Starting phenix.real_space_refine on Wed Aug 5 17:02:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/12jp_76487/08_2026/12jp_76487.cif Found real_map, /net/cci-nas-00/data/ceres_data/12jp_76487/08_2026/12jp_76487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/12jp_76487/08_2026/12jp_76487.map" default_real_map = "/net/cci-nas-00/data/ceres_data/12jp_76487/08_2026/12jp_76487.map" model { file = "/net/cci-nas-00/data/ceres_data/12jp_76487/08_2026/12jp_76487.cif" } default_model = "/net/cci-nas-00/data/ceres_data/12jp_76487/08_2026/12jp_76487.cif" } resolution = 3.46 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= 0.001 sd= 0.030 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: 6 Type Number sf(0) Gaussians Ca 1 9.91 5 Cu 2 5.60 5 S 57 5.16 5 C 6596 2.51 5 N 1747 2.21 5 O 1869 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10272 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 10227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 10227 Classifications: {'peptide': 1263} Link IDs: {'PCIS': 1, 'PTRANS': 61, 'TRANS': 1200} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 45 Unusual residues: {' CA': 1, ' CU': 2, 'NAG': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7598 SG CYS A2000 49.773 50.543 75.230 1.00114.22 S Time building chain proxies: 2.43, per 1000 atoms: 0.24 Number of scatterers: 10272 At special positions: 0 Unit cell: (90.016, 96.512, 140.128, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 2 28.99 Ca 1 19.99 S 57 16.00 O 1869 8.00 N 1747 7.00 C 6596 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 179 " distance=2.03 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 329 " distance=2.03 Simple disulfide: pdb=" SG CYS A 528 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 630 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A1832 " - pdb=" SG CYS A1858 " distance=2.03 Simple disulfide: pdb=" SG CYS A1899 " - pdb=" SG CYS A1903 " distance=2.03 Simple disulfide: pdb=" SG CYS A2021 " - pdb=" SG CYS A2169 " distance=2.03 Simple disulfide: pdb=" SG CYS A2174 " - pdb=" SG CYS A2326 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A2401 " - " ASN A2118 " " NAG A2402 " - " ASN A1810 " " NAG A2403 " - " ASN A 239 " Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 412.0 milliseconds 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2366 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 23 sheets defined 11.2% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 120 through 124 removed outlier: 3.787A pdb=" N GLU A 124 " --> pdb=" O ARG A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 171 removed outlier: 3.896A pdb=" N ASN A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.740A pdb=" N THR A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 removed outlier: 3.512A pdb=" N SER A 207 " --> pdb=" O ASP A 203 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N TRP A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 203 through 208' Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'A' and resid 538 through 544 Processing helix chain 'A' and resid 580 through 584 Processing helix chain 'A' and resid 586 through 595 removed outlier: 3.591A pdb=" N LEU A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 613 Processing helix chain 'A' and resid 694 through 700 removed outlier: 3.656A pdb=" N ARG A 698 " --> pdb=" O ASN A 694 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG A 700 " --> pdb=" O ASP A 696 " (cutoff:3.500A) Processing helix chain 'A' and resid 1713 through 1718 removed outlier: 4.339A pdb=" N VAL A1717 " --> pdb=" O SER A1713 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N LEU A1718 " --> pdb=" O SER A1714 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1713 through 1718' Processing helix chain 'A' and resid 1797 through 1801 removed outlier: 4.153A pdb=" N ALA A1800 " --> pdb=" O ARG A1797 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1824 Processing helix chain 'A' and resid 1842 through 1850 Processing helix chain 'A' and resid 1890 through 1897 removed outlier: 4.327A pdb=" N MET A1895 " --> pdb=" O PHE A1891 " (cutoff:3.500A) Processing helix chain 'A' and resid 1908 through 1915 Processing helix chain 'A' and resid 1920 through 1924 removed outlier: 3.772A pdb=" N GLY A1923 " --> pdb=" O ALA A1920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1949 through 1953 removed outlier: 3.639A pdb=" N ILE A1953 " --> pdb=" O ASN A1950 " (cutoff:3.500A) Processing helix chain 'A' and resid 2002 through 2007 Processing helix chain 'A' and resid 2186 through 2188 No H-bonds generated for 'chain 'A' and resid 2186 through 2188' Processing helix chain 'A' and resid 2204 through 2208 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 54 removed outlier: 4.323A pdb=" N TYR A 6 " --> pdb=" O PHE A 54 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 3 " --> pdb=" O THR A 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A 85 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS A 89 " --> pdb=" O LEU A 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 78 removed outlier: 3.965A pdb=" N VAL A 178 " --> pdb=" O LEU A 154 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 197 through 199 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 removed outlier: 5.869A pdb=" N GLY A 247 " --> pdb=" O ASP A 327 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA6, first strand: chain 'A' and resid 381 through 384 removed outlier: 6.060A pdb=" N TRP A 382 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 464 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS A 384 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS A 466 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE A 386 " --> pdb=" O LYS A 466 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N GLN A 468 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ALA A 388 " --> pdb=" O GLN A 468 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 381 through 384 removed outlier: 6.060A pdb=" N TRP A 382 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N ILE A 464 " --> pdb=" O TRP A 382 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS A 384 " --> pdb=" O ILE A 464 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N LYS A 466 " --> pdb=" O HIS A 384 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP A 482 " --> pdb=" O THR A 514 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 453 through 456 removed outlier: 7.090A pdb=" N LEU A 453 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N CYS A 554 " --> pdb=" O LEU A 453 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLY A 455 " --> pdb=" O CYS A 554 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N SER A 534 " --> pdb=" O TYR A 476 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 572 through 575 removed outlier: 6.080A pdb=" N ASN A 572 " --> pdb=" O TYR A 638 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 640 " --> pdb=" O ASN A 572 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE A 574 " --> pdb=" O LEU A 640 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER A 674 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 578 through 579 Processing sheet with id=AB2, first strand: chain 'A' and resid 626 through 628 removed outlier: 5.679A pdb=" N LEU A 627 " --> pdb=" O LYS A 707 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 649 through 651 Processing sheet with id=AB4, first strand: chain 'A' and resid 658 through 660 Processing sheet with id=AB5, first strand: chain 'A' and resid 1733 through 1738 removed outlier: 4.354A pdb=" N PHE A1699 " --> pdb=" O PHE A1738 " (cutoff:3.500A) removed outlier: 8.144A pdb=" N ILE A1700 " --> pdb=" O MET A1772 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR A1774 " --> pdb=" O ILE A1700 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N ALA A1702 " --> pdb=" O THR A1774 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N ARG A1776 " --> pdb=" O ALA A1702 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N GLU A1704 " --> pdb=" O ARG A1776 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP A1769 " --> pdb=" O VAL A1819 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU A1811 " --> pdb=" O ASN A1777 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1786 through 1787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1875 through 1880 removed outlier: 3.856A pdb=" N LEU A1944 " --> pdb=" O GLU A1984 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLU A1984 " --> pdb=" O LEU A1944 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1933 through 1935 Processing sheet with id=AB9, first strand: chain 'A' and resid 2037 through 2039 removed outlier: 12.935A pdb=" N ILE A2071 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 11.868A pdb=" N THR A2154 " --> pdb=" O ILE A2071 " (cutoff:3.500A) removed outlier: 12.895A pdb=" N VAL A2073 " --> pdb=" O HIS A2152 " (cutoff:3.500A) removed outlier: 11.666A pdb=" N HIS A2152 " --> pdb=" O VAL A2073 " (cutoff:3.500A) removed outlier: 11.902A pdb=" N LEU A2075 " --> pdb=" O ARG A2150 " (cutoff:3.500A) removed outlier: 12.764A pdb=" N ARG A2150 " --> pdb=" O LEU A2075 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N ALA A2077 " --> pdb=" O TYR A2148 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYR A2148 " --> pdb=" O ALA A2077 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY A2083 " --> pdb=" O PRO A2142 " (cutoff:3.500A) removed outlier: 11.220A pdb=" N LYS A2085 " --> pdb=" O PHE A2140 " (cutoff:3.500A) removed outlier: 10.677A pdb=" N PHE A2140 " --> pdb=" O LYS A2085 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N GLN A2100 " --> pdb=" O THR A2154 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N TYR A2156 " --> pdb=" O ILE A2098 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ILE A2098 " --> pdb=" O TYR A2156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 2037 through 2039 removed outlier: 6.907A pdb=" N MET A2167 " --> pdb=" O HIS A2082 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE A2084 " --> pdb=" O GLU A2165 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N GLU A2165 " --> pdb=" O ILE A2084 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 2089 through 2090 Processing sheet with id=AC3, first strand: chain 'A' and resid 2176 through 2177 removed outlier: 6.954A pdb=" N CYS A2326 " --> pdb=" O VAL A2240 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N VAL A2240 " --> pdb=" O CYS A2326 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLN A2231 " --> pdb=" O ARG A2307 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A2307 " --> pdb=" O GLN A2231 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP A2233 " --> pdb=" O TYR A2305 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A2305 " --> pdb=" O ASP A2233 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN A2235 " --> pdb=" O THR A2303 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N THR A2303 " --> pdb=" O GLN A2235 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR A2237 " --> pdb=" O LEU A2301 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N LEU A2301 " --> pdb=" O THR A2237 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N LYS A2239 " --> pdb=" O PRO A2299 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR A2241 " --> pdb=" O LEU A2297 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A2259 " --> pdb=" O GLN A2311 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TRP A2313 " --> pdb=" O VAL A2257 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A2257 " --> pdb=" O TRP A2313 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 2190 through 2192 removed outlier: 6.690A pdb=" N GLN A2231 " --> pdb=" O ARG A2307 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ARG A2307 " --> pdb=" O GLN A2231 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP A2233 " --> pdb=" O TYR A2305 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N TYR A2305 " --> pdb=" O ASP A2233 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N GLN A2235 " --> pdb=" O THR A2303 " (cutoff:3.500A) removed outlier: 11.015A pdb=" N THR A2303 " --> pdb=" O GLN A2235 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N THR A2237 " --> pdb=" O LEU A2301 " (cutoff:3.500A) removed outlier: 10.586A pdb=" N LEU A2301 " --> pdb=" O THR A2237 " (cutoff:3.500A) removed outlier: 10.144A pdb=" N LYS A2239 " --> pdb=" O PRO A2299 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N THR A2241 " --> pdb=" O LEU A2297 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLU A2259 " --> pdb=" O GLN A2311 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TRP A2313 " --> pdb=" O VAL A2257 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL A2257 " --> pdb=" O TRP A2313 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 2275 through 2276 247 hydrogen bonds defined for protein. 597 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: 2.48 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3264 1.34 - 1.47: 2716 1.47 - 1.59: 4484 1.59 - 1.71: 0 1.71 - 1.83: 95 Bond restraints: 10559 Sorted by residual: bond pdb=" C ALA A1901 " pdb=" N PRO A1902 " ideal model delta sigma weight residual 1.334 1.350 -0.016 8.40e-03 1.42e+04 3.85e+00 bond pdb=" CB PRO A 492 " pdb=" CG PRO A 492 " ideal model delta sigma weight residual 1.492 1.549 -0.057 5.00e-02 4.00e+02 1.28e+00 bond pdb=" CA TRP A 228 " pdb=" C TRP A 228 " ideal model delta sigma weight residual 1.525 1.547 -0.022 2.10e-02 2.27e+03 1.13e+00 bond pdb=" CA LEU A 71 " pdb=" CB LEU A 71 " ideal model delta sigma weight residual 1.524 1.537 -0.013 1.31e-02 5.83e+03 1.06e+00 bond pdb=" C ILE A 258 " pdb=" N GLY A 259 " ideal model delta sigma weight residual 1.332 1.327 0.005 5.00e-03 4.00e+04 9.07e-01 ... (remaining 10554 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 13911 1.79 - 3.58: 345 3.58 - 5.37: 51 5.37 - 7.16: 7 7.16 - 8.95: 2 Bond angle restraints: 14316 Sorted by residual: angle pdb=" N ILE A2032 " pdb=" CA ILE A2032 " pdb=" C ILE A2032 " ideal model delta sigma weight residual 111.48 108.22 3.26 9.40e-01 1.13e+00 1.20e+01 angle pdb=" N ARG A2147 " pdb=" CA ARG A2147 " pdb=" C ARG A2147 " ideal model delta sigma weight residual 114.56 110.48 4.08 1.27e+00 6.20e-01 1.03e+01 angle pdb=" N VAL A 278 " pdb=" CA VAL A 278 " pdb=" C VAL A 278 " ideal model delta sigma weight residual 110.74 107.87 2.87 9.10e-01 1.21e+00 9.95e+00 angle pdb=" CA GLN A 417 " pdb=" CB GLN A 417 " pdb=" CG GLN A 417 " ideal model delta sigma weight residual 114.10 120.11 -6.01 2.00e+00 2.50e-01 9.02e+00 angle pdb=" C HIS A2031 " pdb=" N ILE A2032 " pdb=" CA ILE A2032 " ideal model delta sigma weight residual 122.97 120.28 2.69 9.80e-01 1.04e+00 7.52e+00 ... (remaining 14311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5724 17.95 - 35.91: 445 35.91 - 53.86: 77 53.86 - 71.81: 22 71.81 - 89.76: 14 Dihedral angle restraints: 6282 sinusoidal: 2598 harmonic: 3684 Sorted by residual: dihedral pdb=" CB CYS A2021 " pdb=" SG CYS A2021 " pdb=" SG CYS A2169 " pdb=" CB CYS A2169 " ideal model delta sinusoidal sigma weight residual 93.00 152.88 -59.88 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB CYS A 630 " pdb=" SG CYS A 630 " pdb=" SG CYS A 711 " pdb=" CB CYS A 711 " ideal model delta sinusoidal sigma weight residual 93.00 36.02 56.98 1 1.00e+01 1.00e-02 4.37e+01 dihedral pdb=" CA ILE A1925 " pdb=" C ILE A1925 " pdb=" N MET A1926 " pdb=" CA MET A1926 " ideal model delta harmonic sigma weight residual 180.00 152.44 27.56 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 6279 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1109 0.045 - 0.090: 306 0.090 - 0.135: 112 0.135 - 0.180: 5 0.180 - 0.224: 1 Chirality restraints: 1533 Sorted by residual: chirality pdb=" CB THR A1695 " pdb=" CA THR A1695 " pdb=" OG1 THR A1695 " pdb=" CG2 THR A1695 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CG LEU A2050 " pdb=" CB LEU A2050 " pdb=" CD1 LEU A2050 " pdb=" CD2 LEU A2050 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA VAL A1986 " pdb=" N VAL A1986 " pdb=" C VAL A1986 " pdb=" CB VAL A1986 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.31e-01 ... (remaining 1530 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 202 " 0.018 2.00e-02 2.50e+03 1.42e-02 3.54e+00 pdb=" CG PHE A 202 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE A 202 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 202 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 202 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 202 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 202 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2023 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO A2024 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A2024 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A2024 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 63 " 0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO A 64 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.024 5.00e-02 4.00e+02 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 40 2.64 - 3.21: 9428 3.21 - 3.77: 15058 3.77 - 4.34: 21473 4.34 - 4.90: 34047 Nonbonded interactions: 80046 Sorted by model distance: nonbonded pdb=" ND1 HIS A 315 " pdb="CU CU A2406 " model vdw 2.077 2.320 nonbonded pdb=" CD2 HIS A1954 " pdb="CU CU A2405 " model vdw 2.147 2.460 nonbonded pdb=" ND1 HIS A2005 " pdb="CU CU A2405 " model vdw 2.170 2.320 nonbonded pdb=" CG HIS A 315 " pdb="CU CU A2406 " model vdw 2.285 2.460 nonbonded pdb=" O GLU A 122 " pdb="CA CA A2404 " model vdw 2.309 2.510 ... (remaining 80041 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.960 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 : 0.003 0.057 10570 Z= 0.143 Angle : 0.680 8.947 14341 Z= 0.353 Chirality : 0.046 0.224 1533 Planarity : 0.005 0.043 1821 Dihedral : 13.756 89.764 3892 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.23), residues: 1253 helix: -1.18 (0.59), residues: 68 sheet: -0.53 (0.29), residues: 330 loop : -1.70 (0.21), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1705 TYR 0.015 0.001 TYR A 555 PHE 0.032 0.002 PHE A 202 TRP 0.022 0.002 TRP A 138 HIS 0.008 0.001 HIS A 193 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (10559) covalent geometry : angle 0.67746 / 0.35 (14316) SS BOND : bond 0.00217 / 0.12 ( 8) SS BOND : angle 1.64492 / 1.07 ( 16) hydrogen bonds : bond 0.17331 / 10.95 ( 233) hydrogen bonds : angle 8.63023 / 6.17 ( 597) link_NAG-ASN : bond 0.00247 / 0.12 ( 3) link_NAG-ASN : angle 1.72920 / 1.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 VAL cc_start: 0.9032 (t) cc_final: 0.8797 (m) REVERT: A 15 ASP cc_start: 0.6787 (t0) cc_final: 0.6449 (p0) REVERT: A 134 HIS cc_start: 0.7795 (t70) cc_final: 0.7491 (t70) REVERT: A 136 TYR cc_start: 0.8455 (m-80) cc_final: 0.8250 (m-10) REVERT: A 309 PHE cc_start: 0.7875 (p90) cc_final: 0.7367 (p90) REVERT: A 429 MET cc_start: 0.7765 (tpp) cc_final: 0.7071 (tpp) REVERT: A 567 MET cc_start: 0.4707 (mmp) cc_final: 0.4054 (mmt) REVERT: A 577 SER cc_start: 0.7575 (t) cc_final: 0.7374 (t) REVERT: A 616 SER cc_start: 0.8061 (p) cc_final: 0.7804 (p) REVERT: A 618 ASN cc_start: 0.8739 (m110) cc_final: 0.8341 (t0) REVERT: A 670 LEU cc_start: 0.8253 (mt) cc_final: 0.7226 (mp) REVERT: A 695 SER cc_start: 0.8194 (m) cc_final: 0.7850 (p) REVERT: A 699 ASN cc_start: 0.7322 (p0) cc_final: 0.6533 (p0) REVERT: A 1707 TRP cc_start: 0.5585 (t60) cc_final: 0.5356 (t60) REVERT: A 1729 GLN cc_start: 0.8009 (mm-40) cc_final: 0.7498 (mm110) REVERT: A 1786 TYR cc_start: 0.8397 (t80) cc_final: 0.7649 (t80) REVERT: A 1793 GLU cc_start: 0.7146 (tp30) cc_final: 0.6619 (tp30) REVERT: A 1845 LYS cc_start: 0.8030 (mmmm) cc_final: 0.7646 (mtpt) REVERT: A 1855 LEU cc_start: 0.8711 (tt) cc_final: 0.8484 (tp) REVERT: A 1874 GLN cc_start: 0.7137 (tp40) cc_final: 0.6864 (tp-100) REVERT: A 1887 LYS cc_start: 0.8885 (mtpt) cc_final: 0.8644 (mtpp) REVERT: A 1894 ASN cc_start: 0.8210 (t0) cc_final: 0.7881 (t0) REVERT: A 1936 GLN cc_start: 0.8259 (pp30) cc_final: 0.7876 (pp30) REVERT: A 1950 ASN cc_start: 0.8184 (t0) cc_final: 0.7973 (t0) REVERT: A 1955 SER cc_start: 0.8559 (m) cc_final: 0.8051 (p) REVERT: A 1973 MET cc_start: 0.7823 (mtt) cc_final: 0.7615 (mtp) REVERT: A 1978 LEU cc_start: 0.7185 (mt) cc_final: 0.6816 (mt) REVERT: A 1982 VAL cc_start: 0.8841 (t) cc_final: 0.8379 (p) REVERT: A 2094 SER cc_start: 0.7580 (m) cc_final: 0.7258 (m) REVERT: A 2164 MET cc_start: 0.7225 (ppp) cc_final: 0.6456 (ppp) REVERT: A 2239 LYS cc_start: 0.8442 (tttt) cc_final: 0.8234 (tptt) REVERT: A 2259 GLU cc_start: 0.7276 (mt-10) cc_final: 0.6897 (mt-10) REVERT: A 2284 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7463 (mm-40) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.1114 time to fit residues: 59.6807 Evaluate side-chains 285 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.0170 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 123 optimal weight: 0.2980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 HIS A 280 ASN A 281 HIS A 467 ASN A 468 GLN A 615 HIS ** A 618 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1906 GLN ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2316 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.136086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.118627 restraints weight = 20844.624| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 4.25 r_work: 0.3674 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10570 Z= 0.156 Angle : 0.736 13.006 14341 Z= 0.364 Chirality : 0.047 0.218 1533 Planarity : 0.005 0.056 1821 Dihedral : 5.443 24.331 1440 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 2.32 % Allowed : 12.57 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.23), residues: 1253 helix: -1.40 (0.53), residues: 72 sheet: -0.41 (0.29), residues: 346 loop : -1.76 (0.21), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 471 TYR 0.018 0.001 TYR A1709 PHE 0.025 0.002 PHE A 202 TRP 0.017 0.002 TRP A2313 HIS 0.015 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (10559) covalent geometry : angle 0.72884 / 0.36 (14316) SS BOND : bond 0.00587 / 0.20 ( 8) SS BOND : angle 2.71547 / 1.52 ( 16) hydrogen bonds : bond 0.03635 / 2.33 ( 233) hydrogen bonds : angle 6.91207 / 4.87 ( 597) link_NAG-ASN : bond 0.00547 / 0.26 ( 3) link_NAG-ASN : angle 2.36808 / 1.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 292 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 ARG cc_start: 0.7643 (mtp85) cc_final: 0.7419 (mtp85) REVERT: A 16 TYR cc_start: 0.6639 (OUTLIER) cc_final: 0.6004 (t80) REVERT: A 134 HIS cc_start: 0.7881 (t70) cc_final: 0.7539 (t70) REVERT: A 154 LEU cc_start: 0.9203 (mt) cc_final: 0.8882 (mp) REVERT: A 274 HIS cc_start: 0.7088 (m-70) cc_final: 0.6749 (m-70) REVERT: A 275 THR cc_start: 0.7127 (t) cc_final: 0.5128 (p) REVERT: A 309 PHE cc_start: 0.7775 (p90) cc_final: 0.7110 (p90) REVERT: A 323 TYR cc_start: 0.8206 (m-80) cc_final: 0.7999 (m-80) REVERT: A 429 MET cc_start: 0.7470 (tpp) cc_final: 0.7074 (tpp) REVERT: A 471 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7239 (mtp180) REVERT: A 512 LYS cc_start: 0.7896 (tttp) cc_final: 0.7607 (tttm) REVERT: A 540 GLU cc_start: 0.8495 (mp0) cc_final: 0.8051 (pm20) REVERT: A 552 LEU cc_start: 0.7914 (mt) cc_final: 0.7248 (pp) REVERT: A 567 MET cc_start: 0.4540 (mmp) cc_final: 0.4040 (mmt) REVERT: A 618 ASN cc_start: 0.8708 (m110) cc_final: 0.8295 (t0) REVERT: A 636 TYR cc_start: 0.8081 (m-80) cc_final: 0.7763 (m-80) REVERT: A 661 LYS cc_start: 0.8335 (pttm) cc_final: 0.8009 (ptmt) REVERT: A 671 PHE cc_start: 0.8170 (m-80) cc_final: 0.7798 (m-80) REVERT: A 676 GLU cc_start: 0.6717 (mp0) cc_final: 0.6237 (mp0) REVERT: A 695 SER cc_start: 0.8150 (m) cc_final: 0.7928 (p) REVERT: A 1711 MET cc_start: 0.7618 (ttm) cc_final: 0.7050 (ttm) REVERT: A 1752 LEU cc_start: 0.8794 (tp) cc_final: 0.8568 (tt) REVERT: A 1772 MET cc_start: 0.7753 (ttp) cc_final: 0.7484 (mtp) REVERT: A 1793 GLU cc_start: 0.7269 (tp30) cc_final: 0.6543 (tp30) REVERT: A 1806 PHE cc_start: 0.8013 (t80) cc_final: 0.7785 (t80) REVERT: A 1842 ASP cc_start: 0.6973 (p0) cc_final: 0.6461 (p0) REVERT: A 1874 GLN cc_start: 0.7180 (tp40) cc_final: 0.6780 (tp-100) REVERT: A 1875 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.7964 (pm20) REVERT: A 1887 LYS cc_start: 0.8928 (mtpt) cc_final: 0.8704 (mtpp) REVERT: A 1936 GLN cc_start: 0.8417 (pp30) cc_final: 0.7851 (pp30) REVERT: A 1967 LYS cc_start: 0.8983 (mmtm) cc_final: 0.8574 (mmtm) REVERT: A 1973 MET cc_start: 0.8020 (mtt) cc_final: 0.7698 (mtt) REVERT: A 1982 VAL cc_start: 0.8792 (t) cc_final: 0.8587 (p) REVERT: A 2027 MET cc_start: 0.6431 (ttm) cc_final: 0.5953 (ttm) REVERT: A 2091 GLN cc_start: 0.8391 (pt0) cc_final: 0.7992 (pt0) REVERT: A 2096 LEU cc_start: 0.8159 (mt) cc_final: 0.7892 (mt) REVERT: A 2111 LYS cc_start: 0.8468 (ptpt) cc_final: 0.8048 (ptpt) REVERT: A 2116 ARG cc_start: 0.8499 (ttt180) cc_final: 0.8225 (ttt180) REVERT: A 2164 MET cc_start: 0.7311 (ppp) cc_final: 0.6423 (ppp) REVERT: A 2239 LYS cc_start: 0.8570 (tttt) cc_final: 0.8220 (tptt) outliers start: 26 outliers final: 13 residues processed: 303 average time/residue: 0.1020 time to fit residues: 43.9051 Evaluate side-chains 280 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 264 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 475 ILE Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2289 SER Chi-restraints excluded: chain A residue 2296 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 53 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 114 optimal weight: 0.0020 chunk 80 optimal weight: 0.0870 chunk 75 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.4966 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 413 ASN A 467 ASN A 615 HIS A1729 GLN A1770 ASN ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2137 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.134121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.116917 restraints weight = 21133.330| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 4.15 r_work: 0.3667 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10570 Z= 0.149 Angle : 0.694 12.540 14341 Z= 0.345 Chirality : 0.047 0.181 1533 Planarity : 0.005 0.064 1821 Dihedral : 5.401 22.923 1440 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 3.65 % Allowed : 15.42 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.23), residues: 1253 helix: -1.47 (0.50), residues: 78 sheet: -0.47 (0.28), residues: 358 loop : -1.76 (0.21), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 405 TYR 0.019 0.001 TYR A1709 PHE 0.031 0.002 PHE A 652 TRP 0.023 0.002 TRP A1889 HIS 0.016 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (10559) covalent geometry : angle 0.68997 / 0.34 (14316) SS BOND : bond 0.00606 / 0.20 ( 8) SS BOND : angle 2.02753 / 1.14 ( 16) hydrogen bonds : bond 0.03280 / 2.10 ( 233) hydrogen bonds : angle 6.38735 / 4.50 ( 597) link_NAG-ASN : bond 0.00228 / 0.10 ( 3) link_NAG-ASN : angle 1.63678 / 0.98 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6754 (OUTLIER) cc_final: 0.6045 (t80) REVERT: A 154 LEU cc_start: 0.9130 (mt) cc_final: 0.8878 (mp) REVERT: A 155 THR cc_start: 0.8880 (m) cc_final: 0.8600 (p) REVERT: A 274 HIS cc_start: 0.7152 (m-70) cc_final: 0.6823 (m-70) REVERT: A 275 THR cc_start: 0.7041 (t) cc_final: 0.5067 (p) REVERT: A 309 PHE cc_start: 0.7753 (p90) cc_final: 0.7294 (p90) REVERT: A 429 MET cc_start: 0.7380 (tpp) cc_final: 0.7009 (tpp) REVERT: A 467 ASN cc_start: 0.8545 (OUTLIER) cc_final: 0.8315 (t0) REVERT: A 471 ARG cc_start: 0.7493 (OUTLIER) cc_final: 0.7143 (mtp180) REVERT: A 512 LYS cc_start: 0.7933 (tttp) cc_final: 0.7665 (tttm) REVERT: A 540 GLU cc_start: 0.8631 (mp0) cc_final: 0.8353 (pm20) REVERT: A 552 LEU cc_start: 0.7919 (mt) cc_final: 0.7344 (pp) REVERT: A 567 MET cc_start: 0.4613 (mmp) cc_final: 0.4151 (mmp) REVERT: A 616 SER cc_start: 0.7943 (p) cc_final: 0.7641 (p) REVERT: A 618 ASN cc_start: 0.8731 (m110) cc_final: 0.8303 (t0) REVERT: A 661 LYS cc_start: 0.8340 (pttm) cc_final: 0.8027 (ptmt) REVERT: A 676 GLU cc_start: 0.6753 (mp0) cc_final: 0.6211 (mp0) REVERT: A 695 SER cc_start: 0.8219 (m) cc_final: 0.7942 (p) REVERT: A 1695 THR cc_start: 0.7812 (OUTLIER) cc_final: 0.7450 (t) REVERT: A 1772 MET cc_start: 0.7759 (ttp) cc_final: 0.7347 (mtp) REVERT: A 1793 GLU cc_start: 0.7179 (tp30) cc_final: 0.6381 (tp30) REVERT: A 1811 GLU cc_start: 0.7877 (tp30) cc_final: 0.7395 (tm-30) REVERT: A 1816 PHE cc_start: 0.8431 (t80) cc_final: 0.8074 (t80) REVERT: A 1874 GLN cc_start: 0.7178 (tp40) cc_final: 0.6726 (tp-100) REVERT: A 1875 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8050 (pm20) REVERT: A 1887 LYS cc_start: 0.8991 (mtpt) cc_final: 0.8662 (mtpp) REVERT: A 1936 GLN cc_start: 0.8499 (pp30) cc_final: 0.7981 (pp30) REVERT: A 1967 LYS cc_start: 0.8986 (mmtm) cc_final: 0.8600 (mmtm) REVERT: A 1970 GLU cc_start: 0.8306 (pm20) cc_final: 0.8094 (pm20) REVERT: A 1973 MET cc_start: 0.7906 (mtt) cc_final: 0.7562 (mtm) REVERT: A 1982 VAL cc_start: 0.8824 (t) cc_final: 0.8617 (p) REVERT: A 2027 MET cc_start: 0.6383 (ttm) cc_final: 0.6054 (ttm) REVERT: A 2091 GLN cc_start: 0.8439 (pt0) cc_final: 0.7952 (pt0) REVERT: A 2116 ARG cc_start: 0.8484 (ttt180) cc_final: 0.8144 (ttt180) REVERT: A 2164 MET cc_start: 0.7283 (ppp) cc_final: 0.6422 (ppp) REVERT: A 2209 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7772 (mtt-85) REVERT: A 2258 LYS cc_start: 0.8107 (tppt) cc_final: 0.7885 (tppt) REVERT: A 2284 GLN cc_start: 0.7908 (mm-40) cc_final: 0.7487 (mm-40) outliers start: 41 outliers final: 20 residues processed: 290 average time/residue: 0.1028 time to fit residues: 41.9818 Evaluate side-chains 290 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 467 ASN Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2137 HIS Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 281 HIS A 590 ASN A 615 HIS A1729 GLN A1770 ASN A1961 HIS ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.130547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113283 restraints weight = 21274.881| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 4.21 r_work: 0.3582 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10570 Z= 0.213 Angle : 0.712 11.139 14341 Z= 0.359 Chirality : 0.047 0.205 1533 Planarity : 0.005 0.062 1821 Dihedral : 5.752 29.785 1440 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 4.46 % Allowed : 16.67 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.23), residues: 1253 helix: -1.53 (0.53), residues: 72 sheet: -0.49 (0.28), residues: 361 loop : -1.93 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 405 TYR 0.017 0.002 TYR A 323 PHE 0.027 0.002 PHE A 652 TRP 0.019 0.002 TRP A 138 HIS 0.016 0.001 HIS A2137 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (10559) covalent geometry : angle 0.70816 / 0.36 (14316) SS BOND : bond 0.00982 / 0.30 ( 8) SS BOND : angle 1.89489 / 1.05 ( 16) hydrogen bonds : bond 0.03583 / 2.32 ( 233) hydrogen bonds : angle 6.39392 / 4.47 ( 597) link_NAG-ASN : bond 0.00219 / 0.10 ( 3) link_NAG-ASN : angle 2.10590 / 1.25 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 285 time to evaluate : 0.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.6314 (t80) REVERT: A 47 LYS cc_start: 0.8949 (ttpt) cc_final: 0.8623 (ttmm) REVERT: A 274 HIS cc_start: 0.7453 (m-70) cc_final: 0.7099 (m-70) REVERT: A 275 THR cc_start: 0.7079 (t) cc_final: 0.5095 (p) REVERT: A 309 PHE cc_start: 0.7787 (p90) cc_final: 0.7344 (p90) REVERT: A 320 MET cc_start: 0.8011 (OUTLIER) cc_final: 0.7781 (ptp) REVERT: A 323 TYR cc_start: 0.8351 (m-80) cc_final: 0.8115 (m-80) REVERT: A 429 MET cc_start: 0.7457 (tpp) cc_final: 0.6457 (tpp) REVERT: A 459 ASP cc_start: 0.7734 (m-30) cc_final: 0.7411 (m-30) REVERT: A 471 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7147 (mtp180) REVERT: A 552 LEU cc_start: 0.8005 (mt) cc_final: 0.7295 (pp) REVERT: A 567 MET cc_start: 0.4563 (mmp) cc_final: 0.4096 (mmp) REVERT: A 616 SER cc_start: 0.7961 (p) cc_final: 0.7710 (p) REVERT: A 618 ASN cc_start: 0.8791 (m110) cc_final: 0.8294 (t0) REVERT: A 661 LYS cc_start: 0.8309 (pttm) cc_final: 0.8001 (ptmt) REVERT: A 679 PHE cc_start: 0.8466 (t80) cc_final: 0.8138 (t80) REVERT: A 1695 THR cc_start: 0.7805 (OUTLIER) cc_final: 0.7446 (t) REVERT: A 1772 MET cc_start: 0.7594 (ttp) cc_final: 0.7311 (mtp) REVERT: A 1775 PHE cc_start: 0.7421 (t80) cc_final: 0.6160 (t80) REVERT: A 1793 GLU cc_start: 0.7131 (tp30) cc_final: 0.6283 (tp30) REVERT: A 1804 LYS cc_start: 0.8845 (pptt) cc_final: 0.8606 (ptmm) REVERT: A 1811 GLU cc_start: 0.8035 (tp30) cc_final: 0.7416 (tm-30) REVERT: A 1874 GLN cc_start: 0.7154 (tp40) cc_final: 0.6725 (tp-100) REVERT: A 1875 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: A 1887 LYS cc_start: 0.9062 (mtpt) cc_final: 0.8783 (mtpp) REVERT: A 1936 GLN cc_start: 0.8700 (pp30) cc_final: 0.8149 (pp30) REVERT: A 1938 GLN cc_start: 0.8306 (OUTLIER) cc_final: 0.8010 (tp-100) REVERT: A 1967 LYS cc_start: 0.8891 (mmtm) cc_final: 0.8616 (mmtm) REVERT: A 1973 MET cc_start: 0.7926 (mtt) cc_final: 0.7559 (mtp) REVERT: A 1978 LEU cc_start: 0.7293 (mm) cc_final: 0.7051 (mm) REVERT: A 2027 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.5886 (ttm) REVERT: A 2079 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.7397 (mmm) REVERT: A 2164 MET cc_start: 0.7472 (ppp) cc_final: 0.6518 (ppp) REVERT: A 2209 ARG cc_start: 0.8218 (mtt180) cc_final: 0.7982 (mtt180) REVERT: A 2239 LYS cc_start: 0.8581 (tttt) cc_final: 0.8145 (tptp) REVERT: A 2258 LYS cc_start: 0.8166 (tppt) cc_final: 0.7921 (tppt) REVERT: A 2284 GLN cc_start: 0.7981 (mm-40) cc_final: 0.7610 (mm-40) REVERT: A 2293 VAL cc_start: 0.8522 (t) cc_final: 0.8193 (p) outliers start: 50 outliers final: 26 residues processed: 304 average time/residue: 0.1029 time to fit residues: 44.1260 Evaluate side-chains 297 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 577 SER Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2079 MET Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2114 THR Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2238 MET Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Chi-restraints excluded: chain A residue 2302 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 29 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 97 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN A 693 HIS A1729 GLN A1770 ASN ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.130552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.113094 restraints weight = 21234.383| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 4.21 r_work: 0.3575 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10570 Z= 0.162 Angle : 0.705 11.701 14341 Z= 0.351 Chirality : 0.047 0.183 1533 Planarity : 0.005 0.066 1821 Dihedral : 5.638 32.078 1440 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 5.35 % Allowed : 17.91 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.23), residues: 1253 helix: -1.79 (0.47), residues: 85 sheet: -0.46 (0.28), residues: 358 loop : -2.00 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 405 TYR 0.021 0.002 TYR A 136 PHE 0.028 0.002 PHE A 652 TRP 0.017 0.002 TRP A2313 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 (10559) covalent geometry : angle 0.70222 / 0.35 (14316) SS BOND : bond 0.00491 / 0.16 ( 8) SS BOND : angle 1.49273 / 0.82 ( 16) hydrogen bonds : bond 0.03262 / 2.09 ( 233) hydrogen bonds : angle 6.21778 / 4.39 ( 597) link_NAG-ASN : bond 0.00157 / 0.08 ( 3) link_NAG-ASN : angle 2.07549 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 268 time to evaluate : 0.385 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 16 TYR cc_start: 0.6918 (OUTLIER) cc_final: 0.6218 (t80) REVERT: A 47 LYS cc_start: 0.8944 (ttpt) cc_final: 0.8657 (ttmm) REVERT: A 163 ASP cc_start: 0.8348 (t70) cc_final: 0.8105 (t70) REVERT: A 274 HIS cc_start: 0.7337 (m-70) cc_final: 0.7005 (m-70) REVERT: A 275 THR cc_start: 0.7171 (t) cc_final: 0.5166 (p) REVERT: A 323 TYR cc_start: 0.8427 (m-80) cc_final: 0.8204 (m-80) REVERT: A 429 MET cc_start: 0.7546 (tpp) cc_final: 0.7156 (tpp) REVERT: A 459 ASP cc_start: 0.7734 (m-30) cc_final: 0.7361 (m-30) REVERT: A 471 ARG cc_start: 0.7526 (OUTLIER) cc_final: 0.7119 (mtp180) REVERT: A 552 LEU cc_start: 0.8023 (mt) cc_final: 0.7341 (pp) REVERT: A 616 SER cc_start: 0.7985 (p) cc_final: 0.7738 (p) REVERT: A 618 ASN cc_start: 0.8706 (m110) cc_final: 0.8216 (t0) REVERT: A 661 LYS cc_start: 0.8305 (pttm) cc_final: 0.8001 (ptmt) REVERT: A 676 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6673 (mp0) REVERT: A 679 PHE cc_start: 0.8493 (t80) cc_final: 0.8058 (t80) REVERT: A 700 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7779 (mtp85) REVERT: A 1695 THR cc_start: 0.7779 (OUTLIER) cc_final: 0.7410 (t) REVERT: A 1752 LEU cc_start: 0.8786 (tp) cc_final: 0.8581 (tt) REVERT: A 1772 MET cc_start: 0.7562 (ttp) cc_final: 0.7309 (mtp) REVERT: A 1793 GLU cc_start: 0.7146 (tp30) cc_final: 0.6299 (tp30) REVERT: A 1811 GLU cc_start: 0.8011 (tp30) cc_final: 0.7412 (tm-30) REVERT: A 1839 SER cc_start: 0.7753 (OUTLIER) cc_final: 0.7433 (p) REVERT: A 1875 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8039 (pm20) REVERT: A 1887 LYS cc_start: 0.9070 (mtpt) cc_final: 0.8740 (mtpp) REVERT: A 1936 GLN cc_start: 0.8627 (pp30) cc_final: 0.8090 (pp30) REVERT: A 1938 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7669 (tp-100) REVERT: A 1973 MET cc_start: 0.7877 (mtt) cc_final: 0.7587 (mtt) REVERT: A 1978 LEU cc_start: 0.7269 (mm) cc_final: 0.6983 (mm) REVERT: A 2027 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5877 (ttm) REVERT: A 2091 GLN cc_start: 0.8605 (pt0) cc_final: 0.8022 (pt0) REVERT: A 2164 MET cc_start: 0.7422 (ppp) cc_final: 0.6498 (ppp) REVERT: A 2176 MET cc_start: 0.7213 (ppp) cc_final: 0.6871 (tmm) REVERT: A 2239 LYS cc_start: 0.8612 (tttt) cc_final: 0.8162 (tppt) REVERT: A 2258 LYS cc_start: 0.8035 (tppt) cc_final: 0.7822 (tppt) REVERT: A 2284 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7670 (mm-40) outliers start: 60 outliers final: 40 residues processed: 290 average time/residue: 0.1050 time to fit residues: 42.7774 Evaluate side-chains 308 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 260 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 68 TRP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 700 ARG Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1823 MET Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1891 PHE Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2098 ILE Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2238 MET Chi-restraints excluded: chain A residue 2275 PHE Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 95 optimal weight: 0.0050 chunk 56 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 30 optimal weight: 0.0980 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 305 GLN ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A1770 ASN ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.130926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.113451 restraints weight = 21293.327| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 4.24 r_work: 0.3574 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10570 Z= 0.151 Angle : 0.713 11.520 14341 Z= 0.351 Chirality : 0.046 0.185 1533 Planarity : 0.005 0.069 1821 Dihedral : 5.637 37.377 1440 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 5.08 % Allowed : 20.05 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.23), residues: 1253 helix: -1.81 (0.47), residues: 85 sheet: -0.42 (0.29), residues: 355 loop : -1.90 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 405 TYR 0.021 0.001 TYR A 407 PHE 0.028 0.002 PHE A 652 TRP 0.028 0.002 TRP A1889 HIS 0.006 0.001 HIS A 632 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (10559) covalent geometry : angle 0.70977 / 0.35 (14316) SS BOND : bond 0.00582 / 0.19 ( 8) SS BOND : angle 1.52299 / 0.82 ( 16) hydrogen bonds : bond 0.03116 / 2.03 ( 233) hydrogen bonds : angle 6.14549 / 4.32 ( 597) link_NAG-ASN : bond 0.00150 / 0.07 ( 3) link_NAG-ASN : angle 2.03219 / 1.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 266 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.6298 (t80) REVERT: A 47 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8643 (ttmm) REVERT: A 163 ASP cc_start: 0.8346 (t70) cc_final: 0.7920 (t70) REVERT: A 274 HIS cc_start: 0.7345 (m-70) cc_final: 0.7056 (m-70) REVERT: A 275 THR cc_start: 0.7135 (t) cc_final: 0.5080 (p) REVERT: A 323 TYR cc_start: 0.8513 (m-80) cc_final: 0.8125 (m-80) REVERT: A 429 MET cc_start: 0.7686 (tpp) cc_final: 0.7157 (tpp) REVERT: A 459 ASP cc_start: 0.7790 (m-30) cc_final: 0.7411 (m-30) REVERT: A 471 ARG cc_start: 0.7449 (OUTLIER) cc_final: 0.7036 (mtp180) REVERT: A 512 LYS cc_start: 0.7930 (pttt) cc_final: 0.7562 (pttp) REVERT: A 531 ARG cc_start: 0.7688 (mmt-90) cc_final: 0.7477 (mmt-90) REVERT: A 552 LEU cc_start: 0.8060 (mt) cc_final: 0.7358 (pp) REVERT: A 616 SER cc_start: 0.7976 (p) cc_final: 0.7721 (p) REVERT: A 618 ASN cc_start: 0.8722 (m110) cc_final: 0.8220 (t0) REVERT: A 656 TYR cc_start: 0.6460 (m-10) cc_final: 0.5984 (m-80) REVERT: A 661 LYS cc_start: 0.8341 (pttm) cc_final: 0.8059 (ptmt) REVERT: A 676 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6815 (mp0) REVERT: A 679 PHE cc_start: 0.8459 (t80) cc_final: 0.7970 (t80) REVERT: A 1695 THR cc_start: 0.7810 (OUTLIER) cc_final: 0.7465 (t) REVERT: A 1772 MET cc_start: 0.7520 (ttp) cc_final: 0.7296 (mtp) REVERT: A 1793 GLU cc_start: 0.7140 (tp30) cc_final: 0.6272 (tp30) REVERT: A 1811 GLU cc_start: 0.8050 (tp30) cc_final: 0.7429 (tm-30) REVERT: A 1839 SER cc_start: 0.7793 (OUTLIER) cc_final: 0.7468 (p) REVERT: A 1874 GLN cc_start: 0.7475 (mp10) cc_final: 0.7147 (mp10) REVERT: A 1887 LYS cc_start: 0.9076 (mtpt) cc_final: 0.8811 (mtpp) REVERT: A 1936 GLN cc_start: 0.8596 (pp30) cc_final: 0.8116 (tm-30) REVERT: A 1938 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7731 (tp40) REVERT: A 1973 MET cc_start: 0.7881 (mtt) cc_final: 0.7588 (mtt) REVERT: A 2027 MET cc_start: 0.6464 (ttm) cc_final: 0.6011 (ttm) REVERT: A 2091 GLN cc_start: 0.8624 (pt0) cc_final: 0.8039 (pt0) REVERT: A 2164 MET cc_start: 0.7491 (ppp) cc_final: 0.6556 (ppp) REVERT: A 2176 MET cc_start: 0.7325 (ppp) cc_final: 0.6977 (tmm) REVERT: A 2239 LYS cc_start: 0.8573 (tttt) cc_final: 0.8214 (tppt) REVERT: A 2258 LYS cc_start: 0.7999 (tppt) cc_final: 0.7771 (tppt) REVERT: A 2284 GLN cc_start: 0.8067 (mm-40) cc_final: 0.7740 (mm-40) REVERT: A 2302 LEU cc_start: 0.8714 (mt) cc_final: 0.8503 (mt) REVERT: A 2303 THR cc_start: 0.7968 (p) cc_final: 0.7654 (t) outliers start: 57 outliers final: 40 residues processed: 289 average time/residue: 0.1042 time to fit residues: 42.7192 Evaluate side-chains 292 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 297 GLN Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 708 VAL Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1756 LEU Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1823 MET Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1873 VAL Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2114 THR Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2275 PHE Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 19 optimal weight: 0.0970 chunk 120 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 122 optimal weight: 3.9990 chunk 123 optimal weight: 0.2980 chunk 100 optimal weight: 1.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1770 ASN ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.128798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111130 restraints weight = 21104.520| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 4.21 r_work: 0.3541 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.4951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10570 Z= 0.192 Angle : 0.738 11.520 14341 Z= 0.368 Chirality : 0.047 0.183 1533 Planarity : 0.005 0.072 1821 Dihedral : 5.835 39.358 1440 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 4.72 % Allowed : 21.66 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.23), residues: 1253 helix: -1.70 (0.48), residues: 85 sheet: -0.53 (0.28), residues: 356 loop : -1.95 (0.21), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1997 TYR 0.026 0.002 TYR A 407 PHE 0.026 0.002 PHE A 652 TRP 0.023 0.002 TRP A1889 HIS 0.028 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 (10559) covalent geometry : angle 0.73465 / 0.37 (14316) SS BOND : bond 0.00476 / 0.16 ( 8) SS BOND : angle 1.65017 / 0.90 ( 16) hydrogen bonds : bond 0.03331 / 2.16 ( 233) hydrogen bonds : angle 6.21509 / 4.37 ( 597) link_NAG-ASN : bond 0.00160 / 0.08 ( 3) link_NAG-ASN : angle 2.12186 / 1.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 256 time to evaluate : 0.381 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 16 TYR cc_start: 0.7004 (OUTLIER) cc_final: 0.6378 (t80) REVERT: A 47 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8685 (ttmm) REVERT: A 134 HIS cc_start: 0.7728 (t70) cc_final: 0.6978 (t70) REVERT: A 163 ASP cc_start: 0.8355 (t70) cc_final: 0.7327 (p0) REVERT: A 274 HIS cc_start: 0.7411 (m-70) cc_final: 0.7118 (m-70) REVERT: A 275 THR cc_start: 0.7221 (t) cc_final: 0.5271 (p) REVERT: A 309 PHE cc_start: 0.7768 (p90) cc_final: 0.7181 (p90) REVERT: A 429 MET cc_start: 0.7681 (tpp) cc_final: 0.7060 (tpp) REVERT: A 459 ASP cc_start: 0.7805 (m-30) cc_final: 0.7388 (m-30) REVERT: A 471 ARG cc_start: 0.7541 (OUTLIER) cc_final: 0.7156 (mtp180) REVERT: A 512 LYS cc_start: 0.7981 (pttt) cc_final: 0.7548 (pttp) REVERT: A 552 LEU cc_start: 0.8101 (mt) cc_final: 0.7350 (pp) REVERT: A 577 SER cc_start: 0.8132 (m) cc_final: 0.7591 (t) REVERT: A 618 ASN cc_start: 0.8768 (m110) cc_final: 0.8261 (t0) REVERT: A 632 HIS cc_start: 0.8803 (m90) cc_final: 0.8514 (m90) REVERT: A 661 LYS cc_start: 0.8324 (pttm) cc_final: 0.8098 (ptmt) REVERT: A 676 GLU cc_start: 0.7364 (mm-30) cc_final: 0.6861 (mp0) REVERT: A 1695 THR cc_start: 0.7835 (OUTLIER) cc_final: 0.7570 (t) REVERT: A 1793 GLU cc_start: 0.7210 (tp30) cc_final: 0.6364 (tp30) REVERT: A 1811 GLU cc_start: 0.8044 (tp30) cc_final: 0.7458 (tm-30) REVERT: A 1839 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7576 (p) REVERT: A 1885 GLU cc_start: 0.7861 (pm20) cc_final: 0.7650 (pm20) REVERT: A 1887 LYS cc_start: 0.9050 (mtpt) cc_final: 0.8785 (mtpp) REVERT: A 1936 GLN cc_start: 0.8678 (pp30) cc_final: 0.8129 (pp30) REVERT: A 1938 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.7933 (tp-100) REVERT: A 1973 MET cc_start: 0.7913 (mtt) cc_final: 0.7622 (mtt) REVERT: A 2027 MET cc_start: 0.6586 (OUTLIER) cc_final: 0.5846 (ttt) REVERT: A 2091 GLN cc_start: 0.8642 (pt0) cc_final: 0.8062 (pt0) REVERT: A 2164 MET cc_start: 0.7467 (ppp) cc_final: 0.6541 (ppp) REVERT: A 2176 MET cc_start: 0.7409 (ppp) cc_final: 0.7076 (tmm) REVERT: A 2209 ARG cc_start: 0.8242 (mtt180) cc_final: 0.6890 (mtp180) REVERT: A 2238 MET cc_start: 0.7342 (tpp) cc_final: 0.7050 (tpp) REVERT: A 2239 LYS cc_start: 0.8553 (tttt) cc_final: 0.8152 (tppt) REVERT: A 2284 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7772 (mm-40) REVERT: A 2293 VAL cc_start: 0.8587 (t) cc_final: 0.8202 (p) REVERT: A 2303 THR cc_start: 0.8124 (p) cc_final: 0.7797 (t) outliers start: 53 outliers final: 39 residues processed: 280 average time/residue: 0.1022 time to fit residues: 40.4836 Evaluate side-chains 298 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 253 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 444 HIS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1823 MET Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1873 VAL Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2098 ILE Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2114 THR Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2275 PHE Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 120 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.128582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.111140 restraints weight = 21233.946| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 4.16 r_work: 0.3538 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10570 Z= 0.184 Angle : 0.746 11.783 14341 Z= 0.371 Chirality : 0.047 0.167 1533 Planarity : 0.005 0.074 1821 Dihedral : 5.874 40.849 1440 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 4.19 % Allowed : 22.19 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.28 (0.23), residues: 1253 helix: -1.84 (0.47), residues: 85 sheet: -0.56 (0.29), residues: 344 loop : -2.01 (0.20), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 405 TYR 0.023 0.002 TYR A 323 PHE 0.028 0.002 PHE A 652 TRP 0.022 0.002 TRP A2046 HIS 0.005 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 (10559) covalent geometry : angle 0.74241 / 0.37 (14316) SS BOND : bond 0.00489 / 0.17 ( 8) SS BOND : angle 1.76098 / 0.97 ( 16) hydrogen bonds : bond 0.03351 / 2.17 ( 233) hydrogen bonds : angle 6.20506 / 4.35 ( 597) link_NAG-ASN : bond 0.00201 / 0.10 ( 3) link_NAG-ASN : angle 2.15789 / 1.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7072 (OUTLIER) cc_final: 0.6505 (t80) REVERT: A 47 LYS cc_start: 0.8998 (ttpt) cc_final: 0.8697 (ttmm) REVERT: A 163 ASP cc_start: 0.8251 (t70) cc_final: 0.7297 (p0) REVERT: A 231 MET cc_start: 0.5765 (OUTLIER) cc_final: 0.5428 (mtt) REVERT: A 240 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8613 (ttm110) REVERT: A 274 HIS cc_start: 0.7492 (m-70) cc_final: 0.7208 (m-70) REVERT: A 275 THR cc_start: 0.7203 (t) cc_final: 0.5256 (p) REVERT: A 302 ASP cc_start: 0.8469 (t0) cc_final: 0.8219 (m-30) REVERT: A 309 PHE cc_start: 0.7837 (p90) cc_final: 0.7231 (p90) REVERT: A 323 TYR cc_start: 0.8332 (m-80) cc_final: 0.8089 (m-80) REVERT: A 429 MET cc_start: 0.7705 (tpp) cc_final: 0.7098 (tpp) REVERT: A 459 ASP cc_start: 0.7730 (m-30) cc_final: 0.7337 (m-30) REVERT: A 471 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7271 (mtp180) REVERT: A 512 LYS cc_start: 0.8017 (pttt) cc_final: 0.7625 (pttp) REVERT: A 552 LEU cc_start: 0.8087 (mt) cc_final: 0.7346 (pp) REVERT: A 567 MET cc_start: 0.5337 (mmp) cc_final: 0.4889 (mmp) REVERT: A 577 SER cc_start: 0.8053 (m) cc_final: 0.7632 (t) REVERT: A 618 ASN cc_start: 0.8757 (m110) cc_final: 0.8309 (t0) REVERT: A 626 GLN cc_start: 0.8585 (tt0) cc_final: 0.8120 (tt0) REVERT: A 676 GLU cc_start: 0.7429 (mm-30) cc_final: 0.6949 (mp0) REVERT: A 679 PHE cc_start: 0.8508 (t80) cc_final: 0.8125 (t80) REVERT: A 1695 THR cc_start: 0.7840 (OUTLIER) cc_final: 0.7444 (t) REVERT: A 1772 MET cc_start: 0.7614 (ttp) cc_final: 0.7285 (mtp) REVERT: A 1793 GLU cc_start: 0.7271 (tp30) cc_final: 0.6445 (tp30) REVERT: A 1811 GLU cc_start: 0.7972 (tp30) cc_final: 0.7413 (tm-30) REVERT: A 1839 SER cc_start: 0.8084 (OUTLIER) cc_final: 0.7679 (p) REVERT: A 1887 LYS cc_start: 0.9048 (mtpt) cc_final: 0.8787 (mtpp) REVERT: A 1936 GLN cc_start: 0.8629 (pp30) cc_final: 0.8094 (pp30) REVERT: A 1938 GLN cc_start: 0.8526 (OUTLIER) cc_final: 0.8080 (tp-100) REVERT: A 1973 MET cc_start: 0.7891 (mtt) cc_final: 0.7615 (mtt) REVERT: A 2027 MET cc_start: 0.6599 (OUTLIER) cc_final: 0.5867 (ttt) REVERT: A 2164 MET cc_start: 0.7429 (ppp) cc_final: 0.6525 (ppp) REVERT: A 2176 MET cc_start: 0.7486 (ppp) cc_final: 0.7172 (tmm) REVERT: A 2239 LYS cc_start: 0.8584 (tttt) cc_final: 0.8099 (tppt) REVERT: A 2259 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7472 (tm-30) REVERT: A 2284 GLN cc_start: 0.8020 (mm-40) cc_final: 0.7709 (mm-40) REVERT: A 2293 VAL cc_start: 0.8581 (t) cc_final: 0.8191 (p) REVERT: A 2327 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7737 (tp30) outliers start: 47 outliers final: 37 residues processed: 282 average time/residue: 0.0965 time to fit residues: 38.3726 Evaluate side-chains 305 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 260 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1703 VAL Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1823 MET Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1873 VAL Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2114 THR Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2156 TYR Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 3 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 46 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 115 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 ASN A 281 HIS ** A 582 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 590 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.128794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.111206 restraints weight = 21222.577| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 4.22 r_work: 0.3540 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10570 Z= 0.162 Angle : 0.764 12.415 14341 Z= 0.378 Chirality : 0.047 0.193 1533 Planarity : 0.005 0.068 1821 Dihedral : 5.856 41.312 1440 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 4.63 % Allowed : 23.53 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.32 (0.23), residues: 1253 helix: -1.85 (0.46), residues: 91 sheet: -0.52 (0.29), residues: 352 loop : -2.10 (0.20), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 531 TYR 0.025 0.002 TYR A 323 PHE 0.028 0.002 PHE A 652 TRP 0.020 0.002 TRP A1889 HIS 0.007 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (10559) covalent geometry : angle 0.76054 / 0.38 (14316) SS BOND : bond 0.00921 / 0.29 ( 8) SS BOND : angle 1.77580 / 0.97 ( 16) hydrogen bonds : bond 0.03224 / 2.11 ( 233) hydrogen bonds : angle 6.15287 / 4.33 ( 597) link_NAG-ASN : bond 0.00165 / 0.08 ( 3) link_NAG-ASN : angle 2.06394 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6505 (t80) REVERT: A 47 LYS cc_start: 0.8977 (ttpt) cc_final: 0.8663 (ttmm) REVERT: A 99 HIS cc_start: 0.8084 (t-170) cc_final: 0.7801 (t-90) REVERT: A 110 GLU cc_start: 0.7235 (mp0) cc_final: 0.6966 (mp0) REVERT: A 134 HIS cc_start: 0.7704 (t70) cc_final: 0.7142 (t70) REVERT: A 163 ASP cc_start: 0.8180 (t70) cc_final: 0.7137 (p0) REVERT: A 231 MET cc_start: 0.5740 (OUTLIER) cc_final: 0.5426 (mtt) REVERT: A 274 HIS cc_start: 0.7466 (m-70) cc_final: 0.7196 (m-70) REVERT: A 275 THR cc_start: 0.7052 (t) cc_final: 0.5084 (p) REVERT: A 309 PHE cc_start: 0.7816 (p90) cc_final: 0.7233 (p90) REVERT: A 429 MET cc_start: 0.7753 (tpp) cc_final: 0.7184 (tpp) REVERT: A 459 ASP cc_start: 0.7734 (m-30) cc_final: 0.7344 (m-30) REVERT: A 471 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7276 (mtp180) REVERT: A 512 LYS cc_start: 0.8020 (pttt) cc_final: 0.7643 (pttp) REVERT: A 552 LEU cc_start: 0.8100 (mt) cc_final: 0.7411 (pp) REVERT: A 567 MET cc_start: 0.5188 (mmp) cc_final: 0.4674 (mmp) REVERT: A 577 SER cc_start: 0.8042 (m) cc_final: 0.7632 (t) REVERT: A 618 ASN cc_start: 0.8702 (m110) cc_final: 0.8443 (m-40) REVERT: A 626 GLN cc_start: 0.8586 (tt0) cc_final: 0.8124 (tt0) REVERT: A 676 GLU cc_start: 0.7394 (mm-30) cc_final: 0.6892 (mp0) REVERT: A 1695 THR cc_start: 0.7856 (OUTLIER) cc_final: 0.7437 (t) REVERT: A 1772 MET cc_start: 0.7635 (ttp) cc_final: 0.7298 (mtp) REVERT: A 1793 GLU cc_start: 0.7296 (tp30) cc_final: 0.6444 (tp30) REVERT: A 1811 GLU cc_start: 0.7941 (tp30) cc_final: 0.7385 (tm-30) REVERT: A 1839 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7635 (p) REVERT: A 1885 GLU cc_start: 0.7846 (pm20) cc_final: 0.7573 (pm20) REVERT: A 1887 LYS cc_start: 0.9042 (mtpt) cc_final: 0.8777 (mtpp) REVERT: A 1936 GLN cc_start: 0.8613 (pp30) cc_final: 0.8074 (pp30) REVERT: A 1938 GLN cc_start: 0.8515 (OUTLIER) cc_final: 0.8062 (tp-100) REVERT: A 1973 MET cc_start: 0.7908 (mtt) cc_final: 0.7639 (mtt) REVERT: A 1978 LEU cc_start: 0.7061 (mm) cc_final: 0.6815 (mm) REVERT: A 2027 MET cc_start: 0.6569 (OUTLIER) cc_final: 0.5836 (ttt) REVERT: A 2116 ARG cc_start: 0.8541 (ttt180) cc_final: 0.8261 (ttt180) REVERT: A 2164 MET cc_start: 0.7359 (ppp) cc_final: 0.6448 (ppp) REVERT: A 2176 MET cc_start: 0.7414 (ppp) cc_final: 0.7115 (tmm) REVERT: A 2239 LYS cc_start: 0.8536 (tttt) cc_final: 0.8067 (tppt) REVERT: A 2259 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7469 (tm-30) REVERT: A 2284 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7701 (mm-40) REVERT: A 2293 VAL cc_start: 0.8557 (t) cc_final: 0.8158 (p) outliers start: 52 outliers final: 36 residues processed: 284 average time/residue: 0.0905 time to fit residues: 36.0750 Evaluate side-chains 298 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 625 LEU Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1812 THR Chi-restraints excluded: chain A residue 1823 MET Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1873 VAL Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 1988 MET Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2098 ILE Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2114 THR Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 99 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 73 optimal weight: 0.0870 chunk 27 optimal weight: 0.1980 chunk 45 optimal weight: 2.9990 chunk 65 optimal weight: 0.0870 chunk 114 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 590 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 693 HIS A1859 HIS ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** 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 = 0.3970 r_free = 0.3970 target = 0.127117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.110404 restraints weight = 21199.824| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 4.04 r_work: 0.3594 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10570 Z= 0.139 Angle : 0.771 13.042 14341 Z= 0.378 Chirality : 0.047 0.170 1533 Planarity : 0.005 0.065 1821 Dihedral : 5.710 40.871 1440 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 4.19 % Allowed : 24.33 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.23), residues: 1253 helix: -1.73 (0.48), residues: 91 sheet: -0.36 (0.29), residues: 335 loop : -2.04 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 405 TYR 0.021 0.001 TYR A 407 PHE 0.027 0.002 PHE A 652 TRP 0.025 0.002 TRP A 106 HIS 0.004 0.001 HIS A 384 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10559) covalent geometry : angle 0.76785 / 0.38 (14316) SS BOND : bond 0.00586 / 0.19 ( 8) SS BOND : angle 1.64299 / 0.90 ( 16) hydrogen bonds : bond 0.03005 / 1.94 ( 233) hydrogen bonds : angle 6.07370 / 4.29 ( 597) link_NAG-ASN : bond 0.00141 / 0.07 ( 3) link_NAG-ASN : angle 1.96373 / 1.14 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2506 Ramachandran restraints generated. 1253 Oldfield, 0 Emsley, 1253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 0.308 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: A 16 TYR cc_start: 0.6980 (OUTLIER) cc_final: 0.6439 (t80) REVERT: A 47 LYS cc_start: 0.8984 (ttpt) cc_final: 0.8696 (ttmm) REVERT: A 134 HIS cc_start: 0.7618 (t70) cc_final: 0.7017 (t70) REVERT: A 154 LEU cc_start: 0.9105 (mt) cc_final: 0.8877 (mt) REVERT: A 163 ASP cc_start: 0.8093 (t70) cc_final: 0.7154 (p0) REVERT: A 202 PHE cc_start: 0.8819 (m-80) cc_final: 0.8473 (m-80) REVERT: A 274 HIS cc_start: 0.7249 (m-70) cc_final: 0.7048 (m-70) REVERT: A 275 THR cc_start: 0.7001 (t) cc_final: 0.5001 (p) REVERT: A 309 PHE cc_start: 0.7829 (p90) cc_final: 0.7269 (p90) REVERT: A 323 TYR cc_start: 0.8228 (m-80) cc_final: 0.7926 (t80) REVERT: A 429 MET cc_start: 0.7767 (tpp) cc_final: 0.7261 (tpp) REVERT: A 459 ASP cc_start: 0.7798 (m-30) cc_final: 0.7459 (m-30) REVERT: A 471 ARG cc_start: 0.7553 (OUTLIER) cc_final: 0.7215 (mtp180) REVERT: A 512 LYS cc_start: 0.8158 (pttt) cc_final: 0.7776 (pttp) REVERT: A 567 MET cc_start: 0.5101 (mmp) cc_final: 0.4601 (mmp) REVERT: A 577 SER cc_start: 0.8005 (m) cc_final: 0.7634 (t) REVERT: A 618 ASN cc_start: 0.8558 (m110) cc_final: 0.8344 (m-40) REVERT: A 626 GLN cc_start: 0.8593 (tt0) cc_final: 0.8132 (tt0) REVERT: A 676 GLU cc_start: 0.7392 (mm-30) cc_final: 0.6971 (mp0) REVERT: A 1695 THR cc_start: 0.7789 (OUTLIER) cc_final: 0.7377 (t) REVERT: A 1772 MET cc_start: 0.7689 (ttp) cc_final: 0.7387 (mtp) REVERT: A 1793 GLU cc_start: 0.7271 (tp30) cc_final: 0.6464 (tp30) REVERT: A 1811 GLU cc_start: 0.7867 (tp30) cc_final: 0.7371 (tm-30) REVERT: A 1839 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7633 (p) REVERT: A 1885 GLU cc_start: 0.7749 (pm20) cc_final: 0.7399 (pm20) REVERT: A 1887 LYS cc_start: 0.9001 (mtpt) cc_final: 0.8722 (mtpp) REVERT: A 1936 GLN cc_start: 0.8505 (pp30) cc_final: 0.7983 (pp30) REVERT: A 1938 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8048 (tp-100) REVERT: A 1973 MET cc_start: 0.7811 (mtt) cc_final: 0.7566 (mtt) REVERT: A 1978 LEU cc_start: 0.7066 (mm) cc_final: 0.6813 (mm) REVERT: A 2023 THR cc_start: 0.8739 (p) cc_final: 0.8533 (p) REVERT: A 2027 MET cc_start: 0.6466 (OUTLIER) cc_final: 0.5777 (ttt) REVERT: A 2111 LYS cc_start: 0.8701 (ptpt) cc_final: 0.8401 (ptpt) REVERT: A 2116 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8139 (ttt180) REVERT: A 2164 MET cc_start: 0.7250 (ppp) cc_final: 0.6347 (ppp) REVERT: A 2176 MET cc_start: 0.7437 (ppp) cc_final: 0.7144 (tmm) REVERT: A 2209 ARG cc_start: 0.8113 (mtt180) cc_final: 0.6975 (mtp180) REVERT: A 2239 LYS cc_start: 0.8477 (tttt) cc_final: 0.8058 (tppt) REVERT: A 2259 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7385 (tm-30) REVERT: A 2293 VAL cc_start: 0.8574 (t) cc_final: 0.8318 (m) outliers start: 47 outliers final: 36 residues processed: 279 average time/residue: 0.0831 time to fit residues: 32.7079 Evaluate side-chains 291 residues out of total 1122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 TYR Chi-restraints excluded: chain A residue 77 GLN Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 133 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 248 CYS Chi-restraints excluded: chain A residue 281 HIS Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 329 CYS Chi-restraints excluded: chain A residue 471 ARG Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 570 LYS Chi-restraints excluded: chain A residue 574 ILE Chi-restraints excluded: chain A residue 590 ASN Chi-restraints excluded: chain A residue 652 PHE Chi-restraints excluded: chain A residue 1695 THR Chi-restraints excluded: chain A residue 1709 TYR Chi-restraints excluded: chain A residue 1823 MET Chi-restraints excluded: chain A residue 1839 SER Chi-restraints excluded: chain A residue 1872 THR Chi-restraints excluded: chain A residue 1873 VAL Chi-restraints excluded: chain A residue 1875 GLU Chi-restraints excluded: chain A residue 1921 ILE Chi-restraints excluded: chain A residue 1938 GLN Chi-restraints excluded: chain A residue 1982 VAL Chi-restraints excluded: chain A residue 1989 LEU Chi-restraints excluded: chain A residue 2027 MET Chi-restraints excluded: chain A residue 2076 LEU Chi-restraints excluded: chain A residue 2098 ILE Chi-restraints excluded: chain A residue 2099 SER Chi-restraints excluded: chain A residue 2114 THR Chi-restraints excluded: chain A residue 2127 PHE Chi-restraints excluded: chain A residue 2140 PHE Chi-restraints excluded: chain A residue 2191 THR Chi-restraints excluded: chain A residue 2259 GLU Chi-restraints excluded: chain A residue 2296 SER Chi-restraints excluded: chain A residue 2297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 28 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 0.0970 chunk 125 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 48 optimal weight: 1.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.2974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 ASN ** A 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 HIS A 590 ASN ** A 602 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.130430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.112804 restraints weight = 21239.271| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 4.24 r_work: 0.3579 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10570 Z= 0.139 Angle : 0.781 13.246 14341 Z= 0.384 Chirality : 0.048 0.224 1533 Planarity : 0.005 0.062 1821 Dihedral : 5.721 40.183 1440 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.82 % Favored : 92.10 % Rotamer: Outliers : 4.10 % Allowed : 24.96 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % 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 are not related in a simple way. whole: -2.15 (0.23), residues: 1253 helix: -1.61 (0.50), residues: 90 sheet: -0.33 (0.29), residues: 340 loop : -2.01 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 531 TYR 0.022 0.001 TYR A 407 PHE 0.046 0.002 PHE A1830 TRP 0.023 0.002 TRP A 106 HIS 0.011 0.001 HIS A 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (10559) covalent geometry : angle 0.77583 / 0.38 (14316) SS BOND : bond 0.00387 / 0.14 ( 8) SS BOND : angle 2.41558 / 1.48 ( 16) hydrogen bonds : bond 0.03287 / 1.99 ( 233) hydrogen bonds : angle 5.99501 / 4.22 ( 597) link_NAG-ASN : bond 0.00127 / 0.06 ( 3) link_NAG-ASN : angle 1.93750 / 1.13 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2359.22 seconds wall clock time: 41 minutes 23.51 seconds (2483.51 seconds total)