Starting phenix.real_space_refine on Tue Jun 10 10:38:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0t_18803/06_2025/8r0t_18803.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0t_18803/06_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_18803/06_2025/8r0t_18803.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0t_18803/06_2025/8r0t_18803.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0t_18803/06_2025/8r0t_18803.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0t_18803/06_2025/8r0t_18803.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.66, per 1000 atoms: 1.02 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: 3.03 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 1.60 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: 5.61 Time building geometry restraints manager: 3.52 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: 119.550 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: 0.960 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 37.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 161.530 ------------------------------------------------------------------------------- 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 : 27.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.017 0.001 TRP C2573 HIS 0.005 0.001 HIS C1659 PHE 0.027 0.002 PHE F2553 TYR 0.010 0.001 TYR B1387 ARG 0.003 0.000 ARG C2252 Details of bonding type rmsd link_NAG-ASN : bond 0.01391 ( 7) link_NAG-ASN : angle 4.97829 ( 21) hydrogen bonds : bond 0.23110 ( 241) hydrogen bonds : angle 10.08588 ( 567) SS BOND : bond 0.00298 ( 56) SS BOND : angle 1.05246 ( 112) covalent geometry : bond 0.00543 (11752) covalent geometry : angle 1.08905 (16039) *********************** 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 : 1.281 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 1388 HIS cc_start: 0.6794 (p90) cc_final: 0.6494 (p90) REVERT: B 1487 LEU cc_start: 0.7954 (tp) cc_final: 0.7635 (tt) REVERT: C 2524 VAL cc_start: 0.7380 (OUTLIER) cc_final: 0.7172 (p) outliers start: 85 outliers final: 29 residues processed: 279 average time/residue: 0.2818 time to fit residues: 116.3467 Evaluate side-chains 160 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.595 ------------------------------------------------------------------------------- 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 127 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 77 optimal weight: 0.0980 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 71 optimal weight: 0.8980 chunk 88 optimal weight: 9.9990 chunk 137 optimal weight: 5.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C2313 GLN C2395 HIS ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.092311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.077955 restraints weight = 88513.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.080953 restraints weight = 57410.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.082676 restraints weight = 32716.219| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3770 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3770 r_free = 0.3770 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3770 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6612 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11815 Z= 0.197 Angle : 0.883 12.175 16172 Z= 0.443 Chirality : 0.056 0.511 1763 Planarity : 0.006 0.066 2138 Dihedral : 11.852 105.302 1811 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 21.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 5.56 % Allowed : 19.34 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.20), residues: 1529 helix: -2.08 (0.36), residues: 163 sheet: -1.80 (0.34), residues: 208 loop : -2.04 (0.17), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP C2289 HIS 0.007 0.002 HIS F2395 PHE 0.024 0.003 PHE C2175 TYR 0.030 0.003 TYR B1387 ARG 0.011 0.001 ARG C2290 Details of bonding type rmsd link_NAG-ASN : bond 0.00756 ( 7) link_NAG-ASN : angle 4.69367 ( 21) hydrogen bonds : bond 0.04782 ( 241) hydrogen bonds : angle 8.64458 ( 567) SS BOND : bond 0.00501 ( 56) SS BOND : angle 2.03613 ( 112) covalent geometry : bond 0.00441 (11752) covalent geometry : angle 0.85374 (16039) *********************** 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 212 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 143 time to evaluate : 5.018 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: B 1272 GLN cc_start: 0.6871 (mp10) cc_final: 0.6630 (mp10) REVERT: B 1360 LYS cc_start: 0.7388 (mmtm) cc_final: 0.7145 (mmtm) REVERT: B 1378 ARG cc_start: 0.7734 (ttp-170) cc_final: 0.7323 (ttp-170) REVERT: B 1398 MET cc_start: 0.8641 (tmm) cc_final: 0.7841 (ttm) REVERT: B 1516 LYS cc_start: 0.8294 (ttpp) cc_final: 0.7883 (tmtt) REVERT: B 1517 ILE cc_start: 0.8121 (mt) cc_final: 0.7541 (pt) REVERT: C 1710 ARG cc_start: 0.7233 (mtp85) cc_final: 0.6864 (mtp-110) REVERT: C 2223 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8032 (tt0) REVERT: C 2571 GLU cc_start: 0.7841 (tm-30) cc_final: 0.7603 (tm-30) REVERT: F 2466 ASP cc_start: 0.7517 (m-30) cc_final: 0.7228 (m-30) REVERT: F 2559 ASN cc_start: 0.6824 (OUTLIER) cc_final: 0.6599 (p0) outliers start: 69 outliers final: 39 residues processed: 203 average time/residue: 0.4325 time to fit residues: 131.4581 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 1.781 ------------------------------------------------------------------------------- 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 1381 VAL Chi-restraints excluded: chain B residue 1407 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 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 1951 CYS 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 2436 VAL Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2456 LEU 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 2425 ASP Chi-restraints excluded: chain F residue 2459 VAL 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 90 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 19 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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** C1726 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** C2520 GLN C2557 GLN ** F2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.093152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.078722 restraints weight = 86136.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.081187 restraints weight = 58593.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.082738 restraints weight = 37550.651| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6694 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11815 Z= 0.172 Angle : 0.857 13.698 16172 Z= 0.427 Chirality : 0.054 0.469 1763 Planarity : 0.006 0.060 2138 Dihedral : 11.047 106.088 1794 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 5.72 % Allowed : 20.71 % Favored : 73.57 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.20), residues: 1529 helix: -1.97 (0.37), residues: 157 sheet: -1.95 (0.34), residues: 209 loop : -2.02 (0.18), residues: 1163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C2289 HIS 0.008 0.001 HIS F2395 PHE 0.020 0.002 PHE C1668 TYR 0.040 0.002 TYR B1387 ARG 0.007 0.001 ARG C1710 Details of bonding type rmsd link_NAG-ASN : bond 0.00831 ( 7) link_NAG-ASN : angle 4.19035 ( 21) hydrogen bonds : bond 0.04427 ( 241) hydrogen bonds : angle 8.16451 ( 567) SS BOND : bond 0.00410 ( 56) SS BOND : angle 2.55252 ( 112) covalent geometry : bond 0.00390 (11752) covalent geometry : angle 0.81968 (16039) *********************** 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 204 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 133 time to evaluate : 1.580 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: 0.7552 (p90) cc_final: 0.7258 (p90) REVERT: B 1272 GLN cc_start: 0.7041 (mp10) cc_final: 0.6794 (mp10) REVERT: B 1378 ARG cc_start: 0.7590 (ttp-170) cc_final: 0.7023 (ttp-170) REVERT: B 1388 HIS cc_start: 0.7976 (p90) cc_final: 0.7594 (p90) REVERT: C 1710 ARG cc_start: 0.6984 (mtp85) cc_final: 0.6575 (mtp-110) REVERT: C 2058 TYR cc_start: 0.7785 (m-10) cc_final: 0.7565 (m-10) REVERT: C 2136 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8432 (mmmm) REVERT: C 2322 LEU cc_start: 0.6464 (tp) cc_final: 0.6262 (tt) REVERT: C 2384 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7483 (tt) REVERT: C 2452 TRP cc_start: 0.7086 (t-100) cc_final: 0.6807 (t-100) REVERT: C 2571 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7673 (tm-30) REVERT: F 2466 ASP cc_start: 0.7585 (m-30) cc_final: 0.7255 (m-30) REVERT: F 2545 MET cc_start: 0.8174 (mmp) cc_final: 0.7536 (mmm) outliers start: 71 outliers final: 51 residues processed: 187 average time/residue: 0.3365 time to fit residues: 95.1813 Evaluate side-chains 171 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 119 time to evaluate : 4.089 ------------------------------------------------------------------------------- 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 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 1381 VAL Chi-restraints excluded: chain B residue 1472 CYS Chi-restraints excluded: chain B residue 1501 GLN 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 1726 GLN 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 1944 GLU Chi-restraints excluded: chain C residue 1951 CYS Chi-restraints excluded: chain C residue 1952 VAL Chi-restraints excluded: chain C residue 1997 CYS Chi-restraints excluded: chain C residue 2003 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 2148 ILE Chi-restraints excluded: chain C residue 2211 CYS 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 2384 LEU Chi-restraints excluded: chain C residue 2436 VAL Chi-restraints excluded: chain C residue 2443 CYS Chi-restraints excluded: chain C residue 2456 LEU Chi-restraints excluded: chain C residue 2526 VAL Chi-restraints excluded: chain C residue 2558 THR Chi-restraints excluded: chain C residue 2568 THR Chi-restraints excluded: chain F residue 2406 CYS Chi-restraints excluded: chain F residue 2459 VAL Chi-restraints excluded: chain F residue 2480 LEU 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 2581 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 126 optimal weight: 3.9990 chunk 14 optimal weight: 0.4980 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 119 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 133 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 132 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** ** B1523 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1613 HIS C1726 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** C2492 ASN F2520 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.094920 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.079631 restraints weight = 122180.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.082729 restraints weight = 63830.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.085111 restraints weight = 38622.258| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3796 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3796 r_free = 0.3796 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3796 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11815 Z= 0.146 Angle : 0.820 18.102 16172 Z= 0.405 Chirality : 0.053 0.455 1763 Planarity : 0.005 0.059 2138 Dihedral : 10.611 105.631 1792 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 4.92 % Allowed : 22.24 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.20), residues: 1529 helix: -1.72 (0.38), residues: 155 sheet: -1.95 (0.33), residues: 207 loop : -1.99 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C2289 HIS 0.009 0.001 HIS F2395 PHE 0.019 0.002 PHE C1668 TYR 0.029 0.002 TYR B1387 ARG 0.004 0.000 ARG C2128 Details of bonding type rmsd link_NAG-ASN : bond 0.00782 ( 7) link_NAG-ASN : angle 4.33710 ( 21) hydrogen bonds : bond 0.03957 ( 241) hydrogen bonds : angle 7.72337 ( 567) SS BOND : bond 0.00383 ( 56) SS BOND : angle 2.42607 ( 112) covalent geometry : bond 0.00331 (11752) covalent geometry : angle 0.78227 (16039) *********************** 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 195 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 134 time to evaluate : 1.492 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: 0.8164 (m-80) cc_final: 0.7791 (m-80) REVERT: B 1272 GLN cc_start: 0.6978 (mp10) cc_final: 0.6631 (mp10) REVERT: B 1388 HIS cc_start: 0.7974 (p90) cc_final: 0.7599 (p90) REVERT: B 1398 MET cc_start: 0.8622 (tmm) cc_final: 0.7740 (ttm) REVERT: B 1441 CYS cc_start: 0.3996 (p) cc_final: 0.3785 (p) REVERT: C 1710 ARG cc_start: 0.6872 (mtp85) cc_final: 0.6509 (mtp-110) REVERT: C 2136 LYS cc_start: 0.8948 (mmtp) cc_final: 0.8534 (mmmm) REVERT: C 2258 MET cc_start: 0.2562 (ptt) cc_final: 0.2099 (ptt) REVERT: C 2384 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7426 (tt) REVERT: C 2452 TRP cc_start: 0.7101 (t-100) cc_final: 0.6743 (t-100) REVERT: C 2571 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7627 (tm-30) REVERT: F 2410 ARG cc_start: 0.7648 (mmp80) cc_final: 0.7284 (mmp80) REVERT: F 2466 ASP cc_start: 0.7477 (m-30) cc_final: 0.7122 (m-30) REVERT: F 2540 ASP cc_start: 0.8234 (t0) cc_final: 0.7651 (t0) REVERT: F 2545 MET cc_start: 0.8114 (mmp) cc_final: 0.7502 (mmm) outliers start: 61 outliers final: 46 residues processed: 182 average time/residue: 0.2459 time to fit residues: 67.2002 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 1407 VAL 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 1528 ILE 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 1726 GLN 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 1951 CYS Chi-restraints excluded: chain C residue 1997 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 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 2272 LEU 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 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 2474 ILE 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 2581 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 1 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 34 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 116 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1262 ASN ** B1356 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1370 GLN ** B1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1438 GLN C1726 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** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2473 HIS ** F2552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2576 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.087903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.073363 restraints weight = 104171.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.076445 restraints weight = 59815.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.078042 restraints weight = 35727.076| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3652 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.06 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3652 r_free = 0.3652 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3652 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 11815 Z= 0.318 Angle : 1.003 12.756 16172 Z= 0.511 Chirality : 0.059 0.457 1763 Planarity : 0.007 0.064 2138 Dihedral : 10.944 108.404 1791 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 29.92 Ramachandran Plot: Outliers : 0.07 % Allowed : 11.99 % Favored : 87.94 % Rotamer: Outliers : 6.53 % Allowed : 22.64 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.20), residues: 1529 helix: -2.31 (0.37), residues: 146 sheet: -2.08 (0.33), residues: 203 loop : -2.31 (0.17), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C2490 HIS 0.008 0.002 HIS B1402 PHE 0.047 0.004 PHE F2475 TYR 0.041 0.003 TYR B1387 ARG 0.006 0.001 ARG C2101 Details of bonding type rmsd link_NAG-ASN : bond 0.00832 ( 7) link_NAG-ASN : angle 5.07059 ( 21) hydrogen bonds : bond 0.05631 ( 241) hydrogen bonds : angle 8.70700 ( 567) SS BOND : bond 0.00758 ( 56) SS BOND : angle 2.00893 ( 112) covalent geometry : bond 0.00694 (11752) covalent geometry : angle 0.97602 (16039) *********************** 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 208 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 127 time to evaluate : 1.336 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: B 1388 HIS cc_start: 0.8301 (p90) cc_final: 0.7810 (p90) REVERT: C 2258 MET cc_start: 0.2911 (ptt) cc_final: 0.2191 (ptt) REVERT: C 2384 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7597 (tt) REVERT: F 2466 ASP cc_start: 0.7549 (m-30) cc_final: 0.7133 (m-30) outliers start: 81 outliers final: 58 residues processed: 200 average time/residue: 0.2043 time to fit residues: 61.8947 Evaluate side-chains 170 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 111 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1262 ASN 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 1381 VAL 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 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 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 1726 GLN 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 1824 GLU 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 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1941 VAL Chi-restraints excluded: chain C residue 1944 GLU 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 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 2228 CYS Chi-restraints excluded: chain C residue 2241 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 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 C residue 2526 VAL 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 2501 THR Chi-restraints excluded: chain F residue 2518 VAL Chi-restraints excluded: chain F residue 2568 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 21 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 133 optimal weight: 30.0000 chunk 75 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** C1700 HIS C1726 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** ** C2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2473 HIS C2559 ASN ** F2559 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.091383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.076862 restraints weight = 108891.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.079875 restraints weight = 58840.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.081727 restraints weight = 36652.282| |-----------------------------------------------------------------------------| r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3726 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3726 r_free = 0.3726 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3726 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11815 Z= 0.171 Angle : 0.841 11.600 16172 Z= 0.421 Chirality : 0.054 0.437 1763 Planarity : 0.006 0.066 2138 Dihedral : 10.368 108.478 1790 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 19.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 5.56 % Allowed : 24.90 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.20), residues: 1529 helix: -2.01 (0.39), residues: 154 sheet: -1.98 (0.34), residues: 205 loop : -2.25 (0.17), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C2289 HIS 0.019 0.001 HIS C1700 PHE 0.033 0.002 PHE C2476 TYR 0.027 0.002 TYR B1387 ARG 0.009 0.000 ARG C1710 Details of bonding type rmsd link_NAG-ASN : bond 0.00768 ( 7) link_NAG-ASN : angle 4.57109 ( 21) hydrogen bonds : bond 0.04283 ( 241) hydrogen bonds : angle 7.99673 ( 567) SS BOND : bond 0.00398 ( 56) SS BOND : angle 1.56215 ( 112) covalent geometry : bond 0.00386 (11752) covalent geometry : angle 0.81730 (16039) *********************** 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 191 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 122 time to evaluate : 1.410 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: B 1388 HIS cc_start: 0.8090 (p90) cc_final: 0.7723 (p90) REVERT: B 1398 MET cc_start: 0.8712 (tmm) cc_final: 0.7830 (ttm) REVERT: B 1408 PHE cc_start: 0.7535 (m-80) cc_final: 0.6611 (m-80) REVERT: C 2163 LEU cc_start: 0.7012 (mt) cc_final: 0.6804 (mt) REVERT: C 2307 ILE cc_start: 0.8892 (mt) cc_final: 0.8658 (mt) REVERT: C 2384 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7426 (tt) REVERT: C 2452 TRP cc_start: 0.7110 (t-100) cc_final: 0.6752 (t-100) REVERT: F 2410 ARG cc_start: 0.7727 (mmp80) cc_final: 0.7417 (mmp80) REVERT: F 2466 ASP cc_start: 0.7578 (m-30) cc_final: 0.7194 (m-30) outliers start: 69 outliers final: 49 residues processed: 179 average time/residue: 0.2156 time to fit residues: 58.0525 Evaluate side-chains 163 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 113 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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 1370 GLN Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1374 ASP Chi-restraints excluded: chain B residue 1379 VAL Chi-restraints excluded: chain B residue 1407 VAL Chi-restraints excluded: chain B residue 1441 CYS Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1461 LEU Chi-restraints excluded: chain B residue 1472 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 1726 GLN Chi-restraints excluded: chain C residue 1752 ILE Chi-restraints excluded: chain C residue 1775 VAL Chi-restraints excluded: chain C residue 1824 GLU 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 1913 CYS Chi-restraints excluded: chain C residue 1926 CYS Chi-restraints excluded: chain C residue 1944 GLU 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 2228 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2295 CYS 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 C residue 2526 VAL 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 2568 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 72 optimal weight: 0.8980 chunk 136 optimal weight: 0.0470 chunk 22 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- 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** C1726 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** ** F2559 ASN ** 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 = 0.3980 r_free = 0.3980 target = 0.093235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.078511 restraints weight = 102760.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081905 restraints weight = 57258.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.083810 restraints weight = 33701.849| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11815 Z= 0.148 Angle : 0.820 11.726 16172 Z= 0.405 Chirality : 0.053 0.439 1763 Planarity : 0.005 0.067 2138 Dihedral : 9.944 105.530 1788 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 5.00 % Allowed : 25.62 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.20), residues: 1529 helix: -1.83 (0.39), residues: 160 sheet: -1.97 (0.34), residues: 196 loop : -2.21 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C2289 HIS 0.004 0.001 HIS F2395 PHE 0.030 0.002 PHE F2578 TYR 0.025 0.002 TYR B1311 ARG 0.008 0.000 ARG C1710 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 7) link_NAG-ASN : angle 4.29898 ( 21) hydrogen bonds : bond 0.04028 ( 241) hydrogen bonds : angle 7.62599 ( 567) SS BOND : bond 0.00315 ( 56) SS BOND : angle 1.47762 ( 112) covalent geometry : bond 0.00335 (11752) covalent geometry : angle 0.79924 (16039) *********************** 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 178 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 116 time to evaluate : 1.223 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: A 1249 TYR cc_start: 0.7482 (p90) cc_final: 0.7142 (p90) REVERT: B 1388 HIS cc_start: 0.8005 (p90) cc_final: 0.7562 (p90) REVERT: B 1398 MET cc_start: 0.8628 (tmm) cc_final: 0.7838 (ttm) REVERT: C 2258 MET cc_start: 0.1640 (ptp) cc_final: 0.1229 (ptt) REVERT: C 2307 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8709 (mt) REVERT: C 2384 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7450 (tt) REVERT: C 2452 TRP cc_start: 0.7043 (t-100) cc_final: 0.6749 (t-100) REVERT: F 2466 ASP cc_start: 0.7553 (m-30) cc_final: 0.7186 (m-30) outliers start: 62 outliers final: 41 residues processed: 167 average time/residue: 0.1976 time to fit residues: 49.9423 Evaluate side-chains 152 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 109 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 1374 ASP 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 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 1726 GLN 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 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 2228 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 2436 VAL Chi-restraints excluded: chain C residue 2443 CYS 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 19 optimal weight: 0.0970 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** C1726 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** C2520 GLN ** F2395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F2559 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 = 0.3983 r_free = 0.3983 target = 0.093021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.079146 restraints weight = 84382.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081825 restraints weight = 55690.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.083417 restraints weight = 33857.148| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3762 r_free = 0.3762 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11815 Z= 0.152 Angle : 0.818 11.303 16172 Z= 0.405 Chirality : 0.053 0.440 1763 Planarity : 0.005 0.068 2138 Dihedral : 9.787 104.569 1788 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 4.51 % Allowed : 25.95 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.20), residues: 1529 helix: -1.75 (0.39), residues: 160 sheet: -1.92 (0.33), residues: 216 loop : -2.23 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C2289 HIS 0.008 0.001 HIS F2395 PHE 0.021 0.002 PHE C2476 TYR 0.025 0.002 TYR B1311 ARG 0.004 0.000 ARG C2101 Details of bonding type rmsd link_NAG-ASN : bond 0.00717 ( 7) link_NAG-ASN : angle 4.27048 ( 21) hydrogen bonds : bond 0.03819 ( 241) hydrogen bonds : angle 7.39128 ( 567) SS BOND : bond 0.00377 ( 56) SS BOND : angle 1.53243 ( 112) covalent geometry : bond 0.00347 (11752) covalent geometry : angle 0.79629 (16039) *********************** 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 173 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 117 time to evaluate : 1.228 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: A 1249 TYR cc_start: 0.7462 (p90) cc_final: 0.7137 (p90) REVERT: B 1388 HIS cc_start: 0.7890 (p90) cc_final: 0.7443 (p90) REVERT: B 1398 MET cc_start: 0.8625 (tmm) cc_final: 0.7826 (ttm) REVERT: B 1412 THR cc_start: 0.7775 (OUTLIER) cc_final: 0.7538 (m) REVERT: C 1723 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.8047 (mt) REVERT: C 2258 MET cc_start: 0.1575 (ptp) cc_final: 0.1242 (ptt) REVERT: C 2307 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8743 (mt) REVERT: C 2384 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7516 (tt) REVERT: C 2452 TRP cc_start: 0.7021 (t-100) cc_final: 0.6745 (t-100) REVERT: F 2448 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6348 (mtpt) REVERT: F 2466 ASP cc_start: 0.7570 (m-30) cc_final: 0.7202 (m-30) outliers start: 56 outliers final: 41 residues processed: 164 average time/residue: 0.2008 time to fit residues: 50.4972 Evaluate side-chains 153 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 108 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 1412 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 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 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 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 2123 VAL Chi-restraints excluded: chain C residue 2170 ASN Chi-restraints excluded: chain C residue 2211 CYS Chi-restraints excluded: chain C residue 2279 CYS Chi-restraints excluded: chain C residue 2307 ILE Chi-restraints excluded: chain C residue 2325 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 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 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 2572 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 14 optimal weight: 0.9980 chunk 143 optimal weight: 0.0970 chunk 136 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 123 optimal weight: 0.2980 chunk 77 optimal weight: 0.9990 chunk 58 optimal weight: 0.0060 chunk 50 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1303 ASN ** 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** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2407 GLN ** 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 = 0.4007 r_free = 0.4007 target = 0.094293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.079123 restraints weight = 99742.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.082585 restraints weight = 55988.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.084906 restraints weight = 32755.918| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3803 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3803 r_free = 0.3803 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3803 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6708 moved from start: 0.6405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11815 Z= 0.139 Angle : 0.799 11.151 16172 Z= 0.396 Chirality : 0.052 0.432 1763 Planarity : 0.005 0.068 2138 Dihedral : 9.616 103.305 1788 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.76 % Favored : 90.24 % Rotamer: Outliers : 3.87 % Allowed : 25.95 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.20), residues: 1529 helix: -1.66 (0.39), residues: 160 sheet: -1.85 (0.34), residues: 209 loop : -2.18 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C2289 HIS 0.009 0.001 HIS F2395 PHE 0.020 0.002 PHE B1457 TYR 0.025 0.002 TYR B1311 ARG 0.006 0.000 ARG C1710 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 7) link_NAG-ASN : angle 4.15311 ( 21) hydrogen bonds : bond 0.03619 ( 241) hydrogen bonds : angle 7.16459 ( 567) SS BOND : bond 0.00324 ( 56) SS BOND : angle 1.36655 ( 112) covalent geometry : bond 0.00317 (11752) covalent geometry : angle 0.77964 (16039) *********************** 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: 48 poor density : 123 time to evaluate : 1.411 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: A 1249 TYR cc_start: 0.7443 (p90) cc_final: 0.7136 (p90) REVERT: B 1388 HIS cc_start: 0.7823 (p90) cc_final: 0.7409 (p90) REVERT: B 1398 MET cc_start: 0.8547 (tmm) cc_final: 0.7870 (ttp) REVERT: B 1412 THR cc_start: 0.7677 (OUTLIER) cc_final: 0.7459 (m) REVERT: C 2258 MET cc_start: 0.1460 (ptp) cc_final: 0.1049 (ptt) REVERT: C 2307 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8745 (mt) REVERT: C 2384 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7383 (tt) REVERT: C 2452 TRP cc_start: 0.7037 (t-100) cc_final: 0.6709 (t-100) REVERT: C 2467 LYS cc_start: 0.8759 (ptpt) cc_final: 0.8478 (tttp) REVERT: F 2466 ASP cc_start: 0.7517 (m-30) cc_final: 0.7157 (m-30) outliers start: 48 outliers final: 40 residues processed: 165 average time/residue: 0.2009 time to fit residues: 51.3550 Evaluate side-chains 153 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 110 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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 1303 ASN Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1412 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 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 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 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 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 2279 CYS Chi-restraints excluded: chain C residue 2307 ILE 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 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 2474 ILE Chi-restraints excluded: chain F residue 2501 THR Chi-restraints excluded: chain F residue 2568 THR Chi-restraints excluded: chain F residue 2572 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 100 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 119 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 129 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2304 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 = 0.4009 r_free = 0.4009 target = 0.094282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.079453 restraints weight = 123305.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.082441 restraints weight = 63696.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.084668 restraints weight = 39394.635| |-----------------------------------------------------------------------------| r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3788 r_free = 0.3788 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3788 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.6530 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= 0.142 Angle : 0.810 11.182 16172 Z= 0.402 Chirality : 0.052 0.427 1763 Planarity : 0.005 0.067 2138 Dihedral : 9.534 102.466 1787 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.46 % Allowed : 26.83 % Favored : 69.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.20), residues: 1529 helix: -1.52 (0.40), residues: 160 sheet: -1.69 (0.34), residues: 220 loop : -2.18 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C2289 HIS 0.004 0.001 HIS F2395 PHE 0.019 0.002 PHE F2476 TYR 0.024 0.002 TYR B1311 ARG 0.005 0.000 ARG C1710 Details of bonding type rmsd link_NAG-ASN : bond 0.00716 ( 7) link_NAG-ASN : angle 4.16817 ( 21) hydrogen bonds : bond 0.03596 ( 241) hydrogen bonds : angle 7.07311 ( 567) SS BOND : bond 0.00335 ( 56) SS BOND : angle 1.49626 ( 112) covalent geometry : bond 0.00325 (11752) covalent geometry : angle 0.78916 (16039) ********************** 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 158 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 1.241 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: 0.7450 (p90) cc_final: 0.7163 (p90) REVERT: B 1290 GLU cc_start: 0.6602 (pm20) cc_final: 0.6367 (pm20) REVERT: B 1388 HIS cc_start: 0.7811 (p90) cc_final: 0.7428 (p90) REVERT: B 1398 MET cc_start: 0.8625 (tmm) cc_final: 0.7924 (ptm) REVERT: B 1412 THR cc_start: 0.7886 (OUTLIER) cc_final: 0.7676 (m) REVERT: C 2258 MET cc_start: 0.1714 (ptp) cc_final: 0.1319 (ptt) REVERT: C 2307 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8769 (mt) REVERT: C 2384 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7347 (tt) REVERT: C 2452 TRP cc_start: 0.7140 (t-100) cc_final: 0.6749 (t-100) REVERT: C 2467 LYS cc_start: 0.8786 (ptpt) cc_final: 0.8481 (tttt) REVERT: F 2466 ASP cc_start: 0.7587 (m-30) cc_final: 0.7232 (m-30) outliers start: 43 outliers final: 38 residues processed: 153 average time/residue: 0.1999 time to fit residues: 47.1845 Evaluate side-chains 150 residues out of total 1239 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 109 time to evaluate : 1.266 ------------------------------------------------------------------------------- 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 1303 ASN Chi-restraints excluded: chain B residue 1364 GLU Chi-restraints excluded: chain B residue 1372 THR Chi-restraints excluded: chain B residue 1412 THR Chi-restraints excluded: chain B residue 1449 VAL Chi-restraints excluded: chain B residue 1472 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 1802 LEU 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 1970 CYS Chi-restraints excluded: chain C residue 2064 CYS 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 2279 CYS Chi-restraints excluded: chain C residue 2307 ILE 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 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 2568 THR Chi-restraints excluded: chain F residue 2572 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 104 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 105 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 64 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 113 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** ** C2147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2280 GLN ** 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 = 0.4054 r_free = 0.4054 target = 0.094986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.080411 restraints weight = 119558.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.083962 restraints weight = 62410.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.085303 restraints weight = 36199.162| |-----------------------------------------------------------------------------| r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.6628 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= 0.138 Angle : 0.797 11.077 16172 Z= 0.396 Chirality : 0.052 0.425 1763 Planarity : 0.005 0.065 2138 Dihedral : 9.465 101.962 1787 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.90 % Favored : 90.10 % Rotamer: Outliers : 3.46 % Allowed : 26.99 % Favored : 69.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.21), residues: 1529 helix: -1.45 (0.41), residues: 158 sheet: -1.73 (0.34), residues: 227 loop : -2.15 (0.18), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C2289 HIS 0.004 0.001 HIS F2395 PHE 0.024 0.002 PHE B1408 TYR 0.026 0.002 TYR B1311 ARG 0.009 0.000 ARG B1304 Details of bonding type rmsd link_NAG-ASN : bond 0.00713 ( 7) link_NAG-ASN : angle 4.11808 ( 21) hydrogen bonds : bond 0.03558 ( 241) hydrogen bonds : angle 6.98901 ( 567) SS BOND : bond 0.00296 ( 56) SS BOND : angle 1.34130 ( 112) covalent geometry : bond 0.00316 (11752) covalent geometry : angle 0.77845 (16039) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4883.74 seconds wall clock time: 88 minutes 7.11 seconds (5287.11 seconds total)