Starting phenix.real_space_refine on Thu Jul 31 23:11:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7moc_23924/07_2025/7moc_23924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7moc_23924/07_2025/7moc_23924.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7moc_23924/07_2025/7moc_23924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7moc_23924/07_2025/7moc_23924.map" model { file = "/net/cci-nas-00/data/ceres_data/7moc_23924/07_2025/7moc_23924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7moc_23924/07_2025/7moc_23924.cif" } resolution = 4.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 4 Type Number sf(0) Gaussians S 98 5.16 5 C 8943 2.51 5 N 2321 2.21 5 O 2521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 82 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 13883 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1082, 8562 Classifications: {'peptide': 1082} Link IDs: {'PTRANS': 32, 'TRANS': 1049} Chain breaks: 28 Chain: "B" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5321 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 27, 'TRANS': 645} Chain breaks: 6 Time building chain proxies: 9.32, per 1000 atoms: 0.67 Number of scatterers: 13883 At special positions: 0 Unit cell: (146.862, 157.608, 113.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 98 16.00 O 2521 8.00 N 2321 7.00 C 8943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 4.10 Conformation dependent library (CDL) restraints added in 2.4 seconds 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 0 sheets defined 87.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 5 through 20 removed outlier: 3.697A pdb=" N TRP A 9 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 48 Processing helix chain 'A' and resid 50 through 67 Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 107 through 112 Processing helix chain 'A' and resid 112 through 121 removed outlier: 3.952A pdb=" N GLU A 116 " --> pdb=" O GLN A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 166 removed outlier: 4.227A pdb=" N ASN A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASN A 151 " --> pdb=" O CYS A 147 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 166 " --> pdb=" O GLN A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 183 removed outlier: 3.600A pdb=" N GLU A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 179 " --> pdb=" O HIS A 175 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N GLN A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 202 removed outlier: 4.440A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 227 Processing helix chain 'A' and resid 227 through 235 removed outlier: 3.689A pdb=" N TYR A 235 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 259 through 276 Proline residue: A 268 - end of helix removed outlier: 3.587A pdb=" N ILE A 272 " --> pdb=" O PRO A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 285 Processing helix chain 'A' and resid 293 through 308 Processing helix chain 'A' and resid 313 through 333 removed outlier: 3.757A pdb=" N TYR A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 358 removed outlier: 4.879A pdb=" N VAL A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N ASP A 352 " --> pdb=" O SER A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 387 Processing helix chain 'A' and resid 392 through 399 Processing helix chain 'A' and resid 403 through 420 Processing helix chain 'A' and resid 428 through 434 removed outlier: 3.618A pdb=" N ALA A 431 " --> pdb=" O LYS A 428 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS A 434 " --> pdb=" O ALA A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 453 Processing helix chain 'A' and resid 484 through 503 Processing helix chain 'A' and resid 504 through 510 removed outlier: 3.843A pdb=" N ASN A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 533 Processing helix chain 'A' and resid 538 through 553 Processing helix chain 'A' and resid 554 through 561 removed outlier: 3.855A pdb=" N LEU A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 586 Processing helix chain 'A' and resid 593 through 614 Processing helix chain 'A' and resid 679 through 696 removed outlier: 4.140A pdb=" N TRP A 696 " --> pdb=" O TYR A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 723 removed outlier: 3.766A pdb=" N ARG A 711 " --> pdb=" O MET A 707 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 712 " --> pdb=" O SER A 708 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL A 723 " --> pdb=" O ILE A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 744 Processing helix chain 'A' and resid 753 through 766 removed outlier: 3.722A pdb=" N ARG A 765 " --> pdb=" O ALA A 761 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE A 766 " --> pdb=" O LEU A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 792 Processing helix chain 'A' and resid 834 through 848 Processing helix chain 'A' and resid 849 through 852 Processing helix chain 'A' and resid 890 through 903 removed outlier: 4.191A pdb=" N VAL A 903 " --> pdb=" O LEU A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 925 removed outlier: 3.590A pdb=" N LEU A 925 " --> pdb=" O VAL A 921 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 929 through 943 Processing helix chain 'A' and resid 956 through 974 Processing helix chain 'A' and resid 978 through 984 removed outlier: 3.681A pdb=" N HIS A 982 " --> pdb=" O GLY A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1002 removed outlier: 3.858A pdb=" N VAL A1001 " --> pdb=" O ARG A 997 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A1002 " --> pdb=" O TYR A 998 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1025 Processing helix chain 'A' and resid 1026 through 1028 No H-bonds generated for 'chain 'A' and resid 1026 through 1028' Processing helix chain 'A' and resid 1033 through 1049 removed outlier: 3.519A pdb=" N ASP A1047 " --> pdb=" O GLU A1043 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N TRP A1048 " --> pdb=" O TYR A1044 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1080 Processing helix chain 'A' and resid 1093 through 1118 Processing helix chain 'A' and resid 1134 through 1156 Processing helix chain 'A' and resid 1156 through 1170 removed outlier: 5.918A pdb=" N MET A1162 " --> pdb=" O ASP A1158 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N HIS A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A1166 " --> pdb=" O MET A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1172 through 1190 Processing helix chain 'A' and resid 1830 through 1842 removed outlier: 3.558A pdb=" N GLY A1842 " --> pdb=" O LEU A1838 " (cutoff:3.500A) Processing helix chain 'A' and resid 1845 through 1863 Processing helix chain 'A' and resid 1883 through 1898 Processing helix chain 'A' and resid 1900 through 1916 removed outlier: 4.689A pdb=" N GLU A1904 " --> pdb=" O HIS A1900 " (cutoff:3.500A) Processing helix chain 'A' and resid 1917 through 1941 Proline residue: A1930 - end of helix removed outlier: 4.412A pdb=" N SER A1933 " --> pdb=" O THR A1929 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASN A1934 " --> pdb=" O PRO A1930 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LEU A1935 " --> pdb=" O TRP A1931 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL A1936 " --> pdb=" O LEU A1932 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG A1937 " --> pdb=" O SER A1933 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N PHE A1938 " --> pdb=" O ASN A1934 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS A1939 " --> pdb=" O LEU A1935 " (cutoff:3.500A) Processing helix chain 'A' and resid 1943 through 1964 Processing helix chain 'A' and resid 1967 through 1981 removed outlier: 3.699A pdb=" N GLY A1977 " --> pdb=" O ALA A1973 " (cutoff:3.500A) Processing helix chain 'A' and resid 1986 through 1998 Processing helix chain 'A' and resid 2006 through 2020 removed outlier: 3.522A pdb=" N VAL A2015 " --> pdb=" O ALA A2011 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA A2016 " --> pdb=" O ASP A2012 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER A2019 " --> pdb=" O VAL A2015 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY A2020 " --> pdb=" O ALA A2016 " (cutoff:3.500A) Processing helix chain 'B' and resid 1830 through 1843 Processing helix chain 'B' and resid 1883 through 1898 Processing helix chain 'B' and resid 1900 through 1916 removed outlier: 4.206A pdb=" N GLU B1904 " --> pdb=" O HIS B1900 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS B1915 " --> pdb=" O SER B1911 " (cutoff:3.500A) Processing helix chain 'B' and resid 1917 through 1929 Processing helix chain 'B' and resid 1930 through 1933 removed outlier: 3.625A pdb=" N SER B1933 " --> pdb=" O PRO B1930 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1930 through 1933' Processing helix chain 'B' and resid 1934 through 1940 removed outlier: 4.028A pdb=" N PHE B1938 " --> pdb=" O ASN B1934 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS B1939 " --> pdb=" O LEU B1935 " (cutoff:3.500A) Processing helix chain 'B' and resid 1943 through 1964 removed outlier: 3.730A pdb=" N ARG B1947 " --> pdb=" O ASP B1943 " (cutoff:3.500A) Processing helix chain 'B' and resid 1967 through 1981 Processing helix chain 'B' and resid 1982 through 1984 No H-bonds generated for 'chain 'B' and resid 1982 through 1984' Processing helix chain 'B' and resid 1985 through 1999 Processing helix chain 'B' and resid 2004 through 2021 removed outlier: 3.784A pdb=" N VAL B2015 " --> pdb=" O ALA B2011 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ALA B2016 " --> pdb=" O ASP B2012 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLY B2020 " --> pdb=" O ALA B2016 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ASN B2021 " --> pdb=" O LEU B2017 " (cutoff:3.500A) Processing helix chain 'B' and resid 2021 through 2043 removed outlier: 3.764A pdb=" N CYS B2041 " --> pdb=" O ILE B2037 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B2043 " --> pdb=" O LYS B2039 " (cutoff:3.500A) Processing helix chain 'B' and resid 2047 through 2051 Processing helix chain 'B' and resid 2053 through 2090 removed outlier: 3.849A pdb=" N PHE B2069 " --> pdb=" O LEU B2065 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B2070 " --> pdb=" O MET B2066 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LEU B2073 " --> pdb=" O PHE B2069 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA B2076 " --> pdb=" O SER B2072 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ALA B2077 " --> pdb=" O LEU B2073 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N HIS B2078 " --> pdb=" O ASP B2074 " (cutoff:3.500A) Proline residue: B2080 - end of helix Processing helix chain 'B' and resid 2094 through 2114 Processing helix chain 'B' and resid 2121 through 2136 Processing helix chain 'B' and resid 2137 through 2144 Processing helix chain 'B' and resid 2151 through 2157 removed outlier: 3.816A pdb=" N ILE B2155 " --> pdb=" O SER B2151 " (cutoff:3.500A) Processing helix chain 'B' and resid 2177 through 2199 removed outlier: 3.720A pdb=" N LEU B2181 " --> pdb=" O ALA B2177 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASP B2198 " --> pdb=" O ALA B2194 " (cutoff:3.500A) Processing helix chain 'B' and resid 2203 through 2218 Processing helix chain 'B' and resid 2223 through 2235 Processing helix chain 'B' and resid 2239 through 2259 Processing helix chain 'B' and resid 2265 through 2281 Processing helix chain 'B' and resid 2282 through 2284 No H-bonds generated for 'chain 'B' and resid 2282 through 2284' Processing helix chain 'B' and resid 2289 through 2304 removed outlier: 3.533A pdb=" N PHE B2295 " --> pdb=" O HIS B2291 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP B2296 " --> pdb=" O LYS B2292 " (cutoff:3.500A) Processing helix chain 'B' and resid 2306 through 2327 Processing helix chain 'B' and resid 2328 through 2333 removed outlier: 4.136A pdb=" N ASP B2332 " --> pdb=" O ILE B2329 " (cutoff:3.500A) Processing helix chain 'B' and resid 2334 through 2358 removed outlier: 3.641A pdb=" N ILE B2342 " --> pdb=" O VAL B2338 " (cutoff:3.500A) Proline residue: B2345 - end of helix removed outlier: 4.655A pdb=" N TRP B2348 " --> pdb=" O ASN B2344 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N HIS B2349 " --> pdb=" O PRO B2345 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLN B2352 " --> pdb=" O TRP B2348 " (cutoff:3.500A) Processing helix chain 'B' and resid 2364 through 2379 removed outlier: 3.693A pdb=" N LYS B2375 " --> pdb=" O GLY B2371 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLY B2376 " --> pdb=" O HIS B2372 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR B2377 " --> pdb=" O LEU B2373 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG B2378 " --> pdb=" O LEU B2374 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N HIS B2379 " --> pdb=" O LYS B2375 " (cutoff:3.500A) Processing helix chain 'B' and resid 2381 through 2404 removed outlier: 3.944A pdb=" N ARG B2403 " --> pdb=" O VAL B2399 " (cutoff:3.500A) Processing helix chain 'B' and resid 2414 through 2422 Processing helix chain 'B' and resid 2425 through 2430 Processing helix chain 'B' and resid 2592 through 2609 Processing helix chain 'B' and resid 2611 through 2629 Processing helix chain 'B' and resid 2633 through 2651 removed outlier: 3.578A pdb=" N HIS B2637 " --> pdb=" O PHE B2633 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN B2638 " --> pdb=" O PRO B2634 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N LEU B2639 " --> pdb=" O VAL B2635 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B2642 " --> pdb=" O ASN B2638 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS B2643 " --> pdb=" O LEU B2639 " (cutoff:3.500A) Processing helix chain 'B' and resid 2653 through 2670 Proline residue: B2659 - end of helix Processing helix chain 'B' and resid 2679 through 2686 removed outlier: 4.337A pdb=" N GLN B2683 " --> pdb=" O THR B2679 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE B2685 " --> pdb=" O TYR B2681 " (cutoff:3.500A) Processing helix chain 'B' and resid 2688 through 2694 removed outlier: 4.328A pdb=" N ARG B2692 " --> pdb=" O ASN B2688 " (cutoff:3.500A) Processing helix chain 'B' and resid 2704 through 2722 1042 hydrogen bonds defined for protein. 3105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3492 1.33 - 1.45: 2703 1.45 - 1.58: 7776 1.58 - 1.70: 1 1.70 - 1.82: 148 Bond restraints: 14120 Sorted by residual: bond pdb=" C LEU A1187 " pdb=" N GLN A1188 " ideal model delta sigma weight residual 1.333 1.443 -0.110 1.49e-02 4.50e+03 5.46e+01 bond pdb=" CA MET A 108 " pdb=" C MET A 108 " ideal model delta sigma weight residual 1.522 1.585 -0.063 1.39e-02 5.18e+03 2.06e+01 bond pdb=" CB THR A1832 " pdb=" OG1 THR A1832 " ideal model delta sigma weight residual 1.433 1.375 0.058 1.60e-02 3.91e+03 1.33e+01 bond pdb=" CA PHE B2069 " pdb=" C PHE B2069 " ideal model delta sigma weight residual 1.524 1.568 -0.044 1.27e-02 6.20e+03 1.19e+01 bond pdb=" CA GLN A1188 " pdb=" C GLN A1188 " ideal model delta sigma weight residual 1.522 1.567 -0.045 1.37e-02 5.33e+03 1.08e+01 ... (remaining 14115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 15194 2.22 - 4.44: 3498 4.44 - 6.66: 349 6.66 - 8.88: 41 8.88 - 11.11: 12 Bond angle restraints: 19094 Sorted by residual: angle pdb=" N ASP B2074 " pdb=" CA ASP B2074 " pdb=" C ASP B2074 " ideal model delta sigma weight residual 111.36 122.45 -11.09 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N THR A1893 " pdb=" CA THR A1893 " pdb=" C THR A1893 " ideal model delta sigma weight residual 111.14 101.97 9.17 1.08e+00 8.57e-01 7.21e+01 angle pdb=" N LEU A 109 " pdb=" CA LEU A 109 " pdb=" C LEU A 109 " ideal model delta sigma weight residual 111.07 102.16 8.91 1.07e+00 8.73e-01 6.94e+01 angle pdb=" N PHE B2693 " pdb=" CA PHE B2693 " pdb=" C PHE B2693 " ideal model delta sigma weight residual 111.28 119.93 -8.65 1.09e+00 8.42e-01 6.30e+01 angle pdb=" N SER A1891 " pdb=" CA SER A1891 " pdb=" C SER A1891 " ideal model delta sigma weight residual 111.11 120.47 -9.36 1.20e+00 6.94e-01 6.08e+01 ... (remaining 19089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.39: 7945 18.39 - 36.78: 508 36.78 - 55.16: 72 55.16 - 73.55: 26 73.55 - 91.94: 11 Dihedral angle restraints: 8562 sinusoidal: 3413 harmonic: 5149 Sorted by residual: dihedral pdb=" C ASN A 734 " pdb=" N ASN A 734 " pdb=" CA ASN A 734 " pdb=" CB ASN A 734 " ideal model delta harmonic sigma weight residual -122.60 -142.60 20.00 0 2.50e+00 1.60e-01 6.40e+01 dihedral pdb=" C HIS B2078 " pdb=" N HIS B2078 " pdb=" CA HIS B2078 " pdb=" CB HIS B2078 " ideal model delta harmonic sigma weight residual -122.60 -139.87 17.27 0 2.50e+00 1.60e-01 4.77e+01 dihedral pdb=" C ASN B2071 " pdb=" N ASN B2071 " pdb=" CA ASN B2071 " pdb=" CB ASN B2071 " ideal model delta harmonic sigma weight residual -122.60 -138.92 16.32 0 2.50e+00 1.60e-01 4.26e+01 ... (remaining 8559 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.158: 2085 0.158 - 0.316: 184 0.316 - 0.474: 18 0.474 - 0.631: 6 0.631 - 0.789: 5 Chirality restraints: 2298 Sorted by residual: chirality pdb=" CA ASN A 734 " pdb=" N ASN A 734 " pdb=" C ASN A 734 " pdb=" CB ASN A 734 " both_signs ideal model delta sigma weight residual False 2.51 1.72 0.79 2.00e-01 2.50e+01 1.56e+01 chirality pdb=" CA HIS B2078 " pdb=" N HIS B2078 " pdb=" C HIS B2078 " pdb=" CB HIS B2078 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CB VAL B2606 " pdb=" CA VAL B2606 " pdb=" CG1 VAL B2606 " pdb=" CG2 VAL B2606 " both_signs ideal model delta sigma weight residual False -2.63 -1.92 -0.71 2.00e-01 2.50e+01 1.27e+01 ... (remaining 2295 not shown) Planarity restraints: 2351 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1853 " -0.244 2.00e-02 2.50e+03 1.35e-01 3.66e+02 pdb=" CG TYR A1853 " 0.076 2.00e-02 2.50e+03 pdb=" CD1 TYR A1853 " 0.094 2.00e-02 2.50e+03 pdb=" CD2 TYR A1853 " 0.107 2.00e-02 2.50e+03 pdb=" CE1 TYR A1853 " 0.075 2.00e-02 2.50e+03 pdb=" CE2 TYR A1853 " 0.076 2.00e-02 2.50e+03 pdb=" CZ TYR A1853 " 0.035 2.00e-02 2.50e+03 pdb=" OH TYR A1853 " -0.219 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B2693 " -0.137 2.00e-02 2.50e+03 8.35e-02 1.22e+02 pdb=" CG PHE B2693 " 0.106 2.00e-02 2.50e+03 pdb=" CD1 PHE B2693 " 0.074 2.00e-02 2.50e+03 pdb=" CD2 PHE B2693 " 0.081 2.00e-02 2.50e+03 pdb=" CE1 PHE B2693 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 PHE B2693 " -0.031 2.00e-02 2.50e+03 pdb=" CZ PHE B2693 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 49 " -0.146 2.00e-02 2.50e+03 7.51e-02 1.13e+02 pdb=" CG TYR A 49 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TYR A 49 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR A 49 " 0.061 2.00e-02 2.50e+03 pdb=" CE1 TYR A 49 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TYR A 49 " 0.030 2.00e-02 2.50e+03 pdb=" CZ TYR A 49 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR A 49 " -0.094 2.00e-02 2.50e+03 ... (remaining 2348 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 683 2.75 - 3.29: 15455 3.29 - 3.82: 23828 3.82 - 4.36: 29247 4.36 - 4.90: 48291 Nonbonded interactions: 117504 Sorted by model distance: nonbonded pdb=" CD1 LEU B1839 " pdb=" CD1 LEU B1920 " model vdw 2.211 3.880 nonbonded pdb=" OG SER B1916 " pdb=" CD2 LEU B1920 " model vdw 2.375 3.460 nonbonded pdb=" O LEU B2065 " pdb=" OG SER B2068 " model vdw 2.512 3.040 nonbonded pdb=" OD1 ASP A1845 " pdb=" OG SER A1847 " model vdw 2.515 3.040 nonbonded pdb=" OD1 ASN A 974 " pdb=" OG1 THR A 976 " model vdw 2.530 3.040 ... (remaining 117499 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 36.750 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 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 : 0.012 0.110 14120 Z= 0.718 Angle : 1.821 11.105 19094 Z= 1.229 Chirality : 0.106 0.789 2298 Planarity : 0.016 0.135 2351 Dihedral : 13.173 91.938 5172 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.19 % Allowed : 2.61 % Favored : 97.20 % Cbeta Deviations : 1.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 1683 helix: 0.25 (0.12), residues: 1344 sheet: None (None), residues: 0 loop : -0.65 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.121 0.025 TRP B1931 HIS 0.013 0.003 HIS B2379 PHE 0.137 0.016 PHE B2693 TYR 0.244 0.030 TYR A1853 ARG 0.011 0.001 ARG A 385 Details of bonding type rmsd hydrogen bonds : bond 0.15396 ( 1042) hydrogen bonds : angle 6.99371 ( 3105) covalent geometry : bond 0.01178 (14120) covalent geometry : angle 1.82141 (19094) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 711 time to evaluate : 1.545 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 ILE cc_start: 0.8545 (mm) cc_final: 0.8235 (mp) REVERT: A 190 LEU cc_start: 0.8577 (tp) cc_final: 0.8322 (tp) REVERT: A 194 LEU cc_start: 0.9220 (mt) cc_final: 0.8784 (mt) REVERT: A 217 GLU cc_start: 0.8709 (tt0) cc_final: 0.8202 (tm-30) REVERT: A 231 PHE cc_start: 0.8288 (t80) cc_final: 0.8031 (t80) REVERT: A 250 PHE cc_start: 0.8058 (t80) cc_final: 0.7229 (t80) REVERT: A 303 LEU cc_start: 0.7824 (mt) cc_final: 0.7217 (mt) REVERT: A 305 LYS cc_start: 0.8971 (mttt) cc_final: 0.8606 (pttp) REVERT: A 327 LEU cc_start: 0.9241 (tp) cc_final: 0.9037 (tp) REVERT: A 344 LEU cc_start: 0.7888 (mt) cc_final: 0.7520 (tp) REVERT: A 376 MET cc_start: 0.8922 (mtp) cc_final: 0.8592 (mpp) REVERT: A 379 CYS cc_start: 0.8797 (t) cc_final: 0.8147 (t) REVERT: A 383 CYS cc_start: 0.8352 (m) cc_final: 0.8137 (m) REVERT: A 446 THR cc_start: 0.8837 (m) cc_final: 0.8560 (p) REVERT: A 493 LEU cc_start: 0.8993 (tp) cc_final: 0.8769 (tt) REVERT: A 496 MET cc_start: 0.8263 (mtp) cc_final: 0.7841 (mtp) REVERT: A 524 GLU cc_start: 0.8567 (mt-10) cc_final: 0.7904 (tp30) REVERT: A 540 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7165 (pm20) REVERT: A 543 GLN cc_start: 0.8225 (tp40) cc_final: 0.8005 (tm-30) REVERT: A 546 MET cc_start: 0.8320 (mtm) cc_final: 0.7868 (mtm) REVERT: A 552 LEU cc_start: 0.8923 (mt) cc_final: 0.8549 (mt) REVERT: A 561 TRP cc_start: 0.6680 (m-10) cc_final: 0.6292 (m100) REVERT: A 573 ILE cc_start: 0.8819 (mt) cc_final: 0.7944 (mt) REVERT: A 577 MET cc_start: 0.8233 (ttp) cc_final: 0.7663 (tmm) REVERT: A 581 ILE cc_start: 0.8630 (mm) cc_final: 0.8417 (mm) REVERT: A 604 LEU cc_start: 0.8842 (mt) cc_final: 0.8626 (mt) REVERT: A 691 LEU cc_start: 0.8458 (mt) cc_final: 0.8109 (mt) REVERT: A 700 THR cc_start: 0.9158 (m) cc_final: 0.8779 (p) REVERT: A 707 MET cc_start: 0.7709 (mtt) cc_final: 0.7347 (mtt) REVERT: A 711 ARG cc_start: 0.7931 (ttm110) cc_final: 0.6833 (tpt-90) REVERT: A 739 MET cc_start: 0.8068 (mmm) cc_final: 0.7495 (mmm) REVERT: A 773 ASN cc_start: 0.8184 (p0) cc_final: 0.7956 (p0) REVERT: A 775 GLU cc_start: 0.8502 (tt0) cc_final: 0.7289 (tm-30) REVERT: A 779 ASP cc_start: 0.8585 (m-30) cc_final: 0.7668 (m-30) REVERT: A 837 TRP cc_start: 0.8913 (t60) cc_final: 0.8626 (t60) REVERT: A 840 MET cc_start: 0.8654 (mtm) cc_final: 0.8230 (mtp) REVERT: A 932 MET cc_start: 0.7350 (ttm) cc_final: 0.6322 (mmp) REVERT: A 933 LEU cc_start: 0.8120 (tp) cc_final: 0.7714 (tt) REVERT: A 941 ILE cc_start: 0.9186 (mt) cc_final: 0.8982 (mm) REVERT: A 983 LEU cc_start: 0.8543 (mt) cc_final: 0.8257 (mt) REVERT: A 1002 LEU cc_start: 0.7894 (mt) cc_final: 0.7456 (mt) REVERT: A 1005 MET cc_start: 0.7046 (mtm) cc_final: 0.6290 (mpp) REVERT: A 1010 GLN cc_start: 0.8437 (mt0) cc_final: 0.7940 (mm110) REVERT: A 1017 GLN cc_start: 0.8989 (mt0) cc_final: 0.8770 (mt0) REVERT: A 1039 ASN cc_start: 0.8851 (m-40) cc_final: 0.8465 (m-40) REVERT: A 1042 VAL cc_start: 0.8506 (t) cc_final: 0.7958 (t) REVERT: A 1077 VAL cc_start: 0.8780 (t) cc_final: 0.8547 (t) REVERT: A 1106 TYR cc_start: 0.8345 (m-80) cc_final: 0.7326 (m-80) REVERT: A 1149 MET cc_start: 0.8348 (mtt) cc_final: 0.8123 (mtm) REVERT: A 1158 ASP cc_start: 0.7643 (m-30) cc_final: 0.7319 (t70) REVERT: A 1162 MET cc_start: 0.8522 (pmm) cc_final: 0.8212 (pmm) REVERT: A 1169 TYR cc_start: 0.6732 (m-80) cc_final: 0.6425 (m-10) REVERT: A 1829 VAL cc_start: 0.5970 (t) cc_final: 0.5769 (t) REVERT: A 1848 LEU cc_start: 0.8873 (tp) cc_final: 0.8517 (tt) REVERT: A 1866 LYS cc_start: 0.7251 (mttt) cc_final: 0.6978 (mmmt) REVERT: A 1870 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6795 (pm20) REVERT: A 1872 LEU cc_start: 0.8734 (tp) cc_final: 0.8387 (tp) REVERT: A 1884 THR cc_start: 0.9377 (m) cc_final: 0.9122 (t) REVERT: A 1906 LEU cc_start: 0.9031 (mt) cc_final: 0.8763 (mt) REVERT: A 1923 LEU cc_start: 0.9521 (tp) cc_final: 0.9306 (tp) REVERT: A 1925 LEU cc_start: 0.8980 (mt) cc_final: 0.8431 (mt) REVERT: A 1937 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.8312 (ttm-80) REVERT: A 1960 MET cc_start: 0.8457 (ttp) cc_final: 0.8165 (tmm) REVERT: A 1963 ASN cc_start: 0.7647 (m-40) cc_final: 0.7277 (t0) REVERT: A 2005 ILE cc_start: 0.7438 (mt) cc_final: 0.7007 (mt) REVERT: B 1836 ILE cc_start: 0.8611 (mt) cc_final: 0.8214 (tt) REVERT: B 1918 ILE cc_start: 0.7949 (mt) cc_final: 0.7582 (pt) REVERT: B 1928 MET cc_start: 0.8198 (mtp) cc_final: 0.7719 (mtt) REVERT: B 1954 LEU cc_start: 0.9302 (mt) cc_final: 0.9070 (mt) REVERT: B 1956 LYS cc_start: 0.9090 (mttt) cc_final: 0.8430 (mmmt) REVERT: B 1986 LEU cc_start: 0.8897 (mt) cc_final: 0.8626 (mt) REVERT: B 2006 LYS cc_start: 0.8022 (mptt) cc_final: 0.7548 (mmmm) REVERT: B 2033 MET cc_start: 0.8620 (tpp) cc_final: 0.8015 (tpt) REVERT: B 2053 MET cc_start: 0.9041 (mtp) cc_final: 0.8729 (mtp) REVERT: B 2066 MET cc_start: 0.8717 (mmt) cc_final: 0.8504 (mmp) REVERT: B 2107 ASN cc_start: 0.9125 (m-40) cc_final: 0.8755 (m-40) REVERT: B 2120 PHE cc_start: 0.7831 (m-80) cc_final: 0.7301 (m-80) REVERT: B 2178 LEU cc_start: 0.8711 (mt) cc_final: 0.8337 (mt) REVERT: B 2199 ILE cc_start: 0.8259 (mt) cc_final: 0.7966 (tt) REVERT: B 2223 LEU cc_start: 0.9140 (mt) cc_final: 0.8909 (mt) REVERT: B 2246 ILE cc_start: 0.8921 (mt) cc_final: 0.8640 (tp) REVERT: B 2305 ASP cc_start: 0.6959 (t0) cc_final: 0.6225 (t70) REVERT: B 2310 TYR cc_start: 0.8646 (t80) cc_final: 0.8217 (t80) REVERT: B 2330 PHE cc_start: 0.7710 (m-80) cc_final: 0.7419 (m-10) REVERT: B 2333 LYS cc_start: 0.7232 (mttt) cc_final: 0.6729 (mptt) REVERT: B 2373 LEU cc_start: 0.8685 (mt) cc_final: 0.8267 (mt) REVERT: B 2401 LYS cc_start: 0.7811 (tttt) cc_final: 0.7401 (mmmt) REVERT: B 2418 LEU cc_start: 0.9257 (mt) cc_final: 0.9006 (mt) REVERT: B 2600 THR cc_start: 0.9394 (m) cc_final: 0.9180 (p) REVERT: B 2614 ASP cc_start: 0.8757 (m-30) cc_final: 0.8518 (m-30) REVERT: B 2616 ARG cc_start: 0.6660 (ttt180) cc_final: 0.6395 (tmt170) REVERT: B 2685 PHE cc_start: 0.8709 (p90) cc_final: 0.8412 (p90) REVERT: B 2722 LEU cc_start: 0.8197 (mt) cc_final: 0.7900 (mt) outliers start: 3 outliers final: 0 residues processed: 713 average time/residue: 0.2705 time to fit residues: 282.5585 Evaluate side-chains 466 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 466 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS A 510 ASN A 608 ASN A1115 ASN A1835 ASN ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2319 GLN B2393 HIS B2615 GLN B2670 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.119324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.098038 restraints weight = 34086.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101902 restraints weight = 21301.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.104728 restraints weight = 14663.902| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14120 Z= 0.157 Angle : 0.643 8.118 19094 Z= 0.343 Chirality : 0.040 0.191 2298 Planarity : 0.004 0.044 2351 Dihedral : 5.043 30.116 1819 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.45 % Allowed : 2.48 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.20), residues: 1683 helix: 1.74 (0.13), residues: 1403 sheet: None (None), residues: 0 loop : 0.36 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 9 HIS 0.008 0.001 HIS A1922 PHE 0.027 0.002 PHE A 741 TYR 0.031 0.002 TYR A1927 ARG 0.008 0.001 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.04891 ( 1042) hydrogen bonds : angle 4.49836 ( 3105) covalent geometry : bond 0.00323 (14120) covalent geometry : angle 0.64318 (19094) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 555 time to evaluate : 1.567 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 39 ASN cc_start: 0.8993 (m-40) cc_final: 0.8618 (t0) REVERT: A 231 PHE cc_start: 0.8142 (t80) cc_final: 0.7709 (t80) REVERT: A 245 CYS cc_start: 0.8287 (m) cc_final: 0.8050 (p) REVERT: A 250 PHE cc_start: 0.8432 (t80) cc_final: 0.7901 (t80) REVERT: A 274 LEU cc_start: 0.9206 (tp) cc_final: 0.8951 (mt) REVERT: A 344 LEU cc_start: 0.8327 (mt) cc_final: 0.8008 (tp) REVERT: A 349 MET cc_start: 0.7769 (mmp) cc_final: 0.7548 (mmm) REVERT: A 376 MET cc_start: 0.8938 (mtp) cc_final: 0.8559 (mpp) REVERT: A 383 CYS cc_start: 0.8516 (m) cc_final: 0.8300 (m) REVERT: A 446 THR cc_start: 0.8981 (m) cc_final: 0.8513 (p) REVERT: A 496 MET cc_start: 0.7878 (mtp) cc_final: 0.7447 (mtp) REVERT: A 524 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8013 (tp30) REVERT: A 529 LEU cc_start: 0.9089 (mt) cc_final: 0.8873 (mt) REVERT: A 540 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7540 (pm20) REVERT: A 543 GLN cc_start: 0.8345 (tp40) cc_final: 0.7898 (tm-30) REVERT: A 546 MET cc_start: 0.7754 (mtm) cc_final: 0.7439 (mtm) REVERT: A 552 LEU cc_start: 0.8584 (mt) cc_final: 0.8272 (mt) REVERT: A 561 TRP cc_start: 0.5935 (m-10) cc_final: 0.5710 (m-10) REVERT: A 573 ILE cc_start: 0.8958 (mt) cc_final: 0.8301 (mt) REVERT: A 707 MET cc_start: 0.8087 (mtt) cc_final: 0.7580 (mtt) REVERT: A 760 MET cc_start: 0.8319 (mtm) cc_final: 0.7477 (mtp) REVERT: A 775 GLU cc_start: 0.8305 (tt0) cc_final: 0.7151 (tm-30) REVERT: A 779 ASP cc_start: 0.8607 (m-30) cc_final: 0.7864 (m-30) REVERT: A 833 SER cc_start: 0.6405 (m) cc_final: 0.6019 (t) REVERT: A 837 TRP cc_start: 0.8818 (t60) cc_final: 0.8591 (t60) REVERT: A 840 MET cc_start: 0.8464 (mtm) cc_final: 0.8145 (mtp) REVERT: A 902 MET cc_start: 0.8421 (mtt) cc_final: 0.8058 (mtt) REVERT: A 924 GLU cc_start: 0.7830 (mm-30) cc_final: 0.6657 (mm-30) REVERT: A 992 MET cc_start: 0.8754 (mmm) cc_final: 0.8499 (mmm) REVERT: A 998 TYR cc_start: 0.8451 (t80) cc_final: 0.8184 (t80) REVERT: A 1002 LEU cc_start: 0.8247 (mt) cc_final: 0.7577 (mt) REVERT: A 1005 MET cc_start: 0.7956 (mtm) cc_final: 0.6961 (mpp) REVERT: A 1023 MET cc_start: 0.8177 (mmp) cc_final: 0.7690 (mmt) REVERT: A 1036 LYS cc_start: 0.9051 (tttt) cc_final: 0.8756 (tptp) REVERT: A 1039 ASN cc_start: 0.9183 (m-40) cc_final: 0.8506 (m-40) REVERT: A 1042 VAL cc_start: 0.8498 (t) cc_final: 0.8249 (t) REVERT: A 1066 ARG cc_start: 0.8527 (ttm-80) cc_final: 0.7999 (ttp-170) REVERT: A 1106 TYR cc_start: 0.7909 (m-80) cc_final: 0.7642 (m-80) REVERT: A 1149 MET cc_start: 0.8292 (mtt) cc_final: 0.8064 (tpp) REVERT: A 1167 LEU cc_start: 0.9223 (mt) cc_final: 0.8967 (mt) REVERT: A 1848 LEU cc_start: 0.8751 (tp) cc_final: 0.8471 (tt) REVERT: A 1904 GLU cc_start: 0.9329 (mp0) cc_final: 0.6697 (tt0) REVERT: A 1906 LEU cc_start: 0.9159 (mt) cc_final: 0.8616 (mt) REVERT: A 1926 GLU cc_start: 0.8029 (mm-30) cc_final: 0.7222 (mm-30) REVERT: A 1937 ARG cc_start: 0.8877 (mtt-85) cc_final: 0.8344 (ttp-110) REVERT: A 1960 MET cc_start: 0.9084 (ttp) cc_final: 0.8465 (tmm) REVERT: B 1910 ILE cc_start: 0.8333 (mm) cc_final: 0.8034 (mm) REVERT: B 1918 ILE cc_start: 0.7688 (mt) cc_final: 0.7090 (pt) REVERT: B 1922 HIS cc_start: 0.7770 (m-70) cc_final: 0.7367 (m90) REVERT: B 1947 ARG cc_start: 0.9140 (ptm-80) cc_final: 0.8456 (ptp-110) REVERT: B 1956 LYS cc_start: 0.9176 (mttt) cc_final: 0.8366 (mmmt) REVERT: B 1986 LEU cc_start: 0.9111 (mt) cc_final: 0.8901 (mt) REVERT: B 1987 ASP cc_start: 0.8288 (m-30) cc_final: 0.7997 (p0) REVERT: B 2006 LYS cc_start: 0.8032 (mptt) cc_final: 0.7734 (mttm) REVERT: B 2009 VAL cc_start: 0.8754 (p) cc_final: 0.8517 (p) REVERT: B 2010 MET cc_start: 0.8766 (mmm) cc_final: 0.8176 (mmm) REVERT: B 2015 VAL cc_start: 0.9223 (p) cc_final: 0.8943 (p) REVERT: B 2028 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8383 (tptt) REVERT: B 2107 ASN cc_start: 0.9009 (m-40) cc_final: 0.8783 (m-40) REVERT: B 2196 MET cc_start: 0.7225 (ttm) cc_final: 0.6671 (tpt) REVERT: B 2199 ILE cc_start: 0.7891 (mt) cc_final: 0.7439 (mm) REVERT: B 2209 THR cc_start: 0.8627 (m) cc_final: 0.8329 (m) REVERT: B 2314 THR cc_start: 0.9549 (t) cc_final: 0.9176 (m) REVERT: B 2324 LEU cc_start: 0.8737 (mm) cc_final: 0.8487 (mm) REVERT: B 2333 LYS cc_start: 0.6566 (mttt) cc_final: 0.6244 (mptt) REVERT: B 2356 PHE cc_start: 0.6724 (t80) cc_final: 0.6478 (t80) REVERT: B 2359 LEU cc_start: 0.8924 (mt) cc_final: 0.8679 (mt) REVERT: B 2373 LEU cc_start: 0.8946 (mt) cc_final: 0.8602 (mt) REVERT: B 2401 LYS cc_start: 0.7970 (tttt) cc_final: 0.7464 (mmmt) REVERT: B 2417 TYR cc_start: 0.8952 (m-80) cc_final: 0.8279 (m-80) REVERT: B 2427 GLU cc_start: 0.8146 (tp30) cc_final: 0.7790 (tp30) REVERT: B 2600 THR cc_start: 0.9489 (m) cc_final: 0.9223 (p) REVERT: B 2611 ASP cc_start: 0.7387 (m-30) cc_final: 0.6508 (t70) REVERT: B 2614 ASP cc_start: 0.9000 (m-30) cc_final: 0.8772 (m-30) REVERT: B 2616 ARG cc_start: 0.6748 (ttt180) cc_final: 0.6217 (tmt170) REVERT: B 2632 VAL cc_start: 0.8588 (t) cc_final: 0.8313 (t) REVERT: B 2640 LEU cc_start: 0.7600 (mt) cc_final: 0.7100 (mt) REVERT: B 2669 TYR cc_start: 0.8619 (t80) cc_final: 0.8315 (t80) REVERT: B 2685 PHE cc_start: 0.8505 (p90) cc_final: 0.7986 (p90) REVERT: B 2722 LEU cc_start: 0.8245 (mt) cc_final: 0.7949 (mt) outliers start: 7 outliers final: 0 residues processed: 556 average time/residue: 0.2378 time to fit residues: 200.5715 Evaluate side-chains 418 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 48 optimal weight: 5.9990 chunk 59 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 122 optimal weight: 8.9990 chunk 7 optimal weight: 7.9990 chunk 174 optimal weight: 0.9980 chunk 150 optimal weight: 0.7980 chunk 121 optimal weight: 8.9990 chunk 107 optimal weight: 0.5980 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN A1170 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2303 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.120593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.099631 restraints weight = 34170.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103410 restraints weight = 21727.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.106134 restraints weight = 15097.461| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14120 Z= 0.146 Angle : 0.609 8.617 19094 Z= 0.319 Chirality : 0.039 0.237 2298 Planarity : 0.004 0.045 2351 Dihedral : 4.726 26.609 1819 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.32 % Allowed : 2.55 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.20), residues: 1683 helix: 1.91 (0.13), residues: 1397 sheet: None (None), residues: 0 loop : 0.57 (0.39), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 9 HIS 0.012 0.001 HIS A1922 PHE 0.025 0.002 PHE B1993 TYR 0.025 0.002 TYR B1927 ARG 0.004 0.000 ARG A1137 Details of bonding type rmsd hydrogen bonds : bond 0.04384 ( 1042) hydrogen bonds : angle 4.29701 ( 3105) covalent geometry : bond 0.00314 (14120) covalent geometry : angle 0.60937 (19094) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 498 time to evaluate : 1.574 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 39 ASN cc_start: 0.8891 (m-40) cc_final: 0.8689 (t0) REVERT: A 222 ASN cc_start: 0.8559 (m-40) cc_final: 0.8292 (m-40) REVERT: A 231 PHE cc_start: 0.8199 (t80) cc_final: 0.7703 (t80) REVERT: A 254 ASP cc_start: 0.8716 (m-30) cc_final: 0.8232 (t0) REVERT: A 344 LEU cc_start: 0.8325 (mt) cc_final: 0.8057 (tp) REVERT: A 376 MET cc_start: 0.9005 (mtp) cc_final: 0.8494 (mpp) REVERT: A 383 CYS cc_start: 0.8443 (m) cc_final: 0.8170 (m) REVERT: A 524 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8098 (tp30) REVERT: A 529 LEU cc_start: 0.9034 (mt) cc_final: 0.8814 (mt) REVERT: A 530 VAL cc_start: 0.9104 (t) cc_final: 0.8762 (p) REVERT: A 540 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7384 (pm20) REVERT: A 543 GLN cc_start: 0.8407 (tp40) cc_final: 0.8006 (tm-30) REVERT: A 546 MET cc_start: 0.7750 (mtm) cc_final: 0.7408 (mtm) REVERT: A 707 MET cc_start: 0.8183 (mtt) cc_final: 0.7598 (mtt) REVERT: A 711 ARG cc_start: 0.7881 (ttp-110) cc_final: 0.7661 (ttm170) REVERT: A 775 GLU cc_start: 0.8310 (tt0) cc_final: 0.7333 (tm-30) REVERT: A 779 ASP cc_start: 0.8551 (m-30) cc_final: 0.8107 (m-30) REVERT: A 833 SER cc_start: 0.6473 (m) cc_final: 0.6109 (t) REVERT: A 837 TRP cc_start: 0.8805 (t60) cc_final: 0.8412 (t60) REVERT: A 845 CYS cc_start: 0.9329 (m) cc_final: 0.8512 (p) REVERT: A 902 MET cc_start: 0.8415 (mtt) cc_final: 0.8006 (mtt) REVERT: A 964 THR cc_start: 0.9345 (t) cc_final: 0.8925 (t) REVERT: A 965 ILE cc_start: 0.8869 (mm) cc_final: 0.8551 (mm) REVERT: A 992 MET cc_start: 0.8869 (mmm) cc_final: 0.8490 (mmm) REVERT: A 998 TYR cc_start: 0.8590 (t80) cc_final: 0.8202 (t80) REVERT: A 1005 MET cc_start: 0.7960 (mtm) cc_final: 0.6747 (mpp) REVERT: A 1022 MET cc_start: 0.8603 (ptp) cc_final: 0.8388 (ptp) REVERT: A 1023 MET cc_start: 0.7983 (mmp) cc_final: 0.7294 (mmt) REVERT: A 1039 ASN cc_start: 0.9161 (m-40) cc_final: 0.8708 (m-40) REVERT: A 1066 ARG cc_start: 0.8309 (ttm-80) cc_final: 0.8097 (ptm160) REVERT: A 1182 VAL cc_start: 0.8857 (t) cc_final: 0.8623 (t) REVERT: A 1848 LEU cc_start: 0.8649 (tp) cc_final: 0.8407 (tt) REVERT: A 1880 PRO cc_start: 0.8527 (Cg_endo) cc_final: 0.8168 (Cg_exo) REVERT: A 1898 GLU cc_start: 0.8258 (mp0) cc_final: 0.7734 (mt-10) REVERT: A 1901 LEU cc_start: 0.9264 (mt) cc_final: 0.9062 (mt) REVERT: A 1904 GLU cc_start: 0.9324 (mp0) cc_final: 0.6699 (tt0) REVERT: A 1905 PHE cc_start: 0.7998 (t80) cc_final: 0.7495 (t80) REVERT: A 1922 HIS cc_start: 0.7953 (t70) cc_final: 0.6967 (t70) REVERT: A 1925 LEU cc_start: 0.8728 (mt) cc_final: 0.8478 (mt) REVERT: A 1926 GLU cc_start: 0.7894 (mm-30) cc_final: 0.7220 (mm-30) REVERT: A 1927 TYR cc_start: 0.7868 (p90) cc_final: 0.7599 (p90) REVERT: A 1931 TRP cc_start: 0.7840 (m100) cc_final: 0.6656 (m100) REVERT: A 1937 ARG cc_start: 0.8715 (mtt-85) cc_final: 0.8199 (ttp-110) REVERT: A 1960 MET cc_start: 0.8916 (ttp) cc_final: 0.8447 (tmm) REVERT: A 1964 GLU cc_start: 0.8327 (tp30) cc_final: 0.7724 (tp30) REVERT: A 1967 MET cc_start: 0.7944 (mmm) cc_final: 0.7709 (mmt) REVERT: B 1918 ILE cc_start: 0.7905 (mt) cc_final: 0.7443 (mt) REVERT: B 1956 LYS cc_start: 0.8840 (mttt) cc_final: 0.8276 (mmmt) REVERT: B 1987 ASP cc_start: 0.7979 (m-30) cc_final: 0.7297 (t0) REVERT: B 2015 VAL cc_start: 0.9039 (p) cc_final: 0.8642 (p) REVERT: B 2028 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8065 (mmtt) REVERT: B 2120 PHE cc_start: 0.8022 (m-80) cc_final: 0.7637 (m-80) REVERT: B 2140 PHE cc_start: 0.8366 (m-80) cc_final: 0.8119 (m-80) REVERT: B 2184 VAL cc_start: 0.8233 (t) cc_final: 0.7928 (t) REVERT: B 2209 THR cc_start: 0.8681 (m) cc_final: 0.8384 (m) REVERT: B 2291 HIS cc_start: 0.8805 (m-70) cc_final: 0.8539 (m90) REVERT: B 2314 THR cc_start: 0.9482 (t) cc_final: 0.9159 (m) REVERT: B 2356 PHE cc_start: 0.6551 (t80) cc_final: 0.6344 (t80) REVERT: B 2401 LYS cc_start: 0.8165 (tttt) cc_final: 0.7669 (mmmt) REVERT: B 2407 LYS cc_start: 0.7327 (pttt) cc_final: 0.6990 (ptmt) REVERT: B 2417 TYR cc_start: 0.8868 (m-80) cc_final: 0.8292 (m-10) REVERT: B 2600 THR cc_start: 0.9423 (m) cc_final: 0.9193 (p) REVERT: B 2611 ASP cc_start: 0.7465 (m-30) cc_final: 0.7152 (t70) REVERT: B 2616 ARG cc_start: 0.6495 (ttt180) cc_final: 0.6047 (tmt170) REVERT: B 2640 LEU cc_start: 0.7225 (mt) cc_final: 0.6957 (mt) outliers start: 5 outliers final: 0 residues processed: 498 average time/residue: 0.2331 time to fit residues: 175.7891 Evaluate side-chains 408 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 163 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 173 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 58 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 HIS A 531 GLN A1170 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2119 HIS ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.120925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.100129 restraints weight = 33473.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.103902 restraints weight = 21276.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.106667 restraints weight = 14673.799| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14120 Z= 0.150 Angle : 0.599 8.091 19094 Z= 0.314 Chirality : 0.038 0.193 2298 Planarity : 0.004 0.052 2351 Dihedral : 4.637 27.168 1819 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.13 % Allowed : 1.78 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.20), residues: 1683 helix: 1.90 (0.13), residues: 1395 sheet: None (None), residues: 0 loop : 0.61 (0.39), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 9 HIS 0.008 0.001 HIS A1922 PHE 0.029 0.002 PHE B1913 TYR 0.028 0.002 TYR B1968 ARG 0.007 0.000 ARG B2343 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 1042) hydrogen bonds : angle 4.31654 ( 3105) covalent geometry : bond 0.00325 (14120) covalent geometry : angle 0.59938 (19094) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 468 time to evaluate : 1.501 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 8 GLU cc_start: 0.5484 (mp0) cc_final: 0.4382 (tp30) REVERT: A 50 LYS cc_start: 0.8191 (tttt) cc_final: 0.7964 (tptp) REVERT: A 149 ASN cc_start: 0.8389 (t0) cc_final: 0.8100 (t0) REVERT: A 217 GLU cc_start: 0.8685 (pp20) cc_final: 0.8474 (pp20) REVERT: A 231 PHE cc_start: 0.8180 (t80) cc_final: 0.7653 (t80) REVERT: A 250 PHE cc_start: 0.8351 (t80) cc_final: 0.7540 (t80) REVERT: A 274 LEU cc_start: 0.9196 (tp) cc_final: 0.8799 (mt) REVERT: A 344 LEU cc_start: 0.8445 (mt) cc_final: 0.8166 (tp) REVERT: A 376 MET cc_start: 0.8932 (mtp) cc_final: 0.8387 (mpp) REVERT: A 496 MET cc_start: 0.8002 (mtp) cc_final: 0.7393 (mtp) REVERT: A 524 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8127 (tp30) REVERT: A 533 VAL cc_start: 0.8250 (t) cc_final: 0.8029 (t) REVERT: A 540 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7042 (pm20) REVERT: A 543 GLN cc_start: 0.8392 (tp40) cc_final: 0.8011 (tm-30) REVERT: A 546 MET cc_start: 0.7534 (mtm) cc_final: 0.7212 (mtm) REVERT: A 552 LEU cc_start: 0.8633 (mt) cc_final: 0.8282 (mt) REVERT: A 573 ILE cc_start: 0.8748 (mt) cc_final: 0.8335 (mt) REVERT: A 681 ARG cc_start: 0.7643 (mtt180) cc_final: 0.7391 (mmt180) REVERT: A 711 ARG cc_start: 0.7650 (ttp-110) cc_final: 0.7417 (ttm170) REVERT: A 775 GLU cc_start: 0.8299 (tt0) cc_final: 0.7143 (tm-30) REVERT: A 779 ASP cc_start: 0.8616 (m-30) cc_final: 0.7900 (m-30) REVERT: A 833 SER cc_start: 0.5838 (m) cc_final: 0.5332 (t) REVERT: A 837 TRP cc_start: 0.8760 (t60) cc_final: 0.8482 (t60) REVERT: A 845 CYS cc_start: 0.9207 (m) cc_final: 0.8412 (p) REVERT: A 902 MET cc_start: 0.8463 (mtt) cc_final: 0.8057 (mtt) REVERT: A 965 ILE cc_start: 0.8910 (mm) cc_final: 0.8544 (mm) REVERT: A 968 MET cc_start: 0.7931 (mpp) cc_final: 0.7678 (mpp) REVERT: A 985 GLN cc_start: 0.8059 (mp10) cc_final: 0.7795 (mp10) REVERT: A 992 MET cc_start: 0.8968 (mmm) cc_final: 0.8539 (mmm) REVERT: A 998 TYR cc_start: 0.8714 (t80) cc_final: 0.8261 (t80) REVERT: A 1005 MET cc_start: 0.7955 (mtm) cc_final: 0.6701 (mpp) REVERT: A 1022 MET cc_start: 0.8663 (ptp) cc_final: 0.8036 (ptp) REVERT: A 1023 MET cc_start: 0.7580 (mmp) cc_final: 0.6904 (mmt) REVERT: A 1039 ASN cc_start: 0.9159 (m-40) cc_final: 0.8724 (m-40) REVERT: A 1066 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.7970 (ptm160) REVERT: A 1099 LYS cc_start: 0.8822 (ptpt) cc_final: 0.8582 (pttt) REVERT: A 1848 LEU cc_start: 0.8816 (tp) cc_final: 0.8538 (tp) REVERT: A 1880 PRO cc_start: 0.8905 (Cg_endo) cc_final: 0.8605 (Cg_exo) REVERT: A 1904 GLU cc_start: 0.9326 (mp0) cc_final: 0.6880 (tt0) REVERT: A 1905 PHE cc_start: 0.8121 (t80) cc_final: 0.7828 (t80) REVERT: A 1926 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7616 (mm-30) REVERT: A 1937 ARG cc_start: 0.8699 (mtt-85) cc_final: 0.8175 (ttp-110) REVERT: A 1960 MET cc_start: 0.8907 (ttp) cc_final: 0.8468 (tmm) REVERT: A 1964 GLU cc_start: 0.8307 (tp30) cc_final: 0.8006 (tp30) REVERT: A 1967 MET cc_start: 0.7685 (mmm) cc_final: 0.7344 (mmt) REVERT: B 1928 MET cc_start: 0.7554 (mmp) cc_final: 0.7295 (mmp) REVERT: B 1956 LYS cc_start: 0.8844 (mttt) cc_final: 0.8043 (tptm) REVERT: B 1987 ASP cc_start: 0.7988 (m-30) cc_final: 0.7430 (t0) REVERT: B 2107 ASN cc_start: 0.9021 (m-40) cc_final: 0.8686 (m-40) REVERT: B 2120 PHE cc_start: 0.8130 (m-80) cc_final: 0.7673 (m-80) REVERT: B 2140 PHE cc_start: 0.8455 (m-80) cc_final: 0.8184 (m-80) REVERT: B 2184 VAL cc_start: 0.8224 (t) cc_final: 0.7974 (t) REVERT: B 2209 THR cc_start: 0.8656 (m) cc_final: 0.8348 (m) REVERT: B 2356 PHE cc_start: 0.6647 (t80) cc_final: 0.6343 (t80) REVERT: B 2359 LEU cc_start: 0.9122 (mt) cc_final: 0.8774 (mt) REVERT: B 2365 PHE cc_start: 0.7773 (t80) cc_final: 0.7525 (t80) REVERT: B 2401 LYS cc_start: 0.8207 (tttt) cc_final: 0.7571 (mmmt) REVERT: B 2407 LYS cc_start: 0.7251 (pttt) cc_final: 0.6851 (ptmt) REVERT: B 2417 TYR cc_start: 0.8779 (m-80) cc_final: 0.8345 (m-10) REVERT: B 2423 THR cc_start: 0.7933 (p) cc_final: 0.7503 (p) REVERT: B 2427 GLU cc_start: 0.8382 (tp30) cc_final: 0.8164 (tp30) REVERT: B 2616 ARG cc_start: 0.6652 (ttt180) cc_final: 0.6102 (tmt170) REVERT: B 2685 PHE cc_start: 0.8733 (p90) cc_final: 0.8245 (p90) outliers start: 2 outliers final: 0 residues processed: 469 average time/residue: 0.2404 time to fit residues: 170.6627 Evaluate side-chains 388 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 54 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 162 optimal weight: 0.0870 chunk 74 optimal weight: 2.9990 chunk 13 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 531 GLN ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 781 HIS A1163 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.120332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.098891 restraints weight = 34220.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.102591 restraints weight = 22096.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105353 restraints weight = 15476.802| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14120 Z= 0.153 Angle : 0.601 8.197 19094 Z= 0.312 Chirality : 0.039 0.194 2298 Planarity : 0.004 0.093 2351 Dihedral : 4.570 23.820 1819 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.20), residues: 1683 helix: 1.84 (0.13), residues: 1401 sheet: None (None), residues: 0 loop : 0.31 (0.39), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 9 HIS 0.009 0.001 HIS A1922 PHE 0.021 0.002 PHE A 741 TYR 0.025 0.002 TYR A1927 ARG 0.005 0.000 ARG A1849 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 1042) hydrogen bonds : angle 4.30801 ( 3105) covalent geometry : bond 0.00334 (14120) covalent geometry : angle 0.60090 (19094) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 457 time to evaluate : 1.617 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 8 GLU cc_start: 0.5473 (mp0) cc_final: 0.4432 (tp30) REVERT: A 41 GLU cc_start: 0.9382 (mt-10) cc_final: 0.8875 (mm-30) REVERT: A 116 GLU cc_start: 0.6543 (mm-30) cc_final: 0.6255 (mm-30) REVERT: A 149 ASN cc_start: 0.8395 (t0) cc_final: 0.7945 (t0) REVERT: A 250 PHE cc_start: 0.8225 (t80) cc_final: 0.7732 (t80) REVERT: A 274 LEU cc_start: 0.9110 (tp) cc_final: 0.8807 (mt) REVERT: A 349 MET cc_start: 0.7751 (mmp) cc_final: 0.7549 (mmm) REVERT: A 376 MET cc_start: 0.8887 (mtp) cc_final: 0.8341 (mpp) REVERT: A 408 TYR cc_start: 0.8063 (t80) cc_final: 0.7860 (t80) REVERT: A 496 MET cc_start: 0.8121 (mtp) cc_final: 0.7628 (mtp) REVERT: A 524 GLU cc_start: 0.8928 (mt-10) cc_final: 0.8181 (tp30) REVERT: A 540 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7065 (pm20) REVERT: A 543 GLN cc_start: 0.8533 (tp40) cc_final: 0.8185 (pp30) REVERT: A 546 MET cc_start: 0.7516 (mtm) cc_final: 0.7206 (mtm) REVERT: A 552 LEU cc_start: 0.8631 (mt) cc_final: 0.8305 (mt) REVERT: A 577 MET cc_start: 0.8933 (ttm) cc_final: 0.8530 (tmm) REVERT: A 707 MET cc_start: 0.8562 (ttm) cc_final: 0.8023 (tmm) REVERT: A 712 HIS cc_start: 0.7478 (m-70) cc_final: 0.7182 (m-70) REVERT: A 760 MET cc_start: 0.8575 (mtp) cc_final: 0.8373 (ptp) REVERT: A 775 GLU cc_start: 0.8205 (tt0) cc_final: 0.7276 (tm-30) REVERT: A 779 ASP cc_start: 0.8698 (m-30) cc_final: 0.8361 (m-30) REVERT: A 833 SER cc_start: 0.5861 (m) cc_final: 0.5224 (t) REVERT: A 837 TRP cc_start: 0.8810 (t60) cc_final: 0.8548 (t60) REVERT: A 902 MET cc_start: 0.8432 (mtt) cc_final: 0.8089 (mtt) REVERT: A 924 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 964 THR cc_start: 0.9263 (t) cc_final: 0.9007 (t) REVERT: A 992 MET cc_start: 0.8997 (mmm) cc_final: 0.8762 (mmm) REVERT: A 998 TYR cc_start: 0.8657 (t80) cc_final: 0.8222 (t80) REVERT: A 1005 MET cc_start: 0.8080 (mtm) cc_final: 0.6765 (mpp) REVERT: A 1022 MET cc_start: 0.8754 (ptp) cc_final: 0.8460 (ptp) REVERT: A 1039 ASN cc_start: 0.9237 (m-40) cc_final: 0.8826 (m-40) REVERT: A 1066 ARG cc_start: 0.8517 (ttm-80) cc_final: 0.8167 (ptm160) REVERT: A 1070 GLN cc_start: 0.8249 (tt0) cc_final: 0.7927 (tt0) REVERT: A 1099 LYS cc_start: 0.8716 (ptpt) cc_final: 0.8468 (pttt) REVERT: A 1880 PRO cc_start: 0.8833 (Cg_endo) cc_final: 0.8359 (Cg_exo) REVERT: A 1904 GLU cc_start: 0.9341 (mp0) cc_final: 0.6966 (tt0) REVERT: A 1925 LEU cc_start: 0.8870 (mt) cc_final: 0.8660 (mt) REVERT: A 1937 ARG cc_start: 0.8596 (mtt-85) cc_final: 0.8026 (ttp-110) REVERT: A 1960 MET cc_start: 0.8899 (ttp) cc_final: 0.8496 (tmm) REVERT: A 1964 GLU cc_start: 0.8316 (tp30) cc_final: 0.7967 (tp30) REVERT: A 1967 MET cc_start: 0.7763 (mmm) cc_final: 0.7377 (mmt) REVERT: B 1956 LYS cc_start: 0.8811 (mttt) cc_final: 0.8352 (mtpt) REVERT: B 1987 ASP cc_start: 0.7989 (m-30) cc_final: 0.7360 (t0) REVERT: B 2065 LEU cc_start: 0.8351 (tp) cc_final: 0.8099 (tp) REVERT: B 2107 ASN cc_start: 0.8991 (m-40) cc_final: 0.8739 (t0) REVERT: B 2120 PHE cc_start: 0.8115 (m-80) cc_final: 0.7739 (m-80) REVERT: B 2140 PHE cc_start: 0.8504 (m-80) cc_final: 0.8221 (m-80) REVERT: B 2184 VAL cc_start: 0.8313 (t) cc_final: 0.8014 (t) REVERT: B 2196 MET cc_start: 0.6456 (tpp) cc_final: 0.6216 (tpt) REVERT: B 2209 THR cc_start: 0.8759 (m) cc_final: 0.8471 (m) REVERT: B 2336 GLU cc_start: 0.8755 (mp0) cc_final: 0.8532 (mp0) REVERT: B 2340 MET cc_start: 0.7046 (mmm) cc_final: 0.6582 (mmm) REVERT: B 2356 PHE cc_start: 0.6838 (t80) cc_final: 0.6573 (t80) REVERT: B 2359 LEU cc_start: 0.9192 (mt) cc_final: 0.8654 (mt) REVERT: B 2401 LYS cc_start: 0.8090 (tttt) cc_final: 0.7726 (mmmm) REVERT: B 2407 LYS cc_start: 0.7110 (pttt) cc_final: 0.6782 (ptmt) REVERT: B 2417 TYR cc_start: 0.8901 (m-80) cc_final: 0.8479 (m-10) REVERT: B 2613 PHE cc_start: 0.7203 (t80) cc_final: 0.6996 (t80) REVERT: B 2616 ARG cc_start: 0.6549 (ttt180) cc_final: 0.5993 (tmt170) REVERT: B 2669 TYR cc_start: 0.8343 (t80) cc_final: 0.8135 (t80) REVERT: B 2685 PHE cc_start: 0.8936 (p90) cc_final: 0.8292 (p90) outliers start: 0 outliers final: 0 residues processed: 457 average time/residue: 0.2335 time to fit residues: 163.1411 Evaluate side-chains 393 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 138 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 36 optimal weight: 20.0000 chunk 115 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 HIS A 531 GLN A 912 GLN ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2119 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.120231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.098672 restraints weight = 34302.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.102376 restraints weight = 22482.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.105147 restraints weight = 15827.835| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.5863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14120 Z= 0.153 Angle : 0.608 8.420 19094 Z= 0.314 Chirality : 0.039 0.209 2298 Planarity : 0.004 0.049 2351 Dihedral : 4.504 21.620 1819 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 1683 helix: 1.86 (0.13), residues: 1390 sheet: None (None), residues: 0 loop : 0.15 (0.39), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 221 HIS 0.007 0.001 HIS A1922 PHE 0.027 0.002 PHE B1993 TYR 0.028 0.002 TYR B1968 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.04105 ( 1042) hydrogen bonds : angle 4.31190 ( 3105) covalent geometry : bond 0.00340 (14120) covalent geometry : angle 0.60776 (19094) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 1.695 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 8 GLU cc_start: 0.5398 (mp0) cc_final: 0.4348 (tp30) REVERT: A 41 GLU cc_start: 0.9396 (mt-10) cc_final: 0.8874 (mm-30) REVERT: A 121 LEU cc_start: 0.6915 (mp) cc_final: 0.6629 (mp) REVERT: A 250 PHE cc_start: 0.8176 (t80) cc_final: 0.7903 (t80) REVERT: A 274 LEU cc_start: 0.9122 (tp) cc_final: 0.8804 (mt) REVERT: A 376 MET cc_start: 0.8852 (mtp) cc_final: 0.8305 (mpp) REVERT: A 496 MET cc_start: 0.8150 (mtp) cc_final: 0.7534 (mtp) REVERT: A 524 GLU cc_start: 0.8934 (mt-10) cc_final: 0.8319 (tp30) REVERT: A 540 GLU cc_start: 0.7497 (mt-10) cc_final: 0.6947 (pm20) REVERT: A 543 GLN cc_start: 0.8512 (tp40) cc_final: 0.8142 (pp30) REVERT: A 546 MET cc_start: 0.7568 (mtm) cc_final: 0.7243 (mtm) REVERT: A 577 MET cc_start: 0.8952 (ttm) cc_final: 0.8533 (tmm) REVERT: A 604 LEU cc_start: 0.9132 (mt) cc_final: 0.8910 (mt) REVERT: A 695 LEU cc_start: 0.8230 (mt) cc_final: 0.8027 (mt) REVERT: A 707 MET cc_start: 0.8593 (ttm) cc_final: 0.8259 (ttp) REVERT: A 737 THR cc_start: 0.8894 (m) cc_final: 0.8592 (m) REVERT: A 755 LEU cc_start: 0.8680 (tp) cc_final: 0.8449 (mm) REVERT: A 760 MET cc_start: 0.8569 (mtp) cc_final: 0.8328 (ptp) REVERT: A 775 GLU cc_start: 0.8303 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 779 ASP cc_start: 0.8637 (m-30) cc_final: 0.8297 (m-30) REVERT: A 845 CYS cc_start: 0.9376 (m) cc_final: 0.8631 (p) REVERT: A 902 MET cc_start: 0.8435 (mtt) cc_final: 0.8169 (mtt) REVERT: A 924 GLU cc_start: 0.7846 (mm-30) cc_final: 0.7575 (mm-30) REVERT: A 964 THR cc_start: 0.9230 (t) cc_final: 0.9017 (t) REVERT: A 968 MET cc_start: 0.8067 (mpp) cc_final: 0.7859 (mpp) REVERT: A 991 MET cc_start: 0.7418 (ppp) cc_final: 0.6920 (ppp) REVERT: A 998 TYR cc_start: 0.8675 (t80) cc_final: 0.8221 (t80) REVERT: A 1005 MET cc_start: 0.8076 (mtm) cc_final: 0.6706 (mpp) REVERT: A 1012 LYS cc_start: 0.8507 (mttt) cc_final: 0.7844 (mmtp) REVERT: A 1039 ASN cc_start: 0.9243 (m-40) cc_final: 0.8841 (m-40) REVERT: A 1066 ARG cc_start: 0.8482 (ttm-80) cc_final: 0.8074 (ptm160) REVERT: A 1070 GLN cc_start: 0.8298 (tt0) cc_final: 0.7983 (tt0) REVERT: A 1099 LYS cc_start: 0.8716 (ptpt) cc_final: 0.8456 (pttt) REVERT: A 1880 PRO cc_start: 0.8762 (Cg_endo) cc_final: 0.8418 (Cg_exo) REVERT: A 1904 GLU cc_start: 0.9364 (mp0) cc_final: 0.7020 (tt0) REVERT: A 1905 PHE cc_start: 0.7926 (t80) cc_final: 0.7665 (t80) REVERT: A 1925 LEU cc_start: 0.8697 (mt) cc_final: 0.8453 (mt) REVERT: A 1931 TRP cc_start: 0.7314 (m100) cc_final: 0.6270 (m100) REVERT: A 1937 ARG cc_start: 0.8594 (mtt-85) cc_final: 0.8024 (ttp-110) REVERT: A 1960 MET cc_start: 0.8905 (ttp) cc_final: 0.8504 (tmm) REVERT: A 1961 THR cc_start: 0.8056 (m) cc_final: 0.7552 (p) REVERT: B 1956 LYS cc_start: 0.8808 (mttt) cc_final: 0.8326 (mtpt) REVERT: B 1968 TYR cc_start: 0.8318 (t80) cc_final: 0.7984 (t80) REVERT: B 1982 ILE cc_start: 0.8541 (mt) cc_final: 0.8316 (mt) REVERT: B 1987 ASP cc_start: 0.7806 (m-30) cc_final: 0.7238 (t0) REVERT: B 2107 ASN cc_start: 0.8959 (m-40) cc_final: 0.8719 (t0) REVERT: B 2120 PHE cc_start: 0.7999 (m-80) cc_final: 0.7659 (m-80) REVERT: B 2140 PHE cc_start: 0.8502 (m-80) cc_final: 0.8247 (m-80) REVERT: B 2184 VAL cc_start: 0.8292 (t) cc_final: 0.8050 (t) REVERT: B 2209 THR cc_start: 0.8703 (m) cc_final: 0.8439 (m) REVERT: B 2304 LEU cc_start: 0.8828 (mt) cc_final: 0.8611 (mt) REVERT: B 2333 LYS cc_start: 0.6944 (mttt) cc_final: 0.6180 (mptt) REVERT: B 2336 GLU cc_start: 0.8851 (mp0) cc_final: 0.8607 (mp0) REVERT: B 2340 MET cc_start: 0.7212 (mmm) cc_final: 0.6614 (mmm) REVERT: B 2377 TYR cc_start: 0.7958 (m-80) cc_final: 0.7669 (m-80) REVERT: B 2407 LYS cc_start: 0.7381 (pttt) cc_final: 0.7050 (ptmt) REVERT: B 2417 TYR cc_start: 0.8939 (m-80) cc_final: 0.8541 (m-10) REVERT: B 2423 THR cc_start: 0.7814 (p) cc_final: 0.7410 (p) REVERT: B 2616 ARG cc_start: 0.6523 (ttt180) cc_final: 0.5902 (tmt170) REVERT: B 2670 HIS cc_start: 0.8126 (m-70) cc_final: 0.7852 (m-70) REVERT: B 2685 PHE cc_start: 0.8952 (p90) cc_final: 0.8238 (p90) outliers start: 1 outliers final: 0 residues processed: 437 average time/residue: 0.2294 time to fit residues: 154.4895 Evaluate side-chains 393 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 174 optimal weight: 0.8980 chunk 116 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 40 optimal weight: 0.8980 chunk 164 optimal weight: 0.0670 chunk 9 optimal weight: 5.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 501 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 982 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN B1882 ASN ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.100974 restraints weight = 33867.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.104829 restraints weight = 21684.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.107648 restraints weight = 15049.806| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14120 Z= 0.131 Angle : 0.600 12.875 19094 Z= 0.305 Chirality : 0.038 0.182 2298 Planarity : 0.003 0.044 2351 Dihedral : 4.372 20.412 1819 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.13 % Allowed : 1.15 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.20), residues: 1683 helix: 1.93 (0.14), residues: 1393 sheet: None (None), residues: 0 loop : 0.15 (0.39), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 9 HIS 0.009 0.001 HIS A 38 PHE 0.019 0.001 PHE B2367 TYR 0.028 0.002 TYR B1968 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03876 ( 1042) hydrogen bonds : angle 4.24433 ( 3105) covalent geometry : bond 0.00290 (14120) covalent geometry : angle 0.60049 (19094) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 457 time to evaluate : 2.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.5395 (mp0) cc_final: 0.4106 (tp30) REVERT: A 41 GLU cc_start: 0.9416 (mt-10) cc_final: 0.8877 (mm-30) REVERT: A 50 LYS cc_start: 0.8384 (tttt) cc_final: 0.8106 (tptp) REVERT: A 149 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7908 (t0) REVERT: A 222 ASN cc_start: 0.8511 (m-40) cc_final: 0.8300 (m-40) REVERT: A 231 PHE cc_start: 0.8218 (t80) cc_final: 0.7671 (t80) REVERT: A 250 PHE cc_start: 0.8185 (t80) cc_final: 0.7849 (t80) REVERT: A 274 LEU cc_start: 0.9135 (tp) cc_final: 0.8814 (mt) REVERT: A 376 MET cc_start: 0.8816 (mtp) cc_final: 0.8288 (mpp) REVERT: A 384 PHE cc_start: 0.8621 (t80) cc_final: 0.8338 (t80) REVERT: A 442 MET cc_start: 0.8511 (ttm) cc_final: 0.8123 (tpp) REVERT: A 496 MET cc_start: 0.8266 (mtp) cc_final: 0.7425 (mtp) REVERT: A 524 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8244 (tp30) REVERT: A 533 VAL cc_start: 0.8126 (t) cc_final: 0.7912 (t) REVERT: A 540 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6948 (pm20) REVERT: A 543 GLN cc_start: 0.8480 (tp40) cc_final: 0.8140 (pp30) REVERT: A 546 MET cc_start: 0.7464 (mtm) cc_final: 0.7133 (mtm) REVERT: A 573 ILE cc_start: 0.8326 (tp) cc_final: 0.7911 (tp) REVERT: A 577 MET cc_start: 0.8887 (ttm) cc_final: 0.8679 (tmm) REVERT: A 707 MET cc_start: 0.8727 (ttm) cc_final: 0.8193 (tmm) REVERT: A 712 HIS cc_start: 0.7288 (m-70) cc_final: 0.6902 (m-70) REVERT: A 775 GLU cc_start: 0.8384 (tt0) cc_final: 0.7302 (tm-30) REVERT: A 779 ASP cc_start: 0.8707 (m-30) cc_final: 0.8398 (m-30) REVERT: A 836 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 837 TRP cc_start: 0.8740 (t60) cc_final: 0.8509 (t60) REVERT: A 845 CYS cc_start: 0.9333 (m) cc_final: 0.8671 (p) REVERT: A 902 MET cc_start: 0.8412 (mtt) cc_final: 0.8063 (mtt) REVERT: A 924 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7468 (mm-30) REVERT: A 968 MET cc_start: 0.8112 (mpp) cc_final: 0.7892 (mpp) REVERT: A 991 MET cc_start: 0.7324 (ppp) cc_final: 0.6967 (ppp) REVERT: A 998 TYR cc_start: 0.8620 (t80) cc_final: 0.8160 (t80) REVERT: A 1005 MET cc_start: 0.8074 (mtm) cc_final: 0.6798 (mpp) REVERT: A 1039 ASN cc_start: 0.9274 (m-40) cc_final: 0.8864 (m-40) REVERT: A 1066 ARG cc_start: 0.8547 (ttm-80) cc_final: 0.8094 (ptm160) REVERT: A 1070 GLN cc_start: 0.8234 (tt0) cc_final: 0.7928 (tt0) REVERT: A 1099 LYS cc_start: 0.8686 (ptpt) cc_final: 0.8441 (pttt) REVERT: A 1162 MET cc_start: 0.7995 (pmm) cc_final: 0.7786 (pmm) REVERT: A 1880 PRO cc_start: 0.8647 (Cg_endo) cc_final: 0.8323 (Cg_exo) REVERT: A 1898 GLU cc_start: 0.8284 (mp0) cc_final: 0.7664 (mp0) REVERT: A 1904 GLU cc_start: 0.9311 (mp0) cc_final: 0.7045 (tt0) REVERT: A 1925 LEU cc_start: 0.8565 (mt) cc_final: 0.8320 (mt) REVERT: A 1937 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.7940 (ttp-110) REVERT: A 1960 MET cc_start: 0.8963 (ttp) cc_final: 0.8589 (tmm) REVERT: A 1961 THR cc_start: 0.8010 (m) cc_final: 0.7611 (p) REVERT: A 1964 GLU cc_start: 0.8117 (tp30) cc_final: 0.7823 (tp30) REVERT: A 1967 MET cc_start: 0.7822 (mmm) cc_final: 0.7429 (mmm) REVERT: B 1885 LEU cc_start: 0.8946 (tp) cc_final: 0.8526 (pp) REVERT: B 1894 LEU cc_start: 0.9083 (mt) cc_final: 0.8653 (mt) REVERT: B 1928 MET cc_start: 0.8448 (mmp) cc_final: 0.7461 (mmp) REVERT: B 1956 LYS cc_start: 0.8809 (mttt) cc_final: 0.8053 (tptm) REVERT: B 1968 TYR cc_start: 0.8306 (t80) cc_final: 0.7965 (t80) REVERT: B 2065 LEU cc_start: 0.8322 (tp) cc_final: 0.7334 (pp) REVERT: B 2107 ASN cc_start: 0.8949 (m-40) cc_final: 0.8634 (m-40) REVERT: B 2120 PHE cc_start: 0.7964 (m-80) cc_final: 0.7636 (m-80) REVERT: B 2209 THR cc_start: 0.8635 (m) cc_final: 0.8342 (m) REVERT: B 2210 GLU cc_start: 0.8455 (tt0) cc_final: 0.7793 (tp30) REVERT: B 2333 LYS cc_start: 0.6910 (mttt) cc_final: 0.6171 (mptt) REVERT: B 2340 MET cc_start: 0.7112 (mmm) cc_final: 0.6521 (mmm) REVERT: B 2359 LEU cc_start: 0.9104 (mt) cc_final: 0.8735 (mt) REVERT: B 2377 TYR cc_start: 0.7999 (m-80) cc_final: 0.7600 (m-80) REVERT: B 2400 ASN cc_start: 0.8416 (m110) cc_final: 0.7500 (p0) REVERT: B 2407 LYS cc_start: 0.7414 (pttt) cc_final: 0.6952 (ptmt) REVERT: B 2417 TYR cc_start: 0.8977 (m-80) cc_final: 0.8682 (m-10) REVERT: B 2418 LEU cc_start: 0.9130 (mt) cc_final: 0.8909 (mt) REVERT: B 2423 THR cc_start: 0.7962 (p) cc_final: 0.7443 (p) REVERT: B 2616 ARG cc_start: 0.6475 (ttt180) cc_final: 0.5727 (tmt170) REVERT: B 2618 LEU cc_start: 0.8583 (mm) cc_final: 0.8337 (mm) REVERT: B 2670 HIS cc_start: 0.8216 (m-70) cc_final: 0.7969 (m-70) REVERT: B 2685 PHE cc_start: 0.8729 (p90) cc_final: 0.8005 (p90) outliers start: 2 outliers final: 0 residues processed: 458 average time/residue: 0.2775 time to fit residues: 198.9351 Evaluate side-chains 387 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 386 time to evaluate : 2.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 63 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 151 optimal weight: 0.7980 chunk 57 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN A 501 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.122849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.101953 restraints weight = 33622.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.105753 restraints weight = 21664.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108530 restraints weight = 15116.189| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.6362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14120 Z= 0.137 Angle : 0.629 11.806 19094 Z= 0.319 Chirality : 0.039 0.197 2298 Planarity : 0.004 0.045 2351 Dihedral : 4.415 18.944 1819 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.06 % Allowed : 1.02 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.36 (0.20), residues: 1683 helix: 1.87 (0.14), residues: 1399 sheet: None (None), residues: 0 loop : 0.21 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 777 HIS 0.007 0.001 HIS A1922 PHE 0.061 0.002 PHE A1107 TYR 0.035 0.002 TYR A 433 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03908 ( 1042) hydrogen bonds : angle 4.26885 ( 3105) covalent geometry : bond 0.00307 (14120) covalent geometry : angle 0.62927 (19094) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 442 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.5401 (mp0) cc_final: 0.4111 (tp30) REVERT: A 231 PHE cc_start: 0.8256 (t80) cc_final: 0.7701 (t80) REVERT: A 250 PHE cc_start: 0.8186 (t80) cc_final: 0.7729 (t80) REVERT: A 274 LEU cc_start: 0.9076 (tp) cc_final: 0.8796 (mt) REVERT: A 376 MET cc_start: 0.8714 (mtp) cc_final: 0.8218 (mpp) REVERT: A 496 MET cc_start: 0.8194 (mtp) cc_final: 0.7539 (mtp) REVERT: A 524 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8258 (tp30) REVERT: A 533 VAL cc_start: 0.8225 (t) cc_final: 0.7986 (t) REVERT: A 540 GLU cc_start: 0.7506 (mt-10) cc_final: 0.6998 (pm20) REVERT: A 543 GLN cc_start: 0.8505 (tp40) cc_final: 0.8118 (pp30) REVERT: A 546 MET cc_start: 0.7434 (mtm) cc_final: 0.7076 (mtm) REVERT: A 573 ILE cc_start: 0.8325 (tp) cc_final: 0.7945 (tp) REVERT: A 577 MET cc_start: 0.8878 (ttm) cc_final: 0.8516 (tmm) REVERT: A 604 LEU cc_start: 0.9125 (mt) cc_final: 0.8895 (mt) REVERT: A 707 MET cc_start: 0.8647 (ttm) cc_final: 0.8233 (tmm) REVERT: A 735 TYR cc_start: 0.7148 (t80) cc_final: 0.6909 (t80) REVERT: A 739 MET cc_start: 0.8031 (mmm) cc_final: 0.7721 (mmm) REVERT: A 760 MET cc_start: 0.8587 (ptp) cc_final: 0.8318 (ptp) REVERT: A 775 GLU cc_start: 0.8200 (tt0) cc_final: 0.7192 (tm-30) REVERT: A 779 ASP cc_start: 0.8679 (m-30) cc_final: 0.8393 (m-30) REVERT: A 836 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8453 (mt-10) REVERT: A 845 CYS cc_start: 0.9309 (m) cc_final: 0.8632 (p) REVERT: A 902 MET cc_start: 0.8439 (mtt) cc_final: 0.8034 (mtt) REVERT: A 924 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7545 (mm-30) REVERT: A 964 THR cc_start: 0.9162 (t) cc_final: 0.8802 (t) REVERT: A 965 ILE cc_start: 0.8961 (mm) cc_final: 0.8563 (mm) REVERT: A 991 MET cc_start: 0.7432 (ppp) cc_final: 0.6882 (ppp) REVERT: A 998 TYR cc_start: 0.8591 (t80) cc_final: 0.8172 (t80) REVERT: A 1005 MET cc_start: 0.8047 (mtm) cc_final: 0.6711 (mpp) REVERT: A 1039 ASN cc_start: 0.9257 (m-40) cc_final: 0.8850 (m-40) REVERT: A 1066 ARG cc_start: 0.8378 (ttm-80) cc_final: 0.7985 (ptm160) REVERT: A 1070 GLN cc_start: 0.8266 (tt0) cc_final: 0.7947 (tt0) REVERT: A 1099 LYS cc_start: 0.8645 (ptpt) cc_final: 0.8439 (pttt) REVERT: A 1162 MET cc_start: 0.7977 (pmm) cc_final: 0.7749 (pmm) REVERT: A 1880 PRO cc_start: 0.8645 (Cg_endo) cc_final: 0.8183 (Cg_exo) REVERT: A 1904 GLU cc_start: 0.9290 (mp0) cc_final: 0.7080 (tt0) REVERT: A 1925 LEU cc_start: 0.8547 (mt) cc_final: 0.8293 (mt) REVERT: A 1937 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.7881 (ttm-80) REVERT: A 1960 MET cc_start: 0.8835 (ttp) cc_final: 0.8500 (tmm) REVERT: A 1961 THR cc_start: 0.8170 (m) cc_final: 0.7759 (p) REVERT: A 1964 GLU cc_start: 0.8262 (tp30) cc_final: 0.8041 (tp30) REVERT: A 1967 MET cc_start: 0.7715 (mmm) cc_final: 0.7328 (mmt) REVERT: A 2008 GLU cc_start: 0.7205 (pp20) cc_final: 0.6946 (pt0) REVERT: B 1925 LEU cc_start: 0.8642 (mt) cc_final: 0.7996 (pp) REVERT: B 1956 LYS cc_start: 0.8847 (mttt) cc_final: 0.8077 (tptm) REVERT: B 2064 MET cc_start: 0.7613 (tpt) cc_final: 0.7409 (tpt) REVERT: B 2065 LEU cc_start: 0.8338 (tp) cc_final: 0.7314 (pp) REVERT: B 2107 ASN cc_start: 0.8951 (m-40) cc_final: 0.8584 (m-40) REVERT: B 2120 PHE cc_start: 0.7941 (m-80) cc_final: 0.7636 (m-80) REVERT: B 2209 THR cc_start: 0.8700 (m) cc_final: 0.8315 (m) REVERT: B 2210 GLU cc_start: 0.8395 (tt0) cc_final: 0.7774 (tp30) REVERT: B 2333 LYS cc_start: 0.6842 (mttt) cc_final: 0.6013 (mptt) REVERT: B 2340 MET cc_start: 0.7098 (mmm) cc_final: 0.6470 (mmm) REVERT: B 2356 PHE cc_start: 0.5684 (t80) cc_final: 0.5463 (t80) REVERT: B 2359 LEU cc_start: 0.9146 (mt) cc_final: 0.8831 (mt) REVERT: B 2377 TYR cc_start: 0.7914 (m-80) cc_final: 0.7535 (m-80) REVERT: B 2407 LYS cc_start: 0.7469 (pttt) cc_final: 0.7188 (ptmt) REVERT: B 2417 TYR cc_start: 0.8933 (m-80) cc_final: 0.8695 (m-10) REVERT: B 2418 LEU cc_start: 0.9040 (mt) cc_final: 0.8836 (mt) REVERT: B 2423 THR cc_start: 0.8046 (p) cc_final: 0.7526 (p) REVERT: B 2616 ARG cc_start: 0.6456 (ttt180) cc_final: 0.5704 (tmt170) REVERT: B 2618 LEU cc_start: 0.8600 (mm) cc_final: 0.8337 (mm) REVERT: B 2670 HIS cc_start: 0.8245 (m-70) cc_final: 0.8036 (m-70) REVERT: B 2685 PHE cc_start: 0.8744 (p90) cc_final: 0.8135 (p90) outliers start: 1 outliers final: 0 residues processed: 443 average time/residue: 0.2449 time to fit residues: 166.4586 Evaluate side-chains 381 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 12 optimal weight: 0.5980 chunk 77 optimal weight: 0.8980 chunk 148 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 64 optimal weight: 8.9990 chunk 73 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 0.8980 chunk 99 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN A 412 ASN A 501 HIS ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2070 ASN ** B2110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.123543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.102443 restraints weight = 33332.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.106308 restraints weight = 21459.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.109089 restraints weight = 14917.840| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.6569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14120 Z= 0.134 Angle : 0.628 11.015 19094 Z= 0.320 Chirality : 0.039 0.192 2298 Planarity : 0.004 0.045 2351 Dihedral : 4.364 18.876 1819 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.20), residues: 1683 helix: 1.92 (0.14), residues: 1394 sheet: None (None), residues: 0 loop : 0.13 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 777 HIS 0.009 0.001 HIS A1922 PHE 0.040 0.002 PHE A1107 TYR 0.019 0.002 TYR A 433 ARG 0.004 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.03880 ( 1042) hydrogen bonds : angle 4.24026 ( 3105) covalent geometry : bond 0.00296 (14120) covalent geometry : angle 0.62833 (19094) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 3.589 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 8 GLU cc_start: 0.5343 (mp0) cc_final: 0.4181 (tp30) REVERT: A 149 ASN cc_start: 0.8275 (t0) cc_final: 0.7958 (t0) REVERT: A 250 PHE cc_start: 0.8231 (t80) cc_final: 0.7944 (t80) REVERT: A 270 GLN cc_start: 0.7757 (mm110) cc_final: 0.6513 (mm-40) REVERT: A 274 LEU cc_start: 0.9076 (tp) cc_final: 0.8712 (mt) REVERT: A 376 MET cc_start: 0.8716 (mtp) cc_final: 0.8193 (mpp) REVERT: A 384 PHE cc_start: 0.8730 (t80) cc_final: 0.8435 (t80) REVERT: A 442 MET cc_start: 0.8467 (ttm) cc_final: 0.8235 (tpp) REVERT: A 496 MET cc_start: 0.8311 (mtp) cc_final: 0.7552 (mtp) REVERT: A 524 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8283 (tp30) REVERT: A 533 VAL cc_start: 0.8113 (t) cc_final: 0.7863 (t) REVERT: A 540 GLU cc_start: 0.7534 (mt-10) cc_final: 0.6976 (pm20) REVERT: A 543 GLN cc_start: 0.8500 (tp40) cc_final: 0.8159 (pp30) REVERT: A 546 MET cc_start: 0.7446 (mtm) cc_final: 0.7102 (mtm) REVERT: A 577 MET cc_start: 0.8870 (ttm) cc_final: 0.8575 (tmm) REVERT: A 707 MET cc_start: 0.8710 (ttm) cc_final: 0.8237 (tmm) REVERT: A 712 HIS cc_start: 0.7119 (m-70) cc_final: 0.6776 (m-70) REVERT: A 735 TYR cc_start: 0.6832 (t80) cc_final: 0.6558 (t80) REVERT: A 739 MET cc_start: 0.8001 (mmm) cc_final: 0.7625 (mmm) REVERT: A 760 MET cc_start: 0.8566 (ptp) cc_final: 0.8258 (ptp) REVERT: A 763 LEU cc_start: 0.8844 (mt) cc_final: 0.8118 (tp) REVERT: A 775 GLU cc_start: 0.8273 (tt0) cc_final: 0.7084 (tm-30) REVERT: A 779 ASP cc_start: 0.8710 (m-30) cc_final: 0.7996 (m-30) REVERT: A 837 TRP cc_start: 0.8723 (t60) cc_final: 0.8423 (t60) REVERT: A 845 CYS cc_start: 0.9363 (m) cc_final: 0.8678 (p) REVERT: A 902 MET cc_start: 0.8417 (mtt) cc_final: 0.8040 (mtt) REVERT: A 924 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7591 (mm-30) REVERT: A 964 THR cc_start: 0.9172 (t) cc_final: 0.8835 (t) REVERT: A 965 ILE cc_start: 0.8952 (mm) cc_final: 0.8653 (mm) REVERT: A 968 MET cc_start: 0.8253 (mpp) cc_final: 0.8048 (mpp) REVERT: A 991 MET cc_start: 0.7528 (ppp) cc_final: 0.7003 (ppp) REVERT: A 998 TYR cc_start: 0.8586 (t80) cc_final: 0.8192 (t80) REVERT: A 1005 MET cc_start: 0.8054 (mtm) cc_final: 0.6848 (mpp) REVERT: A 1012 LYS cc_start: 0.8376 (mttt) cc_final: 0.7797 (mmtp) REVERT: A 1039 ASN cc_start: 0.9323 (m-40) cc_final: 0.8850 (m-40) REVERT: A 1066 ARG cc_start: 0.8399 (ttm-80) cc_final: 0.7979 (ptm160) REVERT: A 1070 GLN cc_start: 0.8247 (tt0) cc_final: 0.7932 (tt0) REVERT: A 1083 LEU cc_start: 0.8384 (tp) cc_final: 0.8128 (tp) REVERT: A 1099 LYS cc_start: 0.8656 (ptpt) cc_final: 0.8394 (pttt) REVERT: A 1136 ARG cc_start: 0.7213 (mmp80) cc_final: 0.6784 (mmp-170) REVERT: A 1162 MET cc_start: 0.8001 (pmm) cc_final: 0.7736 (pmm) REVERT: A 1880 PRO cc_start: 0.8498 (Cg_endo) cc_final: 0.8265 (Cg_exo) REVERT: A 1898 GLU cc_start: 0.8240 (mp0) cc_final: 0.8010 (mp0) REVERT: A 1904 GLU cc_start: 0.9297 (mp0) cc_final: 0.7042 (tt0) REVERT: A 1925 LEU cc_start: 0.8651 (mt) cc_final: 0.8416 (mt) REVERT: A 1937 ARG cc_start: 0.8475 (mtt-85) cc_final: 0.7816 (ttm-80) REVERT: A 1960 MET cc_start: 0.8817 (ttp) cc_final: 0.8506 (tmm) REVERT: A 1961 THR cc_start: 0.8164 (m) cc_final: 0.7737 (p) REVERT: A 1964 GLU cc_start: 0.8363 (tp30) cc_final: 0.8068 (tp30) REVERT: A 1967 MET cc_start: 0.7807 (mmm) cc_final: 0.7438 (mmt) REVERT: A 2008 GLU cc_start: 0.7193 (pp20) cc_final: 0.6922 (pt0) REVERT: B 1910 ILE cc_start: 0.8192 (mm) cc_final: 0.7749 (mm) REVERT: B 1925 LEU cc_start: 0.8735 (mt) cc_final: 0.8101 (pp) REVERT: B 1948 GLN cc_start: 0.8975 (mm-40) cc_final: 0.8565 (pp30) REVERT: B 1956 LYS cc_start: 0.8803 (mttt) cc_final: 0.8119 (tptm) REVERT: B 2063 TYR cc_start: 0.7096 (m-80) cc_final: 0.6895 (m-10) REVERT: B 2065 LEU cc_start: 0.8245 (tp) cc_final: 0.7324 (pp) REVERT: B 2083 PHE cc_start: 0.8049 (m-10) cc_final: 0.7523 (m-10) REVERT: B 2107 ASN cc_start: 0.8964 (m-40) cc_final: 0.8680 (t0) REVERT: B 2113 CYS cc_start: 0.9081 (t) cc_final: 0.8794 (t) REVERT: B 2120 PHE cc_start: 0.8048 (m-80) cc_final: 0.7773 (m-80) REVERT: B 2140 PHE cc_start: 0.8469 (m-80) cc_final: 0.7884 (m-80) REVERT: B 2209 THR cc_start: 0.8659 (m) cc_final: 0.8404 (m) REVERT: B 2210 GLU cc_start: 0.8457 (tt0) cc_final: 0.7770 (tp30) REVERT: B 2291 HIS cc_start: 0.8490 (m-70) cc_final: 0.8211 (m170) REVERT: B 2303 GLN cc_start: 0.8092 (tt0) cc_final: 0.7490 (tm-30) REVERT: B 2304 LEU cc_start: 0.8762 (mt) cc_final: 0.8478 (mt) REVERT: B 2333 LYS cc_start: 0.7028 (mttt) cc_final: 0.6239 (mptt) REVERT: B 2340 MET cc_start: 0.7007 (mmm) cc_final: 0.6353 (mmm) REVERT: B 2359 LEU cc_start: 0.9104 (mt) cc_final: 0.8767 (mt) REVERT: B 2377 TYR cc_start: 0.7878 (m-80) cc_final: 0.7433 (m-80) REVERT: B 2417 TYR cc_start: 0.8935 (m-80) cc_final: 0.8671 (m-10) REVERT: B 2418 LEU cc_start: 0.9008 (mt) cc_final: 0.8805 (mt) REVERT: B 2423 THR cc_start: 0.8088 (p) cc_final: 0.7511 (p) REVERT: B 2616 ARG cc_start: 0.6387 (ttt180) cc_final: 0.5514 (tmt170) REVERT: B 2618 LEU cc_start: 0.8544 (mm) cc_final: 0.8242 (mm) REVERT: B 2685 PHE cc_start: 0.8669 (p90) cc_final: 0.8004 (p90) outliers start: 1 outliers final: 0 residues processed: 430 average time/residue: 0.2919 time to fit residues: 193.7285 Evaluate side-chains 376 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 1.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.8980 chunk 154 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 151 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 117 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.123722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.102094 restraints weight = 34225.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.105827 restraints weight = 22451.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.108681 restraints weight = 15931.279| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.6722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14120 Z= 0.142 Angle : 0.650 12.648 19094 Z= 0.330 Chirality : 0.040 0.215 2298 Planarity : 0.004 0.045 2351 Dihedral : 4.460 18.749 1819 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.32 (0.20), residues: 1683 helix: 1.84 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : 0.17 (0.40), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B2296 HIS 0.011 0.001 HIS A1922 PHE 0.038 0.002 PHE A1107 TYR 0.029 0.002 TYR A 408 ARG 0.004 0.000 ARG A1038 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 1042) hydrogen bonds : angle 4.30424 ( 3105) covalent geometry : bond 0.00318 (14120) covalent geometry : angle 0.64951 (19094) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3366 Ramachandran restraints generated. 1683 Oldfield, 0 Emsley, 1683 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.816 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 8 GLU cc_start: 0.5477 (mp0) cc_final: 0.4301 (tp30) REVERT: A 149 ASN cc_start: 0.8321 (t0) cc_final: 0.7988 (t0) REVERT: A 222 ASN cc_start: 0.8320 (m110) cc_final: 0.8118 (m-40) REVERT: A 250 PHE cc_start: 0.8178 (t80) cc_final: 0.7922 (t80) REVERT: A 270 GLN cc_start: 0.7794 (mm110) cc_final: 0.6569 (mm-40) REVERT: A 274 LEU cc_start: 0.9078 (tp) cc_final: 0.8795 (mt) REVERT: A 376 MET cc_start: 0.8663 (mtp) cc_final: 0.8149 (mpp) REVERT: A 384 PHE cc_start: 0.8691 (t80) cc_final: 0.8397 (t80) REVERT: A 524 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8101 (tp30) REVERT: A 533 VAL cc_start: 0.8278 (t) cc_final: 0.8027 (t) REVERT: A 540 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7198 (pm20) REVERT: A 543 GLN cc_start: 0.8354 (tp40) cc_final: 0.8017 (tm-30) REVERT: A 577 MET cc_start: 0.8867 (ttm) cc_final: 0.8651 (tmm) REVERT: A 604 LEU cc_start: 0.9108 (mt) cc_final: 0.8883 (mt) REVERT: A 608 ASN cc_start: 0.8344 (m-40) cc_final: 0.7947 (m-40) REVERT: A 707 MET cc_start: 0.8732 (ttm) cc_final: 0.8355 (ttp) REVERT: A 775 GLU cc_start: 0.8278 (tt0) cc_final: 0.7056 (tm-30) REVERT: A 778 GLU cc_start: 0.8105 (mp0) cc_final: 0.7902 (mp0) REVERT: A 779 ASP cc_start: 0.8735 (m-30) cc_final: 0.8003 (m-30) REVERT: A 845 CYS cc_start: 0.9352 (m) cc_final: 0.8609 (p) REVERT: A 902 MET cc_start: 0.8356 (mtt) cc_final: 0.8007 (mtt) REVERT: A 924 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7432 (mm-30) REVERT: A 964 THR cc_start: 0.9195 (t) cc_final: 0.8846 (t) REVERT: A 965 ILE cc_start: 0.8969 (mm) cc_final: 0.8607 (mm) REVERT: A 991 MET cc_start: 0.7428 (ppp) cc_final: 0.6886 (ppp) REVERT: A 998 TYR cc_start: 0.8574 (t80) cc_final: 0.8190 (t80) REVERT: A 1005 MET cc_start: 0.8247 (mtm) cc_final: 0.6898 (mpp) REVERT: A 1012 LYS cc_start: 0.8433 (mttt) cc_final: 0.7888 (mmtp) REVERT: A 1039 ASN cc_start: 0.9333 (m-40) cc_final: 0.8807 (m-40) REVERT: A 1066 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7962 (ptm160) REVERT: A 1070 GLN cc_start: 0.8287 (tt0) cc_final: 0.7939 (tt0) REVERT: A 1099 LYS cc_start: 0.8632 (ptpt) cc_final: 0.8333 (pttt) REVERT: A 1149 MET cc_start: 0.8908 (ptt) cc_final: 0.8062 (ttt) REVERT: A 1162 MET cc_start: 0.8012 (pmm) cc_final: 0.7732 (pmm) REVERT: A 1848 LEU cc_start: 0.8508 (tp) cc_final: 0.8257 (tt) REVERT: A 1880 PRO cc_start: 0.8552 (Cg_endo) cc_final: 0.8207 (Cg_exo) REVERT: A 1937 ARG cc_start: 0.8474 (mtt-85) cc_final: 0.7813 (ttm-80) REVERT: A 1961 THR cc_start: 0.8199 (m) cc_final: 0.7334 (m) REVERT: A 1964 GLU cc_start: 0.8244 (tp30) cc_final: 0.8038 (tp30) REVERT: A 1967 MET cc_start: 0.7804 (mmm) cc_final: 0.7459 (mmt) REVERT: B 1885 LEU cc_start: 0.8975 (tp) cc_final: 0.8496 (pp) REVERT: B 1910 ILE cc_start: 0.8237 (mm) cc_final: 0.7641 (mm) REVERT: B 1919 GLU cc_start: 0.7980 (mp0) cc_final: 0.7262 (mp0) REVERT: B 1925 LEU cc_start: 0.8785 (mt) cc_final: 0.8113 (pp) REVERT: B 1948 GLN cc_start: 0.8969 (mm-40) cc_final: 0.8553 (pp30) REVERT: B 1956 LYS cc_start: 0.8832 (mttt) cc_final: 0.8068 (tptm) REVERT: B 2063 TYR cc_start: 0.6840 (m-80) cc_final: 0.6625 (m-10) REVERT: B 2065 LEU cc_start: 0.8197 (tp) cc_final: 0.7853 (tt) REVERT: B 2083 PHE cc_start: 0.8241 (m-10) cc_final: 0.7701 (m-10) REVERT: B 2107 ASN cc_start: 0.8930 (m-40) cc_final: 0.8653 (t0) REVERT: B 2113 CYS cc_start: 0.9088 (t) cc_final: 0.8797 (t) REVERT: B 2120 PHE cc_start: 0.7947 (m-80) cc_final: 0.7588 (m-80) REVERT: B 2140 PHE cc_start: 0.8484 (m-80) cc_final: 0.8008 (m-80) REVERT: B 2209 THR cc_start: 0.9004 (m) cc_final: 0.8651 (m) REVERT: B 2210 GLU cc_start: 0.8310 (tt0) cc_final: 0.7876 (tp30) REVERT: B 2303 GLN cc_start: 0.8113 (tt0) cc_final: 0.7592 (tm-30) REVERT: B 2304 LEU cc_start: 0.8682 (mt) cc_final: 0.8433 (mt) REVERT: B 2333 LYS cc_start: 0.7051 (mttt) cc_final: 0.6261 (mptt) REVERT: B 2340 MET cc_start: 0.6932 (mmm) cc_final: 0.6229 (mmm) REVERT: B 2359 LEU cc_start: 0.9146 (mt) cc_final: 0.8829 (mt) REVERT: B 2427 GLU cc_start: 0.8012 (tt0) cc_final: 0.7727 (tt0) REVERT: B 2616 ARG cc_start: 0.6421 (ttt180) cc_final: 0.5558 (tmt170) REVERT: B 2618 LEU cc_start: 0.8493 (mm) cc_final: 0.8201 (mm) REVERT: B 2629 PHE cc_start: 0.8075 (m-80) cc_final: 0.7304 (m-80) REVERT: B 2685 PHE cc_start: 0.8711 (p90) cc_final: 0.8103 (p90) outliers start: 0 outliers final: 0 residues processed: 420 average time/residue: 0.2579 time to fit residues: 168.2267 Evaluate side-chains 372 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 372 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 9 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 151 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 125 optimal weight: 8.9990 chunk 172 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2051 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B2670 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.122940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101255 restraints weight = 34137.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.105078 restraints weight = 22213.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.107855 restraints weight = 15657.411| |-----------------------------------------------------------------------------| r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.6839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14120 Z= 0.144 Angle : 0.662 13.445 19094 Z= 0.336 Chirality : 0.040 0.254 2298 Planarity : 0.004 0.044 2351 Dihedral : 4.456 19.570 1819 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 15.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.20), residues: 1683 helix: 1.81 (0.14), residues: 1396 sheet: None (None), residues: 0 loop : 0.03 (0.40), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 571 HIS 0.010 0.001 HIS A1922 PHE 0.023 0.002 PHE B2356 TYR 0.036 0.002 TYR A1927 ARG 0.004 0.000 ARG A1000 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 1042) hydrogen bonds : angle 4.36208 ( 3105) covalent geometry : bond 0.00326 (14120) covalent geometry : angle 0.66189 (19094) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5371.59 seconds wall clock time: 97 minutes 12.80 seconds (5832.80 seconds total)