99 optimal weight: 4.9990 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 0.0270 chunk 108 optimal weight: 0.0770 chunk 72 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 137 optimal weight: 0.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1301 ASN B1303 ASN ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1860 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F2395 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.094432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.079353 restraints weight = 128249.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.083049 restraints weight = 65921.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.085130 restraints weight = 37590.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.085479 restraints weight = 28155.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.085833 restraints weight = 22875.015| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6667 moved from start: 0.6882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11815 Z= 0.143 Angle : 0.842 11.877 16172 Z= 0.413 Chirality : 0.052 0.415 1763 Planarity : 0.006 0.067 2138 Dihedral : 9.518 104.522 1788 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.44 % Favored : 90.50 % Rotamer: Outliers : 3.63 % Allowed : 26.91 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 aren not related in a simple way. whole: -2.92 (0.20), residues: 1529 helix: -1.71 (0.39), residues: 155 sheet: -1.73 (0.35), residues: 209 loop : -2.18 (0.18), residues: 1165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1378 TYR 0.025 0.002 TYR B1311 PHE 0.029 0.002 PHE B1408 TRP 0.056 0.003 TRP C2289 HIS 0.004 0.001 HIS C2261 Details of bonding type rmsd covalent geometry : bond 0.00325 (11752) covalent geometry : angle 0.82591 (16039) SS BOND : bond 0.00283 ( 56) SS BOND : angle 1.24433 ( 112) hydrogen bonds : bond 0.03458 ( 241) hydrogen bonds : angle 7.10505 ( 567) link_NAG-ASN : bond 0.00717 ( 7) link_NAG-ASN : angle 4.05673 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1832.08 seconds wall clock time: 32 minutes 21.60 seconds (1941.60 seconds total)