Starting phenix.real_space_refine on Tue Jun 17 20:47:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rde_19070/06_2025/8rde_19070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rde_19070/06_2025/8rde_19070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rde_19070/06_2025/8rde_19070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rde_19070/06_2025/8rde_19070.map" model { file = "/net/cci-nas-00/data/ceres_data/8rde_19070/06_2025/8rde_19070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rde_19070/06_2025/8rde_19070.cif" } resolution = 3.7 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= 0.012 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 8 9.91 5 S 242 5.16 5 C 12444 2.51 5 N 3454 2.21 5 O 3902 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 20050 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1342, 9928 Classifications: {'peptide': 1342} Link IDs: {'PTRANS': 100, 'TRANS': 1241} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1342, 9928 Classifications: {'peptide': 1342} Link IDs: {'PTRANS': 100, 'TRANS': 1241} Chain breaks: 2 bond proxies already assigned to first conformer: 10182 Chain: "D" Number of atoms: 9937 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1342, 9928 Classifications: {'peptide': 1342} Link IDs: {'PTRANS': 100, 'TRANS': 1241} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1342, 9928 Classifications: {'peptide': 1342} Link IDs: {'PTRANS': 100, 'TRANS': 1241} Chain breaks: 2 bond proxies already assigned to first conformer: 10182 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Unusual residues: {' CA': 4, 'NAG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AGLU A2012 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU A2012 " occ=0.50 residue: pdb=" N AGLU D2012 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU D2012 " occ=0.50 Time building chain proxies: 21.71, per 1000 atoms: 1.08 Number of scatterers: 20050 At special positions: 0 Unit cell: (165.12, 137.6, 105.78, 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 8 19.99 S 242 16.00 O 3902 8.00 N 3454 7.00 C 12444 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=106, symmetry=0 Simple disulfide: pdb=" SG CYS A1275 " - pdb=" SG CYS A1433 " distance=2.03 Simple disulfide: pdb=" SG CYS A1284 " - pdb=" SG CYS A1392 " distance=2.03 Simple disulfide: pdb=" SG CYS A1437 " - pdb=" SG CYS A1441 " distance=2.04 Simple disulfide: pdb=" SG CYS A1444 " - pdb=" SG CYS A1490 " distance=2.03 Simple disulfide: pdb=" SG CYS A1458 " - pdb=" SG CYS A1485 " distance=2.03 Simple disulfide: pdb=" SG CYS A1472 " - pdb=" SG CYS A1510 " distance=2.03 Simple disulfide: pdb=" SG CYS A1500 " - pdb=" SG CYS A1526 " distance=2.03 Simple disulfide: pdb=" SG CYS A1530 " - pdb=" SG CYS A1567 " distance=2.05 Simple disulfide: pdb=" SG CYS A1539 " - pdb=" SG CYS A1563 " distance=2.03 Simple disulfide: pdb=" SG CYS A1543 " - pdb=" SG CYS A1559 " distance=2.03 Simple disulfide: pdb=" SG CYS A1547 " - pdb=" SG CYS A1587 " distance=2.03 Simple disulfide: pdb=" SG CYS A1569 " - pdb=" SG CYS A1580 " distance=2.03 Simple disulfide: pdb=" SG CYS A1589 " - pdb=" SG CYS A1614 " distance=2.03 Simple disulfide: pdb=" SG CYS A1608 " - pdb=" SG CYS A1634 " distance=2.03 Simple disulfide: pdb=" SG CYS A1612 " - pdb=" SG CYS A1623 " distance=2.03 Simple disulfide: pdb=" SG CYS A1628 " - pdb=" SG CYS A1644 " distance=2.03 Simple disulfide: pdb=" SG CYS A1652 " - pdb=" SG CYS A1791 " distance=2.00 Simple disulfide: pdb=" SG CYS A1674 " - pdb=" SG CYS A1820 " distance=2.03 Simple disulfide: pdb=" SG CYS A1682 " - pdb=" SG CYS A1788 " distance=2.03 Simple disulfide: pdb=" SG CYS A1823 " - pdb=" SG CYS A1828 " distance=2.04 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1877 " distance=2.03 Simple disulfide: pdb=" SG CYS A1846 " - pdb=" SG CYS A1872 " distance=2.03 Simple disulfide: pdb=" SG CYS A1859 " - pdb=" SG CYS A1897 " distance=2.03 Simple disulfide: pdb=" SG CYS A1887 " - pdb=" SG CYS A1913 " distance=2.03 Simple disulfide: pdb=" SG CYS A1917 " - pdb=" SG CYS A1951 " distance=2.03 Simple disulfide: pdb=" SG CYS A1926 " - pdb=" SG CYS A1947 " distance=2.03 Simple disulfide: pdb=" SG CYS A1930 " - pdb=" SG CYS A1943 " distance=2.03 Simple disulfide: pdb=" SG CYS A1934 " - pdb=" SG CYS A1970 " distance=2.03 Simple disulfide: pdb=" SG CYS A1953 " - pdb=" SG CYS A1964 " distance=2.03 Simple disulfide: pdb=" SG CYS A1972 " - pdb=" SG CYS A1997 " distance=2.03 Simple disulfide: pdb=" SG CYS A1991 " - pdb=" SG CYS A2017 " distance=2.03 Simple disulfide: pdb=" SG CYS A1995 " - pdb=" SG CYS A2005 " distance=2.03 Simple disulfide: pdb=" SG CYS A2011 " - pdb=" SG CYS A2026 " distance=2.03 Simple disulfide: pdb=" SG CYS A2034 " - pdb=" SG CYS A2164 " distance=2.03 Simple disulfide: pdb=" SG CYS A2056 " - pdb=" SG CYS A2202 " distance=2.04 Simple disulfide: pdb=" SG CYS A2064 " - pdb=" SG CYS A2161 " distance=2.03 Simple disulfide: pdb=" SG CYS A2206 " - pdb=" SG CYS A2211 " distance=2.04 Simple disulfide: pdb=" SG CYS A2214 " - pdb=" SG CYS A2259 " distance=2.03 Simple disulfide: pdb=" SG CYS A2228 " - pdb=" SG CYS A2254 " distance=2.03 Simple disulfide: pdb=" SG CYS A2241 " - pdb=" SG CYS A2279 " distance=2.03 Simple disulfide: pdb=" SG CYS A2269 " - pdb=" SG CYS A2295 " distance=2.04 Simple disulfide: pdb=" SG CYS A2299 " - pdb=" SG CYS A2333 " distance=2.03 Simple disulfide: pdb=" SG CYS A2308 " - pdb=" SG CYS A2329 " distance=2.03 Simple disulfide: pdb=" SG CYS A2312 " - pdb=" SG CYS A2325 " distance=2.03 Simple disulfide: pdb=" SG CYS A2316 " - pdb=" SG CYS A2352 " distance=2.03 Simple disulfide: pdb=" SG CYS A2335 " - pdb=" SG CYS A2346 " distance=2.03 Simple disulfide: pdb=" SG CYS A2354 " - pdb=" SG CYS A2378 " distance=2.03 Simple disulfide: pdb=" SG CYS A2372 " - pdb=" SG CYS A2397 " distance=2.03 Simple disulfide: pdb=" SG CYS A2376 " - pdb=" SG CYS A2386 " distance=2.03 Simple disulfide: pdb=" SG CYS A2391 " - pdb=" SG CYS A2406 " distance=2.03 Simple disulfide: pdb=" SG CYS A2413 " - pdb=" SG CYS A2550 " distance=2.03 Simple disulfide: pdb=" SG CYS A2443 " - pdb=" SG CYS A2547 " distance=2.03 Simple disulfide: pdb=" SG CYS A2462 " - pdb=" SG CYS D2581 " distance=2.02 Simple disulfide: pdb=" SG CYS A2581 " - pdb=" SG CYS D2462 " distance=2.06 Simple disulfide: pdb=" SG CYS D1275 " - pdb=" SG CYS D1433 " distance=2.03 Simple disulfide: pdb=" SG CYS D1284 " - pdb=" SG CYS D1392 " distance=2.03 Simple disulfide: pdb=" SG CYS D1437 " - pdb=" SG CYS D1441 " distance=2.04 Simple disulfide: pdb=" SG CYS D1444 " - pdb=" SG CYS D1490 " distance=2.03 Simple disulfide: pdb=" SG CYS D1458 " - pdb=" SG CYS D1485 " distance=2.03 Simple disulfide: pdb=" SG CYS D1472 " - pdb=" SG CYS D1510 " distance=2.03 Simple disulfide: pdb=" SG CYS D1500 " - pdb=" SG CYS D1526 " distance=2.03 Simple disulfide: pdb=" SG CYS D1530 " - pdb=" SG CYS D1567 " distance=2.05 Simple disulfide: pdb=" SG CYS D1539 " - pdb=" SG CYS D1563 " distance=2.03 Simple disulfide: pdb=" SG CYS D1543 " - pdb=" SG CYS D1559 " distance=2.03 Simple disulfide: pdb=" SG CYS D1547 " - pdb=" SG CYS D1587 " distance=2.03 Simple disulfide: pdb=" SG CYS D1569 " - pdb=" SG CYS D1580 " distance=2.03 Simple disulfide: pdb=" SG CYS D1589 " - pdb=" SG CYS D1614 " distance=2.03 Simple disulfide: pdb=" SG CYS D1608 " - pdb=" SG CYS D1634 " distance=2.03 Simple disulfide: pdb=" SG CYS D1612 " - pdb=" SG CYS D1623 " distance=2.03 Simple disulfide: pdb=" SG CYS D1628 " - pdb=" SG CYS D1644 " distance=2.03 Simple disulfide: pdb=" SG CYS D1652 " - pdb=" SG CYS D1791 " distance=2.07 Simple disulfide: pdb=" SG CYS D1674 " - pdb=" SG CYS D1820 " distance=2.03 Simple disulfide: pdb=" SG CYS D1682 " - pdb=" SG CYS D1788 " distance=2.03 Simple disulfide: pdb=" SG CYS D1823 " - pdb=" SG CYS D1828 " distance=2.04 Simple disulfide: pdb=" SG CYS D1832 " - pdb=" SG CYS D1877 " distance=2.03 Simple disulfide: pdb=" SG CYS D1846 " - pdb=" SG CYS D1872 " distance=2.03 Simple disulfide: pdb=" SG CYS D1859 " - pdb=" SG CYS D1897 " distance=2.03 Simple disulfide: pdb=" SG CYS D1887 " - pdb=" SG CYS D1913 " distance=2.03 Simple disulfide: pdb=" SG CYS D1917 " - pdb=" SG CYS D1951 " distance=2.03 Simple disulfide: pdb=" SG CYS D1926 " - pdb=" SG CYS D1947 " distance=2.03 Simple disulfide: pdb=" SG CYS D1930 " - pdb=" SG CYS D1943 " distance=2.03 Simple disulfide: pdb=" SG CYS D1934 " - pdb=" SG CYS D1970 " distance=2.03 Simple disulfide: pdb=" SG CYS D1953 " - pdb=" SG CYS D1964 " distance=2.03 Simple disulfide: pdb=" SG CYS D1972 " - pdb=" SG CYS D1997 " distance=2.03 Simple disulfide: pdb=" SG CYS D1991 " - pdb=" SG CYS D2017 " distance=2.03 Simple disulfide: pdb=" SG CYS D1995 " - pdb=" SG CYS D2005 " distance=2.03 Simple disulfide: pdb=" SG CYS D2011 " - pdb=" SG CYS D2026 " distance=2.04 Simple disulfide: pdb=" SG CYS D2034 " - pdb=" SG CYS D2164 " distance=2.03 Simple disulfide: pdb=" SG CYS D2056 " - pdb=" SG CYS D2202 " distance=2.04 Simple disulfide: pdb=" SG CYS D2064 " - pdb=" SG CYS D2161 " distance=2.03 Simple disulfide: pdb=" SG CYS D2206 " - pdb=" SG CYS D2211 " distance=2.04 Simple disulfide: pdb=" SG CYS D2214 " - pdb=" SG CYS D2259 " distance=2.03 Simple disulfide: pdb=" SG CYS D2228 " - pdb=" SG CYS D2254 " distance=2.03 Simple disulfide: pdb=" SG CYS D2241 " - pdb=" SG CYS D2279 " distance=2.03 Simple disulfide: pdb=" SG CYS D2269 " - pdb=" SG CYS D2295 " distance=2.04 Simple disulfide: pdb=" SG CYS D2299 " - pdb=" SG CYS D2333 " distance=2.03 Simple disulfide: pdb=" SG CYS D2308 " - pdb=" SG CYS D2329 " distance=2.03 Simple disulfide: pdb=" SG CYS D2312 " - pdb=" SG CYS D2325 " distance=2.03 Simple disulfide: pdb=" SG CYS D2316 " - pdb=" SG CYS D2352 " distance=2.03 Simple disulfide: pdb=" SG CYS D2335 " - pdb=" SG CYS D2346 " distance=2.03 Simple disulfide: pdb=" SG CYS D2354 " - pdb=" SG CYS D2378 " distance=2.03 Simple disulfide: pdb=" SG CYS D2372 " - pdb=" SG CYS D2397 " distance=2.03 Simple disulfide: pdb=" SG CYS D2376 " - pdb=" SG CYS D2386 " distance=2.03 Simple disulfide: pdb=" SG CYS D2391 " - pdb=" SG CYS D2406 " distance=2.03 Simple disulfide: pdb=" SG CYS D2413 " - pdb=" SG CYS D2550 " distance=2.03 Simple disulfide: pdb=" SG CYS D2443 " - pdb=" SG CYS D2547 " 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=2, symmetry=0 Links applied NAG-ASN " NAG A5601 " - " ASN A1250 " " NAG A5603 " - " ASN A1410 " " NAG A5607 " - " ASN A2364 " " NAG A5608 " - " ASN A2420 " " NAG A5609 " - " ASN A2170 " " NAG A5610 " - " ASN A1693 " " NAG D5601 " - " ASN D1250 " " NAG D5603 " - " ASN D1410 " " NAG D5607 " - " ASN D2364 " " NAG D5608 " - " ASN D2420 " " NAG D5609 " - " ASN D2170 " " NAG D5610 " - " ASN D1693 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.26 Conformation dependent library (CDL) restraints added in 5.2 seconds 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4768 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 40 sheets defined 14.4% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.06 Creating SS restraints... Processing helix chain 'A' and resid 1402 through 1406 removed outlier: 3.724A pdb=" N GLN A1406 " --> pdb=" O GLN A1403 " (cutoff:3.500A) Processing helix chain 'A' and resid 1416 through 1423 Processing helix chain 'A' and resid 1448 through 1454 Processing helix chain 'A' and resid 1471 through 1476 removed outlier: 3.578A pdb=" N HIS A1475 " --> pdb=" O SER A1471 " (cutoff:3.500A) Processing helix chain 'A' and resid 1478 through 1492 Processing helix chain 'A' and resid 1495 through 1512 removed outlier: 3.981A pdb=" N LEU A1499 " --> pdb=" O SER A1495 " (cutoff:3.500A) Processing helix chain 'A' and resid 1520 through 1525 Processing helix chain 'A' and resid 1858 through 1863 removed outlier: 4.324A pdb=" N LEU A1862 " --> pdb=" O PRO A1858 " (cutoff:3.500A) Processing helix chain 'A' and resid 1865 through 1879 removed outlier: 4.109A pdb=" N ALA A1871 " --> pdb=" O GLN A1867 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N CYS A1872 " --> pdb=" O TYR A1868 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU A1873 " --> pdb=" O PHE A1869 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A1874 " --> pdb=" O GLU A1870 " (cutoff:3.500A) Processing helix chain 'A' and resid 1882 through 1900 Proline residue: A1888 - end of helix removed outlier: 4.150A pdb=" N ALA A1900 " --> pdb=" O ALA A1896 " (cutoff:3.500A) Processing helix chain 'A' and resid 2170 through 2175 removed outlier: 3.604A pdb=" N ASP A2174 " --> pdb=" O ASN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2212 through 2221 removed outlier: 4.448A pdb=" N THR A2219 " --> pdb=" O LEU A2215 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN A2220 " --> pdb=" O ALA A2216 " (cutoff:3.500A) Processing helix chain 'A' and resid 2221 through 2233 removed outlier: 4.002A pdb=" N ASN A2225 " --> pdb=" O ALA A2221 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS A2228 " --> pdb=" O LYS A2224 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A2231 " --> pdb=" O ALA A2227 " (cutoff:3.500A) Processing helix chain 'A' and resid 2240 through 2245 Processing helix chain 'A' and resid 2247 through 2257 Processing helix chain 'A' and resid 2265 through 2279 Processing helix chain 'A' and resid 2280 through 2282 No H-bonds generated for 'chain 'A' and resid 2280 through 2282' Processing helix chain 'A' and resid 2323 through 2328 Processing helix chain 'A' and resid 2462 through 2466 removed outlier: 3.762A pdb=" N ASN A2465 " --> pdb=" O CYS A2462 " (cutoff:3.500A) Processing helix chain 'A' and resid 2556 through 2562 Processing helix chain 'A' and resid 2568 through 2573 removed outlier: 3.719A pdb=" N LYS A2572 " --> pdb=" O THR A2568 " (cutoff:3.500A) Processing helix chain 'D' and resid 1402 through 1406 removed outlier: 3.723A pdb=" N GLN D1406 " --> pdb=" O GLN D1403 " (cutoff:3.500A) Processing helix chain 'D' and resid 1416 through 1423 Processing helix chain 'D' and resid 1448 through 1454 Processing helix chain 'D' and resid 1471 through 1476 removed outlier: 3.578A pdb=" N HIS D1475 " --> pdb=" O SER D1471 " (cutoff:3.500A) Processing helix chain 'D' and resid 1478 through 1492 Processing helix chain 'D' and resid 1495 through 1512 removed outlier: 3.982A pdb=" N LEU D1499 " --> pdb=" O SER D1495 " (cutoff:3.500A) Processing helix chain 'D' and resid 1520 through 1525 Processing helix chain 'D' and resid 1858 through 1863 removed outlier: 4.324A pdb=" N LEU D1862 " --> pdb=" O PRO D1858 " (cutoff:3.500A) Processing helix chain 'D' and resid 1865 through 1879 removed outlier: 4.109A pdb=" N ALA D1871 " --> pdb=" O GLN D1867 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N CYS D1872 " --> pdb=" O TYR D1868 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D1873 " --> pdb=" O PHE D1869 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU D1874 " --> pdb=" O GLU D1870 " (cutoff:3.500A) Processing helix chain 'D' and resid 1882 through 1900 Proline residue: D1888 - end of helix removed outlier: 4.149A pdb=" N ALA D1900 " --> pdb=" O ALA D1896 " (cutoff:3.500A) Processing helix chain 'D' and resid 2170 through 2175 removed outlier: 3.604A pdb=" N ASP D2174 " --> pdb=" O ASN D2170 " (cutoff:3.500A) Processing helix chain 'D' and resid 2212 through 2221 removed outlier: 4.449A pdb=" N THR D2219 " --> pdb=" O LEU D2215 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN D2220 " --> pdb=" O ALA D2216 " (cutoff:3.500A) Processing helix chain 'D' and resid 2221 through 2233 removed outlier: 4.002A pdb=" N ASN D2225 " --> pdb=" O ALA D2221 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS D2228 " --> pdb=" O LYS D2224 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE D2231 " --> pdb=" O ALA D2227 " (cutoff:3.500A) Processing helix chain 'D' and resid 2240 through 2245 Processing helix chain 'D' and resid 2247 through 2257 Processing helix chain 'D' and resid 2265 through 2279 Processing helix chain 'D' and resid 2280 through 2282 No H-bonds generated for 'chain 'D' and resid 2280 through 2282' Processing helix chain 'D' and resid 2323 through 2328 Processing helix chain 'D' and resid 2462 through 2466 removed outlier: 3.762A pdb=" N ASN D2465 " --> pdb=" O CYS D2462 " (cutoff:3.500A) Processing helix chain 'D' and resid 2556 through 2562 Processing helix chain 'D' and resid 2568 through 2573 removed outlier: 3.718A pdb=" N LYS D2572 " --> pdb=" O THR D2568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1268 through 1269 removed outlier: 3.822A pdb=" N ARG A1378 " --> pdb=" O ASP A1374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL A1371 " --> pdb=" O LEU A1363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1323 through 1326 removed outlier: 5.352A pdb=" N VAL A1312 " --> pdb=" O GLU A1302 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU A1302 " --> pdb=" O VAL A1312 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN A1314 " --> pdb=" O LYS A1300 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR A1299 " --> pdb=" O LEU A1278 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU A1278 " --> pdb=" O THR A1299 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1535 through 1540 removed outlier: 4.542A pdb=" N CYS A1539 " --> pdb=" O VAL A1564 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL A1564 " --> pdb=" O CYS A1539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1574 through 1576 Processing sheet with id=AA5, first strand: chain 'A' and resid 1613 through 1615 removed outlier: 3.629A pdb=" N SER A1620 " --> pdb=" O GLY A1615 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1632 through 1636 Processing sheet with id=AA7, first strand: chain 'A' and resid 1649 through 1654 removed outlier: 3.628A pdb=" N VAL A1775 " --> pdb=" O ALA A1654 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASN A1760 " --> pdb=" O SER A1749 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1659 through 1661 Processing sheet with id=AA9, first strand: chain 'A' and resid 1676 through 1678 removed outlier: 6.513A pdb=" N THR A1695 " --> pdb=" O VAL A1712 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N VAL A1712 " --> pdb=" O THR A1695 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A1697 " --> pdb=" O ARG A1710 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN A1732 " --> pdb=" O THR A1722 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU A1731 " --> pdb=" O VAL A1738 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1921 through 1927 removed outlier: 4.098A pdb=" N CYS A1926 " --> pdb=" O ARG A1948 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG A1948 " --> pdb=" O CYS A1926 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1972 through 1974 Processing sheet with id=AB3, first strand: chain 'A' and resid 1984 through 1985 Processing sheet with id=AB4, first strand: chain 'A' and resid 2015 through 2020 Processing sheet with id=AB5, first strand: chain 'A' and resid 2032 through 2036 removed outlier: 3.774A pdb=" N ILE A2148 " --> pdb=" O ALA A2036 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2095 through 2097 removed outlier: 3.741A pdb=" N VAL A2089 " --> pdb=" O VAL A2076 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A2076 " --> pdb=" O VAL A2089 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A2091 " --> pdb=" O SER A2074 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A2074 " --> pdb=" O THR A2091 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N PHE A2073 " --> pdb=" O VAL A2063 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL A2063 " --> pdb=" O PHE A2073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA A2061 " --> pdb=" O ILE A2075 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU A2077 " --> pdb=" O VAL A2059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL A2059 " --> pdb=" O LEU A2077 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER A2062 " --> pdb=" O CYS A2161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS A2161 " --> pdb=" O SER A2062 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2303 through 2305 Processing sheet with id=AB8, first strand: chain 'A' and resid 2396 through 2400 removed outlier: 3.963A pdb=" N GLU A2405 " --> pdb=" O GLU A2398 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 2420 through 2422 removed outlier: 4.543A pdb=" N ASN A2420 " --> pdb=" O SER A2416 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER A2416 " --> pdb=" O ASN A2420 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU A2534 " --> pdb=" O ILE A2415 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA A2500 " --> pdb=" O VAL A2508 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2435 through 2441 removed outlier: 3.510A pdb=" N ALA A2457 " --> pdb=" O TYR A2437 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A2455 " --> pdb=" O LEU A2439 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2472 through 2476 removed outlier: 3.570A pdb=" N VAL A2483 " --> pdb=" O VAL A2472 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA A2489 " --> pdb=" O VAL A2496 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 1268 through 1269 removed outlier: 3.508A pdb=" N SER D1251 " --> pdb=" O LEU D1383 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG D1378 " --> pdb=" O ASP D1374 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL D1371 " --> pdb=" O LEU D1363 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 1323 through 1326 removed outlier: 5.351A pdb=" N VAL D1312 " --> pdb=" O GLU D1302 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N GLU D1302 " --> pdb=" O VAL D1312 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLN D1314 " --> pdb=" O LYS D1300 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D1299 " --> pdb=" O LEU D1278 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LEU D1278 " --> pdb=" O THR D1299 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 1535 through 1540 removed outlier: 4.542A pdb=" N CYS D1539 " --> pdb=" O VAL D1564 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL D1564 " --> pdb=" O CYS D1539 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 1574 through 1576 Processing sheet with id=AC7, first strand: chain 'D' and resid 1613 through 1615 removed outlier: 3.630A pdb=" N SER D1620 " --> pdb=" O GLY D1615 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 1632 through 1636 Processing sheet with id=AC9, first strand: chain 'D' and resid 1649 through 1654 removed outlier: 3.572A pdb=" N VAL D1775 " --> pdb=" O ALA D1654 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN D1760 " --> pdb=" O SER D1749 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 1659 through 1661 Processing sheet with id=AD2, first strand: chain 'D' and resid 1676 through 1678 removed outlier: 6.513A pdb=" N THR D1695 " --> pdb=" O VAL D1712 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL D1712 " --> pdb=" O THR D1695 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA D1697 " --> pdb=" O ARG D1710 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLN D1732 " --> pdb=" O THR D1722 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU D1731 " --> pdb=" O VAL D1738 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 1921 through 1927 removed outlier: 4.098A pdb=" N CYS D1926 " --> pdb=" O ARG D1948 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ARG D1948 " --> pdb=" O CYS D1926 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 1972 through 1974 Processing sheet with id=AD5, first strand: chain 'D' and resid 1984 through 1985 Processing sheet with id=AD6, first strand: chain 'D' and resid 2015 through 2020 Processing sheet with id=AD7, first strand: chain 'D' and resid 2032 through 2036 removed outlier: 3.775A pdb=" N ILE D2148 " --> pdb=" O ALA D2036 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 2095 through 2097 removed outlier: 3.740A pdb=" N VAL D2089 " --> pdb=" O VAL D2076 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL D2076 " --> pdb=" O VAL D2089 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR D2091 " --> pdb=" O SER D2074 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER D2074 " --> pdb=" O THR D2091 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N PHE D2073 " --> pdb=" O VAL D2063 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N VAL D2063 " --> pdb=" O PHE D2073 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA D2061 " --> pdb=" O ILE D2075 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU D2077 " --> pdb=" O VAL D2059 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N VAL D2059 " --> pdb=" O LEU D2077 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER D2062 " --> pdb=" O CYS D2161 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS D2161 " --> pdb=" O SER D2062 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 2303 through 2305 Processing sheet with id=AE1, first strand: chain 'D' and resid 2396 through 2400 removed outlier: 3.964A pdb=" N GLU D2405 " --> pdb=" O GLU D2398 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 2420 through 2422 removed outlier: 4.543A pdb=" N ASN D2420 " --> pdb=" O SER D2416 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER D2416 " --> pdb=" O ASN D2420 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N LEU D2534 " --> pdb=" O ILE D2415 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA D2500 " --> pdb=" O VAL D2508 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 2435 through 2441 removed outlier: 3.510A pdb=" N ALA D2457 " --> pdb=" O TYR D2437 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL D2455 " --> pdb=" O LEU D2439 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 2472 through 2476 removed outlier: 3.570A pdb=" N VAL D2483 " --> pdb=" O VAL D2472 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ALA D2489 " --> pdb=" O VAL D2496 " (cutoff:3.500A) 527 hydrogen bonds defined for protein. 1344 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.43 Time building geometry restraints manager: 6.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6672 1.34 - 1.46: 4351 1.46 - 1.58: 9281 1.58 - 1.71: 2 1.71 - 1.83: 266 Bond restraints: 20572 Sorted by residual: bond pdb=" N PRO A1582 " pdb=" CD PRO A1582 " ideal model delta sigma weight residual 1.473 1.601 -0.128 1.40e-02 5.10e+03 8.41e+01 bond pdb=" N PRO D1582 " pdb=" CD PRO D1582 " ideal model delta sigma weight residual 1.473 1.601 -0.128 1.40e-02 5.10e+03 8.36e+01 bond pdb=" N PRO A2234 " pdb=" CD PRO A2234 " ideal model delta sigma weight residual 1.473 1.362 0.111 1.40e-02 5.10e+03 6.24e+01 bond pdb=" N PRO D2234 " pdb=" CD PRO D2234 " ideal model delta sigma weight residual 1.473 1.363 0.110 1.40e-02 5.10e+03 6.23e+01 bond pdb=" N THR D2568 " pdb=" CA THR D2568 " ideal model delta sigma weight residual 1.458 1.494 -0.036 7.40e-03 1.83e+04 2.34e+01 ... (remaining 20567 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 26997 2.31 - 4.62: 942 4.62 - 6.94: 111 6.94 - 9.25: 24 9.25 - 11.56: 12 Bond angle restraints: 28086 Sorted by residual: angle pdb=" C ASP A2292 " pdb=" CA ASP A2292 " pdb=" CB ASP A2292 " ideal model delta sigma weight residual 116.54 105.21 11.33 1.15e+00 7.56e-01 9.71e+01 angle pdb=" C ASP D2292 " pdb=" CA ASP D2292 " pdb=" CB ASP D2292 " ideal model delta sigma weight residual 116.54 105.22 11.32 1.15e+00 7.56e-01 9.68e+01 angle pdb=" N VAL A2107 " pdb=" CA VAL A2107 " pdb=" C VAL A2107 " ideal model delta sigma weight residual 109.58 99.24 10.34 1.29e+00 6.01e-01 6.42e+01 angle pdb=" N VAL D2107 " pdb=" CA VAL D2107 " pdb=" C VAL D2107 " ideal model delta sigma weight residual 109.58 99.25 10.33 1.29e+00 6.01e-01 6.42e+01 angle pdb=" N HIS A1743 " pdb=" CA HIS A1743 " pdb=" C HIS A1743 " ideal model delta sigma weight residual 108.52 120.08 -11.56 1.63e+00 3.76e-01 5.03e+01 ... (remaining 28081 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.92: 11901 24.92 - 49.84: 517 49.84 - 74.76: 110 74.76 - 99.68: 22 99.68 - 124.60: 8 Dihedral angle restraints: 12558 sinusoidal: 5026 harmonic: 7532 Sorted by residual: dihedral pdb=" CB CYS A2462 " pdb=" SG CYS A2462 " pdb=" SG CYS D2581 " pdb=" CB CYS D2581 " ideal model delta sinusoidal sigma weight residual -86.00 -140.79 54.79 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CB CYS A2581 " pdb=" SG CYS A2581 " pdb=" SG CYS D2462 " pdb=" CB CYS D2462 " ideal model delta sinusoidal sigma weight residual -86.00 -139.35 53.35 1 1.00e+01 1.00e-02 3.87e+01 dihedral pdb=" CB CYS A2443 " pdb=" SG CYS A2443 " pdb=" SG CYS A2547 " pdb=" CB CYS A2547 " ideal model delta sinusoidal sigma weight residual 93.00 139.52 -46.52 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 12555 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 2930 0.118 - 0.236: 112 0.236 - 0.354: 18 0.354 - 0.472: 8 0.472 - 0.590: 4 Chirality restraints: 3072 Sorted by residual: chirality pdb=" CA VAL D2107 " pdb=" N VAL D2107 " pdb=" C VAL D2107 " pdb=" CB VAL D2107 " both_signs ideal model delta sigma weight residual False 2.44 3.03 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CA VAL A2107 " pdb=" N VAL A2107 " pdb=" C VAL A2107 " pdb=" CB VAL A2107 " both_signs ideal model delta sigma weight residual False 2.44 3.03 -0.59 2.00e-01 2.50e+01 8.67e+00 chirality pdb=" C1 NAG A5608 " pdb=" ND2 ASN A2420 " pdb=" C2 NAG A5608 " pdb=" O5 NAG A5608 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.45e+00 ... (remaining 3069 not shown) Planarity restraints: 3762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D1581 " -0.050 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO D1582 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D1582 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D1582 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A1581 " 0.050 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO A1582 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A1582 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A1582 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A1548 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.71e+00 pdb=" N PRO A1549 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO A1549 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A1549 " 0.030 5.00e-02 4.00e+02 ... (remaining 3759 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 53 2.28 - 2.94: 9326 2.94 - 3.59: 29763 3.59 - 4.25: 45015 4.25 - 4.90: 72189 Nonbonded interactions: 156346 Sorted by model distance: nonbonded pdb=" OD1 ASP A2233 " pdb=" CD PRO A2234 " model vdw 1.626 3.440 nonbonded pdb=" OD1 ASP D2233 " pdb=" CD PRO D2234 " model vdw 1.627 3.440 nonbonded pdb=" OD1 ASP D1399 " pdb="CA CA D5602 " model vdw 2.001 2.510 nonbonded pdb=" OD1 ASP A1399 " pdb="CA CA A5602 " model vdw 2.002 2.510 nonbonded pdb=" OD1 ASP D1405 " pdb="CA CA D5602 " model vdw 2.010 2.510 ... (remaining 156341 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } 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: 3.170 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: 0.040 Extract box with map and model: 0.860 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 63.900 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.140 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5885 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 : 0.006 0.155 20692 Z= 0.396 Angle : 0.971 16.237 28334 Z= 0.627 Chirality : 0.064 0.590 3072 Planarity : 0.005 0.070 3750 Dihedral : 14.616 124.597 7472 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 5.53 % Allowed : 11.80 % Favored : 82.67 % Cbeta Deviations : 0.17 % 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: -2.02 (0.16), residues: 2678 helix: -0.34 (0.29), residues: 330 sheet: -0.64 (0.24), residues: 524 loop : -1.87 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1727 HIS 0.004 0.001 HIS D2242 PHE 0.012 0.001 PHE A2330 TYR 0.011 0.001 TYR A1751 ARG 0.003 0.000 ARG D2290 Details of bonding type rmsd link_NAG-ASN : bond 0.01465 ( 12) link_NAG-ASN : angle 5.56889 ( 36) hydrogen bonds : bond 0.19295 ( 527) hydrogen bonds : angle 7.71240 ( 1344) SS BOND : bond 0.00709 ( 106) SS BOND : angle 1.24486 ( 212) covalent geometry : bond 0.00534 (20572) covalent geometry : angle 0.94825 (28086) Misc. bond : bond 0.15470 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 248 time to evaluate : 2.257 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: A 1341 MET cc_start: 0.6040 (mmm) cc_final: 0.5318 (mmm) REVERT: A 2011 CYS cc_start: 0.3844 (OUTLIER) cc_final: 0.3639 (p) REVERT: D 1601 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5217 (tm-30) outliers start: 116 outliers final: 29 residues processed: 344 average time/residue: 0.2912 time to fit residues: 159.7577 Evaluate side-chains 146 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 115 time to evaluate : 2.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1369 LEU Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1799 ASN Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 2011 CYS Chi-restraints excluded: chain A residue 2087 ARG Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2170 ASN Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2534 LEU Chi-restraints excluded: chain A residue 2560 ASP Chi-restraints excluded: chain A residue 2567 LYS Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1664 ASP Chi-restraints excluded: chain D residue 1850 THR Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2170 ASN Chi-restraints excluded: chain D residue 2173 ASP Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2560 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 226 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 108 optimal weight: 8.9990 chunk 210 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 chunk 156 optimal weight: 0.0470 chunk 243 optimal weight: 9.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1260 HIS A2037 ASN ** A2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1329 ASN ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1882 HIS ** D2356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.076491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.060581 restraints weight = 199226.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.063768 restraints weight = 99131.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065464 restraints weight = 49234.250| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3542 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3542 r_free = 0.3542 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3542 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20692 Z= 0.144 Angle : 0.785 15.046 28334 Z= 0.392 Chirality : 0.051 0.452 3072 Planarity : 0.006 0.084 3750 Dihedral : 10.663 111.270 3157 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.36 % Allowed : 15.35 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.08 (0.16), residues: 2678 helix: -1.13 (0.26), residues: 340 sheet: -0.41 (0.25), residues: 504 loop : -1.83 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1655 HIS 0.008 0.001 HIS D2463 PHE 0.034 0.002 PHE D1269 TYR 0.021 0.002 TYR A2453 ARG 0.009 0.001 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00833 ( 12) link_NAG-ASN : angle 4.06674 ( 36) hydrogen bonds : bond 0.04460 ( 527) hydrogen bonds : angle 6.41033 ( 1344) SS BOND : bond 0.00365 ( 106) SS BOND : angle 1.56257 ( 212) covalent geometry : bond 0.00327 (20572) covalent geometry : angle 0.76257 (28086) Misc. bond : bond 0.00204 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 140 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1341 MET cc_start: 0.7336 (mmm) cc_final: 0.6752 (mmm) REVERT: A 1573 PHE cc_start: 0.7921 (m-80) cc_final: 0.7708 (m-10) REVERT: A 2368 MET cc_start: 0.7837 (ttp) cc_final: 0.7563 (tpp) REVERT: D 1601 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6317 (tm-30) REVERT: D 2351 ASP cc_start: 0.7427 (t0) cc_final: 0.6826 (t0) REVERT: D 2516 MET cc_start: 0.8366 (mtp) cc_final: 0.8160 (mtt) outliers start: 69 outliers final: 36 residues processed: 196 average time/residue: 0.2562 time to fit residues: 84.8069 Evaluate side-chains 135 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 2.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1495 SER Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2170 ASN Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2361 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2560 ASP Chi-restraints excluded: chain A residue 2567 LYS Chi-restraints excluded: chain D residue 1329 ASN Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1623 CYS Chi-restraints excluded: chain D residue 1736 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 2173 ASP Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2215 LEU Chi-restraints excluded: chain D residue 2345 VAL Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2560 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 135 optimal weight: 4.9990 chunk 204 optimal weight: 20.0000 chunk 221 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 69 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 160 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 256 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1760 ASN A1880 GLN A2041 HIS A2147 HIS ** A2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2520 GLN ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1880 GLN ** 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 = 0.3711 r_free = 0.3711 target = 0.073587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.058105 restraints weight = 201143.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.061083 restraints weight = 91376.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.062874 restraints weight = 48715.857| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 20692 Z= 0.213 Angle : 0.820 15.540 28334 Z= 0.410 Chirality : 0.052 0.498 3072 Planarity : 0.006 0.079 3750 Dihedral : 9.902 111.949 3135 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.59 % Allowed : 16.27 % Favored : 80.14 % Cbeta Deviations : 0.00 % 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: -2.23 (0.15), residues: 2678 helix: -1.32 (0.25), residues: 344 sheet: -0.47 (0.25), residues: 474 loop : -1.90 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D2490 HIS 0.010 0.001 HIS D1327 PHE 0.028 0.002 PHE A2330 TYR 0.018 0.002 TYR A1794 ARG 0.012 0.001 ARG A2157 Details of bonding type rmsd link_NAG-ASN : bond 0.01567 ( 12) link_NAG-ASN : angle 4.80225 ( 36) hydrogen bonds : bond 0.04692 ( 527) hydrogen bonds : angle 6.21418 ( 1344) SS BOND : bond 0.00635 ( 106) SS BOND : angle 1.59671 ( 212) covalent geometry : bond 0.00465 (20572) covalent geometry : angle 0.79360 (28086) Misc. bond : bond 0.00513 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 103 time to evaluate : 2.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1399 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8687 (p0) REVERT: A 1736 GLU cc_start: 0.8860 (pm20) cc_final: 0.8650 (pm20) REVERT: A 2241 CYS cc_start: 0.6117 (OUTLIER) cc_final: 0.5879 (m) REVERT: A 2368 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8219 (tpp) REVERT: D 1601 GLU cc_start: 0.7614 (OUTLIER) cc_final: 0.6089 (tm-30) REVERT: D 1750 VAL cc_start: 0.8674 (t) cc_final: 0.8458 (p) REVERT: D 2351 ASP cc_start: 0.7646 (t0) cc_final: 0.7116 (t0) REVERT: D 2368 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8335 (mmt) REVERT: D 2567 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7473 (mmmt) outliers start: 74 outliers final: 48 residues processed: 163 average time/residue: 0.2557 time to fit residues: 72.5296 Evaluate side-chains 146 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 92 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1399 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1495 SER Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1528 ILE Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2167 PHE Chi-restraints excluded: chain A residue 2170 ASN Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2280 GLN Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2534 LEU Chi-restraints excluded: chain D residue 1274 THR Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1441 CYS Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1623 CYS Chi-restraints excluded: chain D residue 1655 TRP Chi-restraints excluded: chain D residue 1674 CYS Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1772 ASP Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1850 THR Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2173 ASP Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2345 VAL Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2560 ASP Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 204 optimal weight: 7.9990 chunk 245 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 203 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 208 optimal weight: 3.9990 chunk 41 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 37 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1329 ASN A2033 HIS A2133 GLN ** A2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1882 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2133 GLN ** D2356 HIS ** 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 = 0.3632 r_free = 0.3632 target = 0.070496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054547 restraints weight = 200951.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.056794 restraints weight = 93082.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.058297 restraints weight = 57035.093| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 20692 Z= 0.305 Angle : 0.902 13.178 28334 Z= 0.462 Chirality : 0.054 0.543 3072 Planarity : 0.007 0.077 3750 Dihedral : 10.044 116.357 3128 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.29 % Allowed : 16.64 % Favored : 79.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.63 (0.15), residues: 2678 helix: -1.57 (0.25), residues: 328 sheet: -1.03 (0.24), residues: 482 loop : -2.11 (0.13), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D2490 HIS 0.011 0.002 HIS A1553 PHE 0.048 0.003 PHE A2330 TYR 0.025 0.003 TYR A1794 ARG 0.007 0.001 ARG A2157 Details of bonding type rmsd link_NAG-ASN : bond 0.01483 ( 12) link_NAG-ASN : angle 4.30709 ( 36) hydrogen bonds : bond 0.05032 ( 527) hydrogen bonds : angle 6.49297 ( 1344) SS BOND : bond 0.00648 ( 106) SS BOND : angle 1.79461 ( 212) covalent geometry : bond 0.00680 (20572) covalent geometry : angle 0.87861 (28086) Misc. bond : bond 0.00506 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 96 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1341 MET cc_start: 0.8760 (mmm) cc_final: 0.8537 (mmm) REVERT: A 1949 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7383 (tp30) REVERT: A 2368 MET cc_start: 0.8692 (OUTLIER) cc_final: 0.8202 (tpp) REVERT: A 2505 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8904 (p) REVERT: D 1274 THR cc_start: 0.8879 (OUTLIER) cc_final: 0.8579 (p) REVERT: D 1601 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6138 (tm-30) REVERT: D 2351 ASP cc_start: 0.7753 (t0) cc_final: 0.7469 (t0) REVERT: D 2368 MET cc_start: 0.8707 (OUTLIER) cc_final: 0.8292 (mmt) REVERT: D 2511 MET cc_start: 0.9145 (mmm) cc_final: 0.8816 (mmm) outliers start: 89 outliers final: 59 residues processed: 174 average time/residue: 0.2464 time to fit residues: 73.8869 Evaluate side-chains 149 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 84 time to evaluate : 2.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1379 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1528 ILE Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1694 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2167 PHE Chi-restraints excluded: chain A residue 2170 ASN Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2231 ILE Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2280 GLN Chi-restraints excluded: chain A residue 2323 THR Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain D residue 1274 THR Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1356 ASN Chi-restraints excluded: chain D residue 1388 HIS Chi-restraints excluded: chain D residue 1441 CYS Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1557 THR Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1694 VAL Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1850 THR Chi-restraints excluded: chain D residue 1937 LEU Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2161 CYS Chi-restraints excluded: chain D residue 2173 ASP Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2325 CYS Chi-restraints excluded: chain D residue 2339 PHE Chi-restraints excluded: chain D residue 2345 VAL Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2538 VAL Chi-restraints excluded: chain D residue 2560 ASP Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 63 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 114 optimal weight: 8.9990 chunk 181 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 155 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 165 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1653 GLN ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1882 HIS D2133 GLN ** D2356 HIS ** 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 = 0.3683 r_free = 0.3683 target = 0.072530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.057048 restraints weight = 187272.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.059772 restraints weight = 85311.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061537 restraints weight = 47911.678| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20692 Z= 0.141 Angle : 0.750 12.669 28334 Z= 0.374 Chirality : 0.049 0.464 3072 Planarity : 0.006 0.075 3750 Dihedral : 9.206 110.394 3128 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.23 % Allowed : 17.93 % Favored : 78.85 % Cbeta Deviations : 0.00 % 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: -2.40 (0.15), residues: 2678 helix: -1.34 (0.26), residues: 338 sheet: -1.02 (0.23), residues: 506 loop : -1.93 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D2289 HIS 0.006 0.001 HIS A1388 PHE 0.028 0.002 PHE A2330 TYR 0.018 0.002 TYR A1311 ARG 0.006 0.000 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 12) link_NAG-ASN : angle 4.14432 ( 36) hydrogen bonds : bond 0.03997 ( 527) hydrogen bonds : angle 6.01966 ( 1344) SS BOND : bond 0.00351 ( 106) SS BOND : angle 1.43854 ( 212) covalent geometry : bond 0.00325 (20572) covalent geometry : angle 0.72816 (28086) Misc. bond : bond 0.00353 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 104 time to evaluate : 2.161 Fit side-chains REVERT: A 1732 GLN cc_start: 0.7274 (OUTLIER) cc_final: 0.6868 (tp-100) REVERT: A 2368 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8150 (tpp) REVERT: A 2505 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8932 (p) REVERT: D 1601 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6111 (tm-30) REVERT: D 2351 ASP cc_start: 0.7658 (t0) cc_final: 0.7370 (t0) REVERT: D 2368 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8464 (tpp) REVERT: D 2416 SER cc_start: 0.8558 (m) cc_final: 0.8351 (t) REVERT: D 2511 MET cc_start: 0.9043 (mmm) cc_final: 0.8753 (mmm) REVERT: D 2567 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7645 (mmmt) outliers start: 66 outliers final: 43 residues processed: 161 average time/residue: 0.2393 time to fit residues: 68.0820 Evaluate side-chains 143 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 2.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1732 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2167 PHE Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2231 ILE Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1441 CYS Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1736 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1752 ILE Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1850 THR Chi-restraints excluded: chain D residue 1926 CYS Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2335 CYS Chi-restraints excluded: chain D residue 2345 VAL Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 216 optimal weight: 10.0000 chunk 186 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 224 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 56 optimal weight: 0.0670 chunk 204 optimal weight: 0.7980 chunk 258 optimal weight: 4.9990 overall best weight: 1.7122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.072729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.056646 restraints weight = 228455.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.059748 restraints weight = 96998.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.061534 restraints weight = 51049.382| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20692 Z= 0.139 Angle : 0.734 12.509 28334 Z= 0.361 Chirality : 0.048 0.453 3072 Planarity : 0.005 0.074 3750 Dihedral : 8.520 110.453 3121 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 3.32 % Allowed : 17.97 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.28 (0.15), residues: 2678 helix: -1.26 (0.27), residues: 324 sheet: -0.95 (0.23), residues: 504 loop : -1.83 (0.14), residues: 1850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP D2289 HIS 0.008 0.001 HIS A2356 PHE 0.022 0.002 PHE A2330 TYR 0.014 0.001 TYR D1387 ARG 0.005 0.000 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00767 ( 12) link_NAG-ASN : angle 4.27651 ( 36) hydrogen bonds : bond 0.03848 ( 527) hydrogen bonds : angle 5.79804 ( 1344) SS BOND : bond 0.00368 ( 106) SS BOND : angle 1.31602 ( 212) covalent geometry : bond 0.00323 (20572) covalent geometry : angle 0.71213 (28086) Misc. bond : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 101 time to evaluate : 2.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1732 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6936 (mm-40) REVERT: A 2368 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8148 (tpp) REVERT: A 2505 SER cc_start: 0.9110 (OUTLIER) cc_final: 0.8879 (p) REVERT: D 1447 ASP cc_start: 0.8785 (p0) cc_final: 0.8375 (p0) REVERT: D 1601 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.6256 (tm-30) REVERT: D 2351 ASP cc_start: 0.7571 (t0) cc_final: 0.7265 (t0) REVERT: D 2368 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8245 (tpp) REVERT: D 2511 MET cc_start: 0.9026 (mmm) cc_final: 0.8715 (mmm) REVERT: D 2567 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7777 (mmmt) outliers start: 68 outliers final: 50 residues processed: 159 average time/residue: 0.2403 time to fit residues: 68.7063 Evaluate side-chains 150 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 94 time to evaluate : 2.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1495 SER Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1732 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2167 PHE Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2231 ILE Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2505 SER Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1441 CYS Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1693 ASN Chi-restraints excluded: chain D residue 1736 GLU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1926 CYS Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2114 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2325 CYS Chi-restraints excluded: chain D residue 2335 CYS Chi-restraints excluded: chain D residue 2345 VAL Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 118 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 211 optimal weight: 5.9990 chunk 247 optimal weight: 0.0040 chunk 203 optimal weight: 6.9990 chunk 186 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 255 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 139 optimal weight: 7.9990 chunk 52 optimal weight: 7.9990 overall best weight: 2.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1760 ASN ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2356 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 = 0.3660 r_free = 0.3660 target = 0.071531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.056788 restraints weight = 152123.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.059155 restraints weight = 75746.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.060321 restraints weight = 46247.966| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20692 Z= 0.181 Angle : 0.753 11.955 28334 Z= 0.374 Chirality : 0.049 0.453 3072 Planarity : 0.006 0.071 3750 Dihedral : 8.377 111.162 3121 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 3.09 % Allowed : 18.11 % Favored : 78.80 % Cbeta Deviations : 0.00 % 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: -2.32 (0.15), residues: 2678 helix: -1.27 (0.27), residues: 328 sheet: -1.02 (0.23), residues: 508 loop : -1.85 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D2289 HIS 0.006 0.001 HIS A1553 PHE 0.021 0.002 PHE A2330 TYR 0.015 0.002 TYR D1387 ARG 0.004 0.000 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00728 ( 12) link_NAG-ASN : angle 4.20669 ( 36) hydrogen bonds : bond 0.04060 ( 527) hydrogen bonds : angle 5.84566 ( 1344) SS BOND : bond 0.00378 ( 106) SS BOND : angle 1.35255 ( 212) covalent geometry : bond 0.00414 (20572) covalent geometry : angle 0.73199 (28086) Misc. bond : bond 0.00371 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 96 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1732 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6913 (mm-40) REVERT: A 1949 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: A 2138 MET cc_start: 0.8622 (tpt) cc_final: 0.8292 (tmm) REVERT: A 2368 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.8216 (tpp) REVERT: D 1274 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8846 (p) REVERT: D 1447 ASP cc_start: 0.8811 (p0) cc_final: 0.8415 (p0) REVERT: D 1601 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.5931 (tm-30) REVERT: D 2351 ASP cc_start: 0.7623 (t0) cc_final: 0.7366 (t0) REVERT: D 2368 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8251 (mmm) REVERT: D 2511 MET cc_start: 0.8970 (mmm) cc_final: 0.8691 (mmm) REVERT: D 2567 LYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7804 (mmmt) outliers start: 63 outliers final: 50 residues processed: 151 average time/residue: 0.2370 time to fit residues: 63.6300 Evaluate side-chains 150 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 93 time to evaluate : 2.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1495 SER Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1528 ILE Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1732 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2534 LEU Chi-restraints excluded: chain D residue 1274 THR Chi-restraints excluded: chain D residue 1299 THR Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1693 ASN Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1752 ILE Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1926 CYS Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2114 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2325 CYS Chi-restraints excluded: chain D residue 2335 CYS Chi-restraints excluded: chain D residue 2345 VAL Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2538 VAL Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 49 optimal weight: 5.9990 chunk 200 optimal weight: 0.0000 chunk 241 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 156 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 174 optimal weight: 7.9990 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2447 GLN D1475 HIS ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2356 HIS ** 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 = 0.3676 r_free = 0.3676 target = 0.072231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.056433 restraints weight = 208851.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.059246 restraints weight = 92862.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060972 restraints weight = 51122.889| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 20692 Z= 0.147 Angle : 0.726 11.898 28334 Z= 0.357 Chirality : 0.048 0.434 3072 Planarity : 0.005 0.074 3750 Dihedral : 8.078 109.924 3121 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.04 % Allowed : 18.48 % Favored : 78.48 % Cbeta Deviations : 0.00 % 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: -2.23 (0.15), residues: 2678 helix: -1.19 (0.27), residues: 328 sheet: -0.88 (0.23), residues: 502 loop : -1.81 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D2289 HIS 0.005 0.001 HIS D1388 PHE 0.016 0.002 PHE D1869 TYR 0.022 0.001 TYR A1311 ARG 0.005 0.000 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00730 ( 12) link_NAG-ASN : angle 4.13422 ( 36) hydrogen bonds : bond 0.03778 ( 527) hydrogen bonds : angle 5.72820 ( 1344) SS BOND : bond 0.00462 ( 106) SS BOND : angle 1.20953 ( 212) covalent geometry : bond 0.00339 (20572) covalent geometry : angle 0.70632 (28086) Misc. bond : bond 0.00126 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 99 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1732 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6849 (mm-40) REVERT: A 1949 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7065 (tp30) REVERT: A 2368 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8212 (tpp) REVERT: D 1274 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 1447 ASP cc_start: 0.8770 (p0) cc_final: 0.8363 (p0) REVERT: D 1601 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.5934 (tm-30) REVERT: D 2351 ASP cc_start: 0.7492 (t0) cc_final: 0.7181 (t0) REVERT: D 2368 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8299 (tpp) REVERT: D 2511 MET cc_start: 0.8957 (mmm) cc_final: 0.8663 (mmm) REVERT: D 2567 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7848 (mmmt) outliers start: 62 outliers final: 49 residues processed: 152 average time/residue: 0.2387 time to fit residues: 64.2813 Evaluate side-chains 152 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 96 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1495 SER Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1528 ILE Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1732 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2534 LEU Chi-restraints excluded: chain D residue 1274 THR Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1693 ASN Chi-restraints excluded: chain D residue 1694 VAL Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1752 ILE Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1926 CYS Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2114 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2325 CYS Chi-restraints excluded: chain D residue 2335 CYS Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 253 optimal weight: 10.0000 chunk 76 optimal weight: 8.9990 chunk 52 optimal weight: 9.9990 chunk 95 optimal weight: 0.0010 chunk 56 optimal weight: 0.5980 chunk 17 optimal weight: 0.0870 chunk 96 optimal weight: 8.9990 chunk 124 optimal weight: 8.9990 chunk 238 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 overall best weight: 2.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2356 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.072058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.055414 restraints weight = 244288.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.057859 restraints weight = 102634.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.059527 restraints weight = 60233.335| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3333 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3333 r_free = 0.3333 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3333 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.6032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 20692 Z= 0.153 Angle : 0.731 15.519 28334 Z= 0.362 Chirality : 0.048 0.434 3072 Planarity : 0.005 0.071 3750 Dihedral : 7.979 109.948 3121 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.46 % Favored : 91.54 % Rotamer: Outliers : 3.09 % Allowed : 18.25 % Favored : 78.66 % Cbeta Deviations : 0.04 % 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: -2.22 (0.16), residues: 2678 helix: -1.19 (0.27), residues: 328 sheet: -0.86 (0.23), residues: 502 loop : -1.81 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D2289 HIS 0.007 0.001 HIS D2343 PHE 0.052 0.002 PHE D2330 TYR 0.020 0.001 TYR A1311 ARG 0.005 0.000 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00741 ( 12) link_NAG-ASN : angle 4.10774 ( 36) hydrogen bonds : bond 0.03791 ( 527) hydrogen bonds : angle 5.73168 ( 1344) SS BOND : bond 0.00354 ( 106) SS BOND : angle 1.24074 ( 212) covalent geometry : bond 0.00354 (20572) covalent geometry : angle 0.71107 (28086) Misc. bond : bond 0.00154 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 96 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1732 GLN cc_start: 0.7200 (OUTLIER) cc_final: 0.6925 (mm-40) REVERT: A 1949 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7027 (tp30) REVERT: A 2368 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8269 (tpp) REVERT: D 1274 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8876 (p) REVERT: D 1447 ASP cc_start: 0.8828 (p0) cc_final: 0.8456 (p0) REVERT: D 1601 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.6033 (tm-30) REVERT: D 2351 ASP cc_start: 0.7569 (t0) cc_final: 0.7240 (t0) REVERT: D 2368 MET cc_start: 0.8496 (OUTLIER) cc_final: 0.8252 (tpp) REVERT: D 2511 MET cc_start: 0.9052 (mmm) cc_final: 0.8736 (mmm) REVERT: D 2567 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7831 (mmmt) outliers start: 63 outliers final: 55 residues processed: 150 average time/residue: 0.2489 time to fit residues: 66.2894 Evaluate side-chains 157 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 95 time to evaluate : 2.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1495 SER Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1528 ILE Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1732 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2436 VAL Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2534 LEU Chi-restraints excluded: chain D residue 1252 THR Chi-restraints excluded: chain D residue 1274 THR Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1693 ASN Chi-restraints excluded: chain D residue 1694 VAL Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1752 ILE Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1926 CYS Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2114 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2161 CYS Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2325 CYS Chi-restraints excluded: chain D residue 2335 CYS Chi-restraints excluded: chain D residue 2368 MET Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 99 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 102 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 180 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 196 optimal weight: 0.5980 chunk 131 optimal weight: 7.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.072425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.056586 restraints weight = 204204.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.059494 restraints weight = 92383.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.061269 restraints weight = 50221.611| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3382 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 20692 Z= 0.137 Angle : 0.726 13.108 28334 Z= 0.356 Chirality : 0.048 0.426 3072 Planarity : 0.005 0.071 3750 Dihedral : 7.888 109.338 3121 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 3.09 % Allowed : 18.39 % Favored : 78.53 % Cbeta Deviations : 0.00 % 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: -2.15 (0.16), residues: 2678 helix: -1.16 (0.27), residues: 328 sheet: -0.79 (0.23), residues: 508 loop : -1.77 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D2289 HIS 0.005 0.001 HIS D2356 PHE 0.044 0.002 PHE D2330 TYR 0.020 0.001 TYR A1311 ARG 0.005 0.000 ARG A2252 Details of bonding type rmsd link_NAG-ASN : bond 0.00724 ( 12) link_NAG-ASN : angle 3.98998 ( 36) hydrogen bonds : bond 0.03660 ( 527) hydrogen bonds : angle 5.67360 ( 1344) SS BOND : bond 0.00305 ( 106) SS BOND : angle 1.18287 ( 212) covalent geometry : bond 0.00323 (20572) covalent geometry : angle 0.70780 (28086) Misc. bond : bond 0.00111 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5356 Ramachandran restraints generated. 2678 Oldfield, 0 Emsley, 2678 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 96 time to evaluate : 2.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1732 GLN cc_start: 0.7212 (OUTLIER) cc_final: 0.6974 (mm-40) REVERT: A 1949 GLU cc_start: 0.7552 (OUTLIER) cc_final: 0.7052 (tp30) REVERT: A 2368 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8283 (tpp) REVERT: D 1274 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8896 (p) REVERT: D 1447 ASP cc_start: 0.8743 (p0) cc_final: 0.8335 (p0) REVERT: D 1601 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.5986 (tm-30) REVERT: D 2351 ASP cc_start: 0.7474 (t0) cc_final: 0.7174 (t0) REVERT: D 2511 MET cc_start: 0.8952 (mmm) cc_final: 0.8672 (mmm) REVERT: D 2567 LYS cc_start: 0.8198 (OUTLIER) cc_final: 0.7917 (mmmt) outliers start: 63 outliers final: 54 residues processed: 149 average time/residue: 0.3079 time to fit residues: 83.1509 Evaluate side-chains 154 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 94 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1317 VAL Chi-restraints excluded: chain A residue 1345 VAL Chi-restraints excluded: chain A residue 1355 ILE Chi-restraints excluded: chain A residue 1371 VAL Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1528 ILE Chi-restraints excluded: chain A residue 1535 HIS Chi-restraints excluded: chain A residue 1623 CYS Chi-restraints excluded: chain A residue 1726 GLN Chi-restraints excluded: chain A residue 1732 GLN Chi-restraints excluded: chain A residue 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 1949 GLU Chi-restraints excluded: chain A residue 2121 VAL Chi-restraints excluded: chain A residue 2140 VAL Chi-restraints excluded: chain A residue 2150 MET Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2211 CYS Chi-restraints excluded: chain A residue 2335 CYS Chi-restraints excluded: chain A residue 2368 MET Chi-restraints excluded: chain A residue 2376 CYS Chi-restraints excluded: chain A residue 2436 VAL Chi-restraints excluded: chain A residue 2501 THR Chi-restraints excluded: chain A residue 2518 VAL Chi-restraints excluded: chain A residue 2534 LEU Chi-restraints excluded: chain D residue 1252 THR Chi-restraints excluded: chain D residue 1274 THR Chi-restraints excluded: chain D residue 1297 VAL Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1476 VAL Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS Chi-restraints excluded: chain D residue 1601 GLU Chi-restraints excluded: chain D residue 1693 ASN Chi-restraints excluded: chain D residue 1694 VAL Chi-restraints excluded: chain D residue 1731 LEU Chi-restraints excluded: chain D residue 1740 LEU Chi-restraints excluded: chain D residue 1750 VAL Chi-restraints excluded: chain D residue 1752 ILE Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1926 CYS Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2114 LEU Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2161 CYS Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2325 CYS Chi-restraints excluded: chain D residue 2335 CYS Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2501 THR Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Chi-restraints excluded: chain D residue 2538 VAL Chi-restraints excluded: chain D residue 2567 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 158 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 249 optimal weight: 0.7980 chunk 196 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 232 optimal weight: 0.3980 chunk 35 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 130 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D2086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.073765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.057674 restraints weight = 233797.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060775 restraints weight = 99031.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.062094 restraints weight = 52396.894| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20692 Z= 0.115 Angle : 0.704 12.058 28334 Z= 0.343 Chirality : 0.047 0.406 3072 Planarity : 0.005 0.072 3750 Dihedral : 7.599 106.684 3120 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 2.44 % Allowed : 18.99 % Favored : 78.57 % Cbeta Deviations : 0.00 % 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: -2.07 (0.16), residues: 2678 helix: -1.06 (0.28), residues: 336 sheet: -0.82 (0.23), residues: 526 loop : -1.69 (0.14), residues: 1816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D2289 HIS 0.005 0.001 HIS A1388 PHE 0.044 0.001 PHE D2330 TYR 0.021 0.001 TYR A1311 ARG 0.008 0.000 ARG D2375 Details of bonding type rmsd link_NAG-ASN : bond 0.00732 ( 12) link_NAG-ASN : angle 3.80386 ( 36) hydrogen bonds : bond 0.03387 ( 527) hydrogen bonds : angle 5.54566 ( 1344) SS BOND : bond 0.00264 ( 106) SS BOND : angle 1.06889 ( 212) covalent geometry : bond 0.00269 (20572) covalent geometry : angle 0.68725 (28086) Misc. bond : bond 0.00101 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7113.23 seconds wall clock time: 123 minutes 49.02 seconds (7429.02 seconds total)