Starting phenix.real_space_refine on Thu Sep 18 21:31:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rde_19070/09_2025/8rde_19070.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rde_19070/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rde_19070/09_2025/8rde_19070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rde_19070/09_2025/8rde_19070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rde_19070/09_2025/8rde_19070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rde_19070/09_2025/8rde_19070.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 8.61, per 1000 atoms: 0.43 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: 1.36 Conformation dependent library (CDL) restraints added in 1.6 seconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.99 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: 4.44 Time building geometry restraints manager: 1.98 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: 0.04 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: 2.680 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.470 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.100 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.02 (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 ARG 0.003 0.000 ARG D2290 TYR 0.011 0.001 TYR A1751 PHE 0.012 0.001 PHE A2330 TRP 0.014 0.001 TRP A1727 HIS 0.004 0.001 HIS D2242 Details of bonding type rmsd covalent geometry : bond 0.00534 (20572) covalent geometry : angle 0.94825 (28086) SS BOND : bond 0.00709 ( 106) SS BOND : angle 1.24486 ( 212) hydrogen bonds : bond 0.19295 ( 527) hydrogen bonds : angle 7.71240 ( 1344) Misc. bond : bond 0.15470 ( 2) link_NAG-ASN : bond 0.01465 ( 12) link_NAG-ASN : angle 5.56889 ( 36) *********************** 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 : 0.821 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: A 1341 MET cc_start: 0.6040 (mmm) cc_final: 0.5318 (mmm) REVERT: D 1601 GLU cc_start: 0.5922 (OUTLIER) cc_final: 0.5214 (tm-30) outliers start: 116 outliers final: 29 residues processed: 344 average time/residue: 0.1282 time to fit residues: 70.7153 Evaluate side-chains 146 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.601 ------------------------------------------------------------------------------- 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 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 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.3980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.076003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.060330 restraints weight = 183351.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.062659 restraints weight = 86132.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.064229 restraints weight = 52586.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.065309 restraints weight = 37335.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.066061 restraints weight = 29338.349| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3531 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3531 r_free = 0.3531 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3531 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1857 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= 0.148 Angle : 0.793 15.164 28334 Z= 0.397 Chirality : 0.051 0.454 3072 Planarity : 0.006 0.084 3750 Dihedral : 10.693 111.589 3156 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 3.32 % Allowed : 15.62 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.16), residues: 2678 helix: -1.08 (0.26), residues: 340 sheet: -0.42 (0.25), residues: 504 loop : -1.83 (0.14), residues: 1834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1378 TYR 0.021 0.002 TYR A2453 PHE 0.033 0.002 PHE D1269 TRP 0.028 0.002 TRP A1655 HIS 0.008 0.001 HIS D2463 Details of bonding type rmsd covalent geometry : bond 0.00337 (20572) covalent geometry : angle 0.77088 (28086) SS BOND : bond 0.00336 ( 106) SS BOND : angle 1.52788 ( 212) hydrogen bonds : bond 0.04482 ( 527) hydrogen bonds : angle 6.44254 ( 1344) Misc. bond : bond 0.00347 ( 2) link_NAG-ASN : bond 0.00839 ( 12) link_NAG-ASN : angle 4.15147 ( 36) *********************** 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 203 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 135 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1573 PHE cc_start: 0.7928 (m-80) cc_final: 0.7668 (m-10) REVERT: A 2368 MET cc_start: 0.7838 (ttp) cc_final: 0.7637 (tpp) REVERT: D 1601 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.6275 (tm-30) REVERT: D 1750 VAL cc_start: 0.8710 (t) cc_final: 0.8459 (p) REVERT: D 2351 ASP cc_start: 0.7426 (t0) cc_final: 0.6812 (t0) outliers start: 68 outliers final: 38 residues processed: 191 average time/residue: 0.1061 time to fit residues: 35.0754 Evaluate side-chains 143 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 104 time to evaluate : 0.668 ------------------------------------------------------------------------------- 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 2173 ASP Chi-restraints excluded: chain A residue 2241 CYS Chi-restraints excluded: chain A residue 2323 THR Chi-restraints excluded: chain A residue 2361 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 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 1441 CYS 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 1740 LEU Chi-restraints excluded: chain D residue 1765 VAL Chi-restraints excluded: chain D residue 2170 ASN 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 200 optimal weight: 0.5980 chunk 106 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 168 optimal weight: 0.4980 chunk 252 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 45 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 chunk 163 optimal weight: 0.0030 chunk 114 optimal weight: 0.5980 overall best weight: 0.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2147 HIS ** D1475 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 = 0.3789 r_free = 0.3789 target = 0.076646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.060623 restraints weight = 211365.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.063093 restraints weight = 94059.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.064749 restraints weight = 55850.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.065896 restraints weight = 39072.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.066676 restraints weight = 30337.520| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3586 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3586 r_free = 0.3586 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3586 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20692 Z= 0.128 Angle : 0.736 13.288 28334 Z= 0.361 Chirality : 0.049 0.439 3072 Planarity : 0.005 0.080 3750 Dihedral : 9.567 107.486 3136 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 2.95 % Allowed : 16.27 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.16), residues: 2678 helix: -1.26 (0.26), residues: 348 sheet: -0.50 (0.25), residues: 500 loop : -1.74 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A2157 TYR 0.019 0.001 TYR A2453 PHE 0.018 0.002 PHE D2330 TRP 0.018 0.001 TRP D2289 HIS 0.004 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00291 (20572) covalent geometry : angle 0.71230 (28086) SS BOND : bond 0.00349 ( 106) SS BOND : angle 1.32368 ( 212) hydrogen bonds : bond 0.04089 ( 527) hydrogen bonds : angle 6.02388 ( 1344) Misc. bond : bond 0.00478 ( 2) link_NAG-ASN : bond 0.01498 ( 12) link_NAG-ASN : angle 4.49131 ( 36) *********************** 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 188 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 128 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1399 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8729 (p0) REVERT: A 1745 ASP cc_start: 0.8817 (p0) cc_final: 0.8518 (p0) REVERT: A 2368 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7783 (tpp) REVERT: D 1399 ASP cc_start: 0.8951 (OUTLIER) cc_final: 0.8726 (p0) REVERT: D 1601 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6325 (tm-30) REVERT: D 2351 ASP cc_start: 0.7361 (t0) cc_final: 0.6791 (t0) outliers start: 60 outliers final: 39 residues processed: 174 average time/residue: 0.1139 time to fit residues: 33.8414 Evaluate side-chains 148 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 105 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 1399 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1495 SER 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 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2241 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 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 1369 LEU Chi-restraints excluded: chain D residue 1399 ASP Chi-restraints excluded: chain D residue 1441 CYS Chi-restraints excluded: chain D residue 1461 LEU 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 1674 CYS 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 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 2140 VAL Chi-restraints excluded: chain D residue 2173 ASP Chi-restraints excluded: chain D residue 2211 CYS Chi-restraints excluded: chain D residue 2345 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 59 optimal weight: 0.6980 chunk 235 optimal weight: 5.9990 chunk 171 optimal weight: 40.0000 chunk 263 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 chunk 169 optimal weight: 0.0970 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2133 GLN ** D1475 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 = 0.3771 r_free = 0.3771 target = 0.075958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.060324 restraints weight = 204384.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.063746 restraints weight = 91063.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.065223 restraints weight = 46015.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.065340 restraints weight = 35431.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.065479 restraints weight = 31866.683| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3551 r_free = 0.3551 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 20692 Z= 0.133 Angle : 0.715 12.663 28334 Z= 0.351 Chirality : 0.049 0.443 3072 Planarity : 0.005 0.088 3750 Dihedral : 9.128 105.919 3131 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 2.95 % Allowed : 16.59 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.04 (0.16), residues: 2678 helix: -1.16 (0.26), residues: 344 sheet: -0.56 (0.24), residues: 502 loop : -1.72 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A2252 TYR 0.016 0.001 TYR A2453 PHE 0.022 0.002 PHE D2330 TRP 0.017 0.001 TRP D2289 HIS 0.005 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00306 (20572) covalent geometry : angle 0.69422 (28086) SS BOND : bond 0.00315 ( 106) SS BOND : angle 1.27064 ( 212) hydrogen bonds : bond 0.03831 ( 527) hydrogen bonds : angle 5.84916 ( 1344) Misc. bond : bond 0.00395 ( 2) link_NAG-ASN : bond 0.00853 ( 12) link_NAG-ASN : angle 4.16870 ( 36) *********************** 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 162 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 102 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1399 ASP cc_start: 0.8965 (OUTLIER) cc_final: 0.8733 (p0) REVERT: A 1488 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8478 (t70) REVERT: A 1736 GLU cc_start: 0.8841 (pm20) cc_final: 0.8611 (pm20) REVERT: A 1745 ASP cc_start: 0.8849 (p0) cc_final: 0.8569 (p0) REVERT: A 2368 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7929 (tpp) REVERT: D 1399 ASP cc_start: 0.9009 (OUTLIER) cc_final: 0.8803 (p0) REVERT: D 1601 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6322 (tm-30) REVERT: D 2351 ASP cc_start: 0.7463 (t0) cc_final: 0.6835 (t0) REVERT: D 2368 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8610 (tpp) REVERT: D 2511 MET cc_start: 0.9007 (mmm) cc_final: 0.8762 (mmm) outliers start: 60 outliers final: 38 residues processed: 150 average time/residue: 0.1021 time to fit residues: 27.2646 Evaluate side-chains 141 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 97 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 1399 ASP Chi-restraints excluded: chain A residue 1461 LEU Chi-restraints excluded: chain A residue 1488 ASP 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 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2280 GLN 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 A residue 2534 LEU Chi-restraints excluded: chain D residue 1329 ASN Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1369 LEU Chi-restraints excluded: chain D residue 1399 ASP 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 1674 CYS 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 1765 VAL Chi-restraints excluded: chain D residue 1775 VAL Chi-restraints excluded: chain D residue 1938 SER 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 111 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 8 optimal weight: 0.0670 chunk 32 optimal weight: 6.9990 chunk 254 optimal weight: 0.3980 chunk 119 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 overall best weight: 2.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1760 ASN A2033 HIS ** A2407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.073749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.059162 restraints weight = 121144.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.061043 restraints weight = 66732.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.062342 restraints weight = 44554.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.063230 restraints weight = 33702.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.063813 restraints weight = 27711.411| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20692 Z= 0.180 Angle : 0.771 12.189 28334 Z= 0.386 Chirality : 0.050 0.478 3072 Planarity : 0.006 0.072 3750 Dihedral : 8.656 109.146 3122 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.86 % Favored : 92.14 % Rotamer: Outliers : 2.86 % Allowed : 17.19 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.13 (0.16), residues: 2678 helix: -1.07 (0.27), residues: 332 sheet: -0.74 (0.24), residues: 492 loop : -1.78 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D2310 TYR 0.017 0.002 TYR A2562 PHE 0.029 0.002 PHE A2330 TRP 0.025 0.002 TRP D2289 HIS 0.006 0.001 HIS D1388 Details of bonding type rmsd covalent geometry : bond 0.00402 (20572) covalent geometry : angle 0.75041 (28086) SS BOND : bond 0.00414 ( 106) SS BOND : angle 1.37778 ( 212) hydrogen bonds : bond 0.04275 ( 527) hydrogen bonds : angle 5.97687 ( 1344) Misc. bond : bond 0.00323 ( 2) link_NAG-ASN : bond 0.01060 ( 12) link_NAG-ASN : angle 4.23419 ( 36) *********************** 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 161 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 103 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1399 ASP cc_start: 0.8949 (OUTLIER) cc_final: 0.8650 (p0) REVERT: A 1745 ASP cc_start: 0.8980 (p0) cc_final: 0.8767 (p0) REVERT: D 1601 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: D 2351 ASP cc_start: 0.7570 (t0) cc_final: 0.7039 (t0) REVERT: D 2511 MET cc_start: 0.8968 (mmm) cc_final: 0.8709 (mmm) outliers start: 58 outliers final: 39 residues processed: 155 average time/residue: 0.1052 time to fit residues: 29.0622 Evaluate side-chains 134 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 93 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 1399 ASP 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 1557 THR Chi-restraints excluded: chain A residue 1623 CYS 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 1934 CYS Chi-restraints excluded: chain A residue 2167 PHE Chi-restraints excluded: chain A residue 2173 ASP Chi-restraints excluded: chain A residue 2335 CYS 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 2534 LEU 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 1623 CYS Chi-restraints excluded: chain D residue 1655 TRP Chi-restraints excluded: chain D residue 1693 ASN 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 1938 SER 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 2241 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 49 optimal weight: 3.9990 chunk 177 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 179 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1329 ASN A1715 GLN A1880 GLN A2041 HIS ** D1475 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.072258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.056040 restraints weight = 194782.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059347 restraints weight = 98961.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.060659 restraints weight = 48097.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.060913 restraints weight = 34209.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.061097 restraints weight = 34451.563| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 20692 Z= 0.222 Angle : 0.794 12.200 28334 Z= 0.401 Chirality : 0.050 0.478 3072 Planarity : 0.006 0.074 3750 Dihedral : 8.475 110.880 3118 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.18 % Allowed : 17.10 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.15), residues: 2678 helix: -1.18 (0.27), residues: 330 sheet: -0.96 (0.23), residues: 504 loop : -1.82 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A2128 TYR 0.020 0.002 TYR A1311 PHE 0.026 0.002 PHE A2330 TRP 0.036 0.002 TRP D2289 HIS 0.007 0.001 HIS A1553 Details of bonding type rmsd covalent geometry : bond 0.00505 (20572) covalent geometry : angle 0.76793 (28086) SS BOND : bond 0.00483 ( 106) SS BOND : angle 1.70698 ( 212) hydrogen bonds : bond 0.04313 ( 527) hydrogen bonds : angle 6.07896 ( 1344) Misc. bond : bond 0.00643 ( 2) link_NAG-ASN : bond 0.00771 ( 12) link_NAG-ASN : angle 4.38229 ( 36) *********************** 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: 65 poor density : 104 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 2138 MET cc_start: 0.8507 (ppp) cc_final: 0.8085 (tmm) REVERT: A 2368 MET cc_start: 0.8606 (OUTLIER) cc_final: 0.8324 (tpp) REVERT: A 2505 SER cc_start: 0.9189 (OUTLIER) cc_final: 0.8906 (p) REVERT: D 1274 THR cc_start: 0.8912 (OUTLIER) cc_final: 0.8646 (p) REVERT: D 1601 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.6236 (tm-30) REVERT: D 2351 ASP cc_start: 0.7690 (t0) cc_final: 0.7391 (t0) REVERT: D 2511 MET cc_start: 0.8965 (mmm) cc_final: 0.8666 (mmm) REVERT: D 2567 LYS cc_start: 0.7779 (OUTLIER) cc_final: 0.7431 (mmmt) outliers start: 65 outliers final: 47 residues processed: 158 average time/residue: 0.1132 time to fit residues: 31.4347 Evaluate side-chains 150 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 98 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 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 1750 VAL Chi-restraints excluded: chain A residue 1765 VAL Chi-restraints excluded: chain A residue 1823 CYS Chi-restraints excluded: chain A residue 2060 LEU Chi-restraints excluded: chain A residue 2167 PHE Chi-restraints excluded: chain A residue 2173 ASP 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 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 1355 ILE Chi-restraints excluded: chain D residue 1379 VAL 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 1515 ILE 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 1731 LEU 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 1775 VAL Chi-restraints excluded: chain D residue 1938 SER 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 2211 CYS Chi-restraints excluded: chain D residue 2213 VAL Chi-restraints excluded: chain D residue 2339 PHE 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 202 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 211 optimal weight: 7.9990 chunk 30 optimal weight: 20.0000 chunk 143 optimal weight: 7.9990 chunk 22 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 233 optimal weight: 1.9990 chunk 232 optimal weight: 0.0570 chunk 70 optimal weight: 30.0000 chunk 249 optimal weight: 0.5980 overall best weight: 2.1304 ------------------------------------------------------------------------------- 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** ** D1880 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D2520 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.073199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.057479 restraints weight = 207278.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.060310 restraints weight = 92109.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.061625 restraints weight = 50418.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.061776 restraints weight = 39879.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.061960 restraints weight = 36098.990| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 20692 Z= 0.149 Angle : 0.738 12.510 28334 Z= 0.366 Chirality : 0.048 0.450 3072 Planarity : 0.005 0.074 3750 Dihedral : 7.989 109.301 3118 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 3.32 % Allowed : 17.28 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.14 (0.15), residues: 2678 helix: -1.12 (0.27), residues: 330 sheet: -0.92 (0.23), residues: 504 loop : -1.72 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2252 TYR 0.016 0.001 TYR A1311 PHE 0.025 0.002 PHE A2330 TRP 0.028 0.002 TRP D2289 HIS 0.006 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00345 (20572) covalent geometry : angle 0.71501 (28086) SS BOND : bond 0.00391 ( 106) SS BOND : angle 1.38926 ( 212) hydrogen bonds : bond 0.03906 ( 527) hydrogen bonds : angle 5.87300 ( 1344) Misc. bond : bond 0.00146 ( 2) link_NAG-ASN : bond 0.00737 ( 12) link_NAG-ASN : angle 4.36015 ( 36) *********************** 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 177 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 109 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1274 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8487 (p) REVERT: A 2138 MET cc_start: 0.8439 (ppp) cc_final: 0.7927 (tmm) REVERT: A 2505 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8937 (p) REVERT: D 1274 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8636 (p) REVERT: D 1447 ASP cc_start: 0.8805 (p0) cc_final: 0.8412 (p0) REVERT: D 1601 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6253 (tm-30) REVERT: D 2351 ASP cc_start: 0.7535 (t0) cc_final: 0.7146 (t0) REVERT: D 2416 SER cc_start: 0.8722 (m) cc_final: 0.8418 (t) REVERT: D 2511 MET cc_start: 0.8969 (mmm) cc_final: 0.8702 (mmm) REVERT: D 2567 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7578 (mmmt) outliers start: 68 outliers final: 51 residues processed: 168 average time/residue: 0.1124 time to fit residues: 33.4037 Evaluate side-chains 155 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 99 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1274 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 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 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 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 2060 LEU Chi-restraints excluded: chain A residue 2167 PHE 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 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 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 1731 LEU 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 1938 SER Chi-restraints excluded: chain D residue 1959 LEU Chi-restraints excluded: chain D residue 2060 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 2241 CYS Chi-restraints excluded: chain D residue 2339 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 66 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 164 optimal weight: 7.9990 chunk 113 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 248 optimal weight: 0.0870 chunk 15 optimal weight: 0.0980 chunk 158 optimal weight: 4.9990 chunk 266 optimal weight: 0.2980 chunk 264 optimal weight: 2.9990 chunk 166 optimal weight: 8.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1475 HIS D1760 ASN D2356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.073784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.057905 restraints weight = 192075.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.060839 restraints weight = 92427.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062419 restraints weight = 48946.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.062666 restraints weight = 36868.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.062679 restraints weight = 32762.566| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3423 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3423 r_free = 0.3423 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3423 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20692 Z= 0.131 Angle : 0.722 11.738 28334 Z= 0.355 Chirality : 0.048 0.434 3072 Planarity : 0.005 0.073 3750 Dihedral : 7.742 108.135 3116 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.81 % Allowed : 17.83 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.16), residues: 2678 helix: -1.11 (0.27), residues: 336 sheet: -0.82 (0.23), residues: 510 loop : -1.66 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2252 TYR 0.015 0.001 TYR A1311 PHE 0.022 0.002 PHE A2330 TRP 0.027 0.001 TRP D2289 HIS 0.006 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00306 (20572) covalent geometry : angle 0.70020 (28086) SS BOND : bond 0.00299 ( 106) SS BOND : angle 1.25108 ( 212) hydrogen bonds : bond 0.03694 ( 527) hydrogen bonds : angle 5.77455 ( 1344) Misc. bond : bond 0.00124 ( 2) link_NAG-ASN : bond 0.00740 ( 12) link_NAG-ASN : angle 4.30071 ( 36) *********************** 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 162 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 105 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2138 MET cc_start: 0.8424 (ppp) cc_final: 0.7939 (tmm) REVERT: A 2368 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8148 (tpp) REVERT: A 2505 SER cc_start: 0.9193 (OUTLIER) cc_final: 0.8936 (p) REVERT: D 1274 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8758 (p) REVERT: D 1447 ASP cc_start: 0.8769 (p0) cc_final: 0.8351 (p0) REVERT: D 1601 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6176 (tm-30) REVERT: D 1938 SER cc_start: 0.9029 (OUTLIER) cc_final: 0.8535 (t) REVERT: D 2351 ASP cc_start: 0.7438 (t0) cc_final: 0.6999 (t0) REVERT: D 2511 MET cc_start: 0.8944 (mmm) cc_final: 0.8674 (mmm) REVERT: D 2567 LYS cc_start: 0.7898 (OUTLIER) cc_final: 0.7561 (mmmt) outliers start: 57 outliers final: 45 residues processed: 154 average time/residue: 0.1137 time to fit residues: 31.1993 Evaluate side-chains 150 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 99 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 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 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 2167 PHE 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 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 1510 CYS 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 1693 ASN Chi-restraints excluded: chain D residue 1731 LEU 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 1775 VAL Chi-restraints excluded: chain D residue 1938 SER Chi-restraints excluded: chain D residue 2060 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 2241 CYS Chi-restraints excluded: chain D residue 2339 PHE 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 91 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 17 optimal weight: 0.0030 chunk 18 optimal weight: 0.3980 chunk 117 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1303 ASN ** D2086 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.075262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.060048 restraints weight = 144767.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.062174 restraints weight = 73690.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.063598 restraints weight = 47018.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.064571 restraints weight = 34623.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.065248 restraints weight = 27928.753| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20692 Z= 0.116 Angle : 0.701 11.908 28334 Z= 0.343 Chirality : 0.048 0.411 3072 Planarity : 0.005 0.075 3750 Dihedral : 7.498 105.876 3116 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 2.30 % Allowed : 18.29 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.16), residues: 2678 helix: -1.06 (0.28), residues: 336 sheet: -0.73 (0.23), residues: 510 loop : -1.61 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A2252 TYR 0.017 0.001 TYR A1311 PHE 0.017 0.001 PHE A2330 TRP 0.024 0.001 TRP D2289 HIS 0.006 0.001 HIS A1388 Details of bonding type rmsd covalent geometry : bond 0.00268 (20572) covalent geometry : angle 0.68310 (28086) SS BOND : bond 0.00270 ( 106) SS BOND : angle 1.09241 ( 212) hydrogen bonds : bond 0.03431 ( 527) hydrogen bonds : angle 5.63635 ( 1344) Misc. bond : bond 0.00302 ( 2) link_NAG-ASN : bond 0.00706 ( 12) link_NAG-ASN : angle 3.94553 ( 36) *********************** 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 155 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 109 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2138 MET cc_start: 0.8319 (ppp) cc_final: 0.7854 (tmm) REVERT: A 2368 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8093 (tpp) REVERT: A 2505 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8919 (p) REVERT: D 1395 CYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7644 (p) REVERT: D 1447 ASP cc_start: 0.8730 (p0) cc_final: 0.8322 (p0) REVERT: D 2335 CYS cc_start: 0.1159 (t) cc_final: 0.0718 (t) REVERT: D 2351 ASP cc_start: 0.7264 (t0) cc_final: 0.6746 (t0) REVERT: D 2511 MET cc_start: 0.8923 (mmm) cc_final: 0.8675 (mmm) REVERT: D 2567 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7470 (mmmt) outliers start: 46 outliers final: 36 residues processed: 148 average time/residue: 0.1129 time to fit residues: 30.0173 Evaluate side-chains 141 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 0.860 ------------------------------------------------------------------------------- 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 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 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 2167 PHE 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 A residue 2534 LEU Chi-restraints excluded: chain D residue 1345 VAL Chi-restraints excluded: chain D residue 1355 ILE Chi-restraints excluded: chain D residue 1395 CYS Chi-restraints excluded: chain D residue 1510 CYS Chi-restraints excluded: chain D residue 1535 HIS 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 1775 VAL Chi-restraints excluded: chain D residue 2060 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 2241 CYS Chi-restraints excluded: chain D residue 2339 PHE Chi-restraints excluded: chain D residue 2376 CYS 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 208 optimal weight: 0.0070 chunk 51 optimal weight: 0.9980 chunk 175 optimal weight: 8.9990 chunk 236 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 231 optimal weight: 8.9990 chunk 142 optimal weight: 4.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.073663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.057753 restraints weight = 176998.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.059993 restraints weight = 84044.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.061528 restraints weight = 52201.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.062533 restraints weight = 37672.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.063265 restraints weight = 30174.628| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 20692 Z= 0.141 Angle : 0.715 11.353 28334 Z= 0.352 Chirality : 0.048 0.423 3072 Planarity : 0.006 0.090 3750 Dihedral : 7.482 107.757 3112 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.30 % Allowed : 18.66 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.16), residues: 2678 helix: -1.03 (0.28), residues: 336 sheet: -0.69 (0.23), residues: 500 loop : -1.61 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2252 TYR 0.015 0.001 TYR A1311 PHE 0.023 0.002 PHE A2330 TRP 0.023 0.001 TRP D2289 HIS 0.006 0.001 HIS D2356 Details of bonding type rmsd covalent geometry : bond 0.00330 (20572) covalent geometry : angle 0.69584 (28086) SS BOND : bond 0.00308 ( 106) SS BOND : angle 1.24724 ( 212) hydrogen bonds : bond 0.03591 ( 527) hydrogen bonds : angle 5.66393 ( 1344) Misc. bond : bond 0.00110 ( 2) link_NAG-ASN : bond 0.00714 ( 12) link_NAG-ASN : angle 3.88655 ( 36) ********************** 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 147 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 101 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2138 MET cc_start: 0.8394 (ppp) cc_final: 0.7935 (tmm) REVERT: A 2505 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8926 (p) REVERT: D 1274 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8843 (p) REVERT: D 1395 CYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7788 (p) REVERT: D 1447 ASP cc_start: 0.8717 (p0) cc_final: 0.8330 (p0) REVERT: D 2351 ASP cc_start: 0.7417 (t0) cc_final: 0.6979 (t0) REVERT: D 2511 MET cc_start: 0.8917 (mmm) cc_final: 0.8686 (mmm) outliers start: 46 outliers final: 39 residues processed: 140 average time/residue: 0.1130 time to fit residues: 28.5500 Evaluate side-chains 142 residues out of total 2166 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 100 time to evaluate : 0.835 ------------------------------------------------------------------------------- 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 1495 SER Chi-restraints excluded: chain A residue 1500 CYS Chi-restraints excluded: chain A residue 1510 CYS Chi-restraints excluded: chain A residue 1623 CYS 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 1949 GLU Chi-restraints excluded: chain A residue 2167 PHE 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 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 1355 ILE Chi-restraints excluded: chain D residue 1395 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 1623 CYS 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 2060 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 2241 CYS Chi-restraints excluded: chain D residue 2339 PHE Chi-restraints excluded: chain D residue 2376 CYS Chi-restraints excluded: chain D residue 2518 VAL Chi-restraints excluded: chain D residue 2534 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 187 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 260 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 161 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 249 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.073303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.056624 restraints weight = 232020.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.059110 restraints weight = 98292.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.060806 restraints weight = 57872.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.061949 restraints weight = 40319.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.062720 restraints weight = 31517.968| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.5758 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 : 0.713 11.538 28334 Z= 0.352 Chirality : 0.048 0.419 3072 Planarity : 0.006 0.076 3750 Dihedral : 7.534 108.274 3112 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 2.17 % Allowed : 18.71 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.16), residues: 2678 helix: -1.09 (0.27), residues: 340 sheet: -0.81 (0.23), residues: 518 loop : -1.58 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2252 TYR 0.014 0.001 TYR A1311 PHE 0.016 0.002 PHE A2330 TRP 0.022 0.001 TRP D2289 HIS 0.005 0.001 HIS D1388 Details of bonding type rmsd covalent geometry : bond 0.00331 (20572) covalent geometry : angle 0.69513 (28086) SS BOND : bond 0.00306 ( 106) SS BOND : angle 1.24783 ( 212) hydrogen bonds : bond 0.03623 ( 527) hydrogen bonds : angle 5.67030 ( 1344) Misc. bond : bond 0.00120 ( 2) link_NAG-ASN : bond 0.00655 ( 12) link_NAG-ASN : angle 3.71518 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3990.96 seconds wall clock time: 69 minutes 26.95 seconds (4166.95 seconds total)