Starting phenix.real_space_refine on Wed Mar 4 13:25:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7moc_23924/03_2026/7moc_23924.cif Found real_map, /net/cci-nas-00/data/ceres_data/7moc_23924/03_2026/7moc_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_23924/03_2026/7moc_23924.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7moc_23924/03_2026/7moc_23924.map" model { file = "/net/cci-nas-00/data/ceres_data/7moc_23924/03_2026/7moc_23924.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7moc_23924/03_2026/7moc_23924.cif" } resolution = 4.56 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 2.96, per 1000 atoms: 0.21 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: 0.87 Conformation dependent library (CDL) restraints added in 467.9 milliseconds 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: 0.42 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: 2.39 Time building geometry restraints manager: 1.20 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.940 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.680 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -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 ARG 0.011 0.001 ARG A 385 TYR 0.244 0.030 TYR A1853 PHE 0.137 0.016 PHE B2693 TRP 0.121 0.025 TRP B1931 HIS 0.013 0.003 HIS B2379 Details of bonding type rmsd covalent geometry : bond 0.01178 (14120) covalent geometry : angle 1.82141 (19094) hydrogen bonds : bond 0.15396 ( 1042) hydrogen bonds : angle 6.99371 ( 3105) *********************** 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 : 0.528 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: 0.8233 (mp) REVERT: A 190 LEU cc_start: 0.8577 (tp) cc_final: 0.8303 (tp) REVERT: A 194 LEU cc_start: 0.9220 (mt) cc_final: 0.8808 (mt) REVERT: A 217 GLU cc_start: 0.8709 (tt0) cc_final: 0.8203 (tm-30) REVERT: A 231 PHE cc_start: 0.8288 (t80) cc_final: 0.8020 (t80) REVERT: A 250 PHE cc_start: 0.8058 (t80) cc_final: 0.7297 (t80) REVERT: A 303 LEU cc_start: 0.7824 (mt) cc_final: 0.7196 (mt) REVERT: A 305 LYS cc_start: 0.8971 (mttt) cc_final: 0.8604 (pttp) REVERT: A 327 LEU cc_start: 0.9241 (tp) cc_final: 0.9038 (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: 0.8591 (mpp) REVERT: A 379 CYS cc_start: 0.8797 (t) cc_final: 0.8154 (t) REVERT: A 383 CYS cc_start: 0.8352 (m) cc_final: 0.8134 (m) REVERT: A 446 THR cc_start: 0.8837 (m) cc_final: 0.8557 (p) REVERT: A 493 LEU cc_start: 0.8993 (tp) cc_final: 0.8772 (tt) REVERT: A 496 MET cc_start: 0.8263 (mtp) cc_final: 0.7842 (mtp) REVERT: A 524 GLU cc_start: 0.8568 (mt-10) cc_final: 0.7906 (tp30) REVERT: A 540 GLU cc_start: 0.7434 (mt-10) cc_final: 0.7160 (pm20) REVERT: A 543 GLN cc_start: 0.8225 (tp40) cc_final: 0.8006 (tm-30) REVERT: A 546 MET cc_start: 0.8320 (mtm) cc_final: 0.7875 (mtm) REVERT: A 552 LEU cc_start: 0.8923 (mt) cc_final: 0.8546 (mt) REVERT: A 561 TRP cc_start: 0.6680 (m-10) cc_final: 0.6290 (m100) REVERT: A 573 ILE cc_start: 0.8819 (mt) cc_final: 0.7947 (mt) REVERT: A 577 MET cc_start: 0.8233 (ttp) cc_final: 0.7669 (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: 0.8624 (mt) REVERT: A 691 LEU cc_start: 0.8458 (mt) cc_final: 0.8123 (mt) REVERT: A 700 THR cc_start: 0.9158 (m) cc_final: 0.8766 (p) REVERT: A 707 MET cc_start: 0.7709 (mtt) cc_final: 0.7338 (mtt) REVERT: A 711 ARG cc_start: 0.7931 (ttm110) cc_final: 0.6842 (tpt-90) REVERT: A 739 MET cc_start: 0.8068 (mmm) cc_final: 0.7499 (mmm) REVERT: A 773 ASN cc_start: 0.8184 (p0) cc_final: 0.7945 (p0) REVERT: A 775 GLU cc_start: 0.8502 (tt0) cc_final: 0.7295 (tm-30) REVERT: A 779 ASP cc_start: 0.8585 (m-30) cc_final: 0.7664 (m-30) REVERT: A 837 TRP cc_start: 0.8913 (t60) cc_final: 0.8628 (t60) REVERT: A 840 MET cc_start: 0.8654 (mtm) cc_final: 0.8212 (mtp) REVERT: A 932 MET cc_start: 0.7350 (ttm) cc_final: 0.6324 (mmp) REVERT: A 933 LEU cc_start: 0.8120 (tp) cc_final: 0.7707 (tt) REVERT: A 941 ILE cc_start: 0.9186 (mt) cc_final: 0.8980 (mm) REVERT: A 983 LEU cc_start: 0.8543 (mt) cc_final: 0.8250 (mt) REVERT: A 1002 LEU cc_start: 0.7894 (mt) cc_final: 0.7458 (mt) REVERT: A 1005 MET cc_start: 0.7046 (mtm) cc_final: 0.6298 (mpp) REVERT: A 1010 GLN cc_start: 0.8437 (mt0) cc_final: 0.7931 (mm110) REVERT: A 1039 ASN cc_start: 0.8851 (m-40) cc_final: 0.8461 (m-40) REVERT: A 1042 VAL cc_start: 0.8506 (t) cc_final: 0.7980 (t) REVERT: A 1077 VAL cc_start: 0.8780 (t) cc_final: 0.8555 (t) REVERT: A 1106 TYR cc_start: 0.8345 (m-80) cc_final: 0.7334 (m-80) REVERT: A 1149 MET cc_start: 0.8348 (mtt) cc_final: 0.8124 (mtm) REVERT: A 1158 ASP cc_start: 0.7644 (m-30) cc_final: 0.7288 (t70) REVERT: A 1162 MET cc_start: 0.8522 (pmm) cc_final: 0.8222 (pmm) REVERT: A 1169 TYR cc_start: 0.6732 (m-80) cc_final: 0.6421 (m-10) REVERT: A 1848 LEU cc_start: 0.8873 (tp) cc_final: 0.8525 (tt) REVERT: A 1866 LYS cc_start: 0.7251 (mttt) cc_final: 0.6977 (mmmt) REVERT: A 1870 GLN cc_start: 0.7034 (mm-40) cc_final: 0.6796 (pm20) REVERT: A 1872 LEU cc_start: 0.8734 (tp) cc_final: 0.8382 (tp) REVERT: A 1884 THR cc_start: 0.9377 (m) cc_final: 0.9118 (t) REVERT: A 1906 LEU cc_start: 0.9031 (mt) cc_final: 0.8766 (mt) REVERT: A 1923 LEU cc_start: 0.9521 (tp) cc_final: 0.9309 (tp) REVERT: A 1925 LEU cc_start: 0.8980 (mt) cc_final: 0.8434 (mt) REVERT: A 1937 ARG cc_start: 0.8843 (mtt-85) cc_final: 0.8309 (ttm-80) REVERT: A 1960 MET cc_start: 0.8457 (ttp) cc_final: 0.8156 (tmm) REVERT: A 1963 ASN cc_start: 0.7647 (m-40) cc_final: 0.7280 (t0) REVERT: A 2005 ILE cc_start: 0.7438 (mt) cc_final: 0.6991 (mt) REVERT: B 1836 ILE cc_start: 0.8611 (mt) cc_final: 0.8218 (tt) REVERT: B 1918 ILE cc_start: 0.7949 (mt) cc_final: 0.7584 (pt) REVERT: B 1928 MET cc_start: 0.8199 (mtp) cc_final: 0.7715 (mtt) REVERT: B 1954 LEU cc_start: 0.9302 (mt) cc_final: 0.9072 (mt) REVERT: B 1956 LYS cc_start: 0.9090 (mttt) cc_final: 0.8432 (mmmt) REVERT: B 1986 LEU cc_start: 0.8897 (mt) cc_final: 0.8633 (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: 0.8740 (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: 0.8756 (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: 0.8345 (mt) REVERT: B 2199 ILE cc_start: 0.8259 (mt) cc_final: 0.7967 (tt) REVERT: B 2223 LEU cc_start: 0.9140 (mt) cc_final: 0.8898 (mt) REVERT: B 2246 ILE cc_start: 0.8921 (mt) cc_final: 0.8635 (tp) REVERT: B 2305 ASP cc_start: 0.6959 (t0) cc_final: 0.6241 (t70) REVERT: B 2310 TYR cc_start: 0.8646 (t80) cc_final: 0.8206 (t80) REVERT: B 2314 THR cc_start: 0.9453 (p) cc_final: 0.8186 (t) REVERT: B 2330 PHE cc_start: 0.7710 (m-80) cc_final: 0.7420 (m-10) REVERT: B 2333 LYS cc_start: 0.7232 (mttt) cc_final: 0.6719 (mptt) REVERT: B 2373 LEU cc_start: 0.8685 (mt) cc_final: 0.8272 (mt) REVERT: B 2401 LYS cc_start: 0.7811 (tttt) cc_final: 0.7395 (mmmt) REVERT: B 2418 LEU cc_start: 0.9257 (mt) cc_final: 0.8995 (mt) REVERT: B 2425 SER cc_start: 0.7427 (t) cc_final: 0.7150 (m) REVERT: B 2600 THR cc_start: 0.9394 (m) cc_final: 0.9189 (p) REVERT: B 2614 ASP cc_start: 0.8757 (m-30) cc_final: 0.8516 (m-30) REVERT: B 2616 ARG cc_start: 0.6660 (ttt180) cc_final: 0.6399 (tmt170) REVERT: B 2685 PHE cc_start: 0.8709 (p90) cc_final: 0.8430 (p90) REVERT: B 2722 LEU cc_start: 0.8197 (mt) cc_final: 0.7897 (mt) outliers start: 3 outliers final: 0 residues processed: 713 average time/residue: 0.1087 time to fit residues: 115.0009 Evaluate side-chains 464 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 464 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** B2670 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.116237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.095559 restraints weight = 34893.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.099319 restraints weight = 21712.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.102022 restraints weight = 14872.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103932 restraints weight = 10888.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.105347 restraints weight = 8481.513| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14120 Z= 0.182 Angle : 0.670 8.080 19094 Z= 0.356 Chirality : 0.041 0.201 2298 Planarity : 0.005 0.044 2351 Dihedral : 5.168 30.563 1819 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 0.45 % Allowed : 2.67 % Favored : 96.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.20), residues: 1683 helix: 1.57 (0.13), residues: 1403 sheet: None (None), residues: 0 loop : 0.20 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1137 TYR 0.029 0.002 TYR A1927 PHE 0.032 0.002 PHE B2365 TRP 0.031 0.002 TRP A 9 HIS 0.007 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00387 (14120) covalent geometry : angle 0.66985 (19094) hydrogen bonds : bond 0.05013 ( 1042) hydrogen bonds : angle 4.61858 ( 3105) *********************** 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 549 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 542 time to evaluate : 0.513 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: 0.5893 (mp0) cc_final: 0.5591 (mp0) REVERT: A 39 ASN cc_start: 0.8946 (m-40) cc_final: 0.8588 (t0) REVERT: A 80 TYR cc_start: 0.6855 (m-80) cc_final: 0.6541 (m-80) REVERT: A 217 GLU cc_start: 0.8832 (tt0) cc_final: 0.8560 (tm-30) REVERT: A 250 PHE cc_start: 0.8400 (t80) cc_final: 0.7746 (t80) REVERT: A 274 LEU cc_start: 0.9242 (tp) cc_final: 0.9034 (mt) REVERT: A 303 LEU cc_start: 0.7615 (mt) cc_final: 0.7299 (mt) REVERT: A 344 LEU cc_start: 0.8336 (mt) cc_final: 0.8003 (tp) REVERT: A 383 CYS cc_start: 0.8566 (m) cc_final: 0.8338 (m) REVERT: A 446 THR cc_start: 0.8952 (m) cc_final: 0.8391 (p) REVERT: A 496 MET cc_start: 0.7887 (mtp) cc_final: 0.7480 (mtp) REVERT: A 524 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8490 (pt0) REVERT: A 540 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7588 (pm20) REVERT: A 543 GLN cc_start: 0.8347 (tp40) cc_final: 0.7905 (tm-30) REVERT: A 546 MET cc_start: 0.7726 (mtm) cc_final: 0.7360 (mtm) REVERT: A 552 LEU cc_start: 0.8594 (mt) cc_final: 0.8275 (mt) REVERT: A 573 ILE cc_start: 0.8940 (mt) cc_final: 0.8324 (mt) REVERT: A 707 MET cc_start: 0.8050 (mtt) cc_final: 0.7606 (mtt) REVERT: A 760 MET cc_start: 0.8677 (mtp) cc_final: 0.8460 (mtm) REVERT: A 775 GLU cc_start: 0.8273 (tt0) cc_final: 0.7102 (tm-30) REVERT: A 779 ASP cc_start: 0.8565 (m-30) cc_final: 0.7740 (m-30) REVERT: A 833 SER cc_start: 0.6368 (m) cc_final: 0.5887 (t) REVERT: A 836 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8403 (mt-10) REVERT: A 840 MET cc_start: 0.8297 (mtm) cc_final: 0.7967 (mtp) REVERT: A 902 MET cc_start: 0.8460 (mtt) cc_final: 0.8055 (mtt) REVERT: A 924 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7291 (mm-30) REVERT: A 992 MET cc_start: 0.8704 (mmm) cc_final: 0.8381 (mmm) REVERT: A 998 TYR cc_start: 0.8562 (t80) cc_final: 0.8254 (t80) REVERT: A 1005 MET cc_start: 0.7956 (mtm) cc_final: 0.6861 (mpp) REVERT: A 1036 LYS cc_start: 0.9077 (tttt) cc_final: 0.8848 (tptp) REVERT: A 1039 ASN cc_start: 0.9187 (m-40) cc_final: 0.8571 (m-40) REVERT: A 1042 VAL cc_start: 0.8531 (t) cc_final: 0.8243 (t) REVERT: A 1066 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.7881 (ttp-170) REVERT: A 1083 LEU cc_start: 0.8715 (tp) cc_final: 0.8457 (tp) REVERT: A 1096 MET cc_start: 0.8802 (tpp) cc_final: 0.8555 (tpp) REVERT: A 1099 LYS cc_start: 0.8833 (ptpt) cc_final: 0.8618 (pttt) REVERT: A 1106 TYR cc_start: 0.7910 (m-80) cc_final: 0.7622 (m-80) REVERT: A 1149 MET cc_start: 0.8301 (mtt) cc_final: 0.7939 (tpp) REVERT: A 1167 LEU cc_start: 0.9271 (mt) cc_final: 0.8852 (mt) REVERT: A 1841 LEU cc_start: 0.8889 (mt) cc_final: 0.8597 (mt) REVERT: A 1870 GLN cc_start: 0.7297 (mm-40) cc_final: 0.7015 (tp40) REVERT: A 1871 LEU cc_start: 0.7783 (mt) cc_final: 0.7461 (pt) REVERT: A 1904 GLU cc_start: 0.9326 (mp0) cc_final: 0.6665 (tt0) REVERT: A 1906 LEU cc_start: 0.9109 (mt) cc_final: 0.8514 (mt) REVERT: A 1925 LEU cc_start: 0.8782 (mt) cc_final: 0.8500 (mt) REVERT: A 1926 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7084 (mm-30) REVERT: A 1937 ARG cc_start: 0.8846 (mtt-85) cc_final: 0.8342 (ttp-110) REVERT: A 1960 MET cc_start: 0.9039 (ttp) cc_final: 0.8453 (tmm) REVERT: B 1832 THR cc_start: 0.9146 (p) cc_final: 0.8927 (p) REVERT: B 1910 ILE cc_start: 0.8326 (mm) cc_final: 0.8024 (mm) REVERT: B 1918 ILE cc_start: 0.7858 (mt) cc_final: 0.7386 (pt) REVERT: B 1922 HIS cc_start: 0.7585 (m-70) cc_final: 0.7318 (m90) REVERT: B 1947 ARG cc_start: 0.9139 (ptm-80) cc_final: 0.8476 (ptp-110) REVERT: B 1956 LYS cc_start: 0.9183 (mttt) cc_final: 0.8383 (mmmt) REVERT: B 1987 ASP cc_start: 0.8201 (m-30) cc_final: 0.7960 (p0) REVERT: B 2010 MET cc_start: 0.8751 (mmm) cc_final: 0.8132 (mmm) REVERT: B 2028 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8412 (tptt) REVERT: B 2151 SER cc_start: 0.8419 (t) cc_final: 0.8180 (p) REVERT: B 2203 LYS cc_start: 0.8474 (mmpt) cc_final: 0.8222 (mmmt) REVERT: B 2204 TRP cc_start: 0.8337 (m-10) cc_final: 0.7895 (m-10) REVERT: B 2209 THR cc_start: 0.8570 (m) cc_final: 0.8271 (m) REVERT: B 2291 HIS cc_start: 0.8563 (m-70) cc_final: 0.8180 (m170) REVERT: B 2306 GLU cc_start: 0.5443 (mp0) cc_final: 0.5208 (mp0) REVERT: B 2314 THR cc_start: 0.9359 (p) cc_final: 0.9140 (p) REVERT: B 2320 ASN cc_start: 0.8399 (t0) cc_final: 0.7971 (t0) REVERT: B 2324 LEU cc_start: 0.8725 (mm) cc_final: 0.8425 (mm) REVERT: B 2333 LYS cc_start: 0.6855 (mttt) cc_final: 0.6492 (mptt) REVERT: B 2356 PHE cc_start: 0.6646 (t80) cc_final: 0.6439 (t80) REVERT: B 2359 LEU cc_start: 0.8920 (mt) cc_final: 0.8637 (mt) REVERT: B 2373 LEU cc_start: 0.8952 (mt) cc_final: 0.8640 (mt) REVERT: B 2375 LYS cc_start: 0.8430 (tttp) cc_final: 0.8142 (tttp) REVERT: B 2401 LYS cc_start: 0.8081 (tttt) cc_final: 0.7586 (mmmt) REVERT: B 2417 TYR cc_start: 0.8878 (m-80) cc_final: 0.8276 (m-10) REVERT: B 2427 GLU cc_start: 0.8507 (tp30) cc_final: 0.8079 (tp30) REVERT: B 2600 THR cc_start: 0.9476 (m) cc_final: 0.9235 (p) REVERT: B 2611 ASP cc_start: 0.7443 (m-30) cc_final: 0.6477 (t70) REVERT: B 2616 ARG cc_start: 0.7007 (ttt180) cc_final: 0.6197 (tmt170) REVERT: B 2632 VAL cc_start: 0.8683 (t) cc_final: 0.8421 (t) REVERT: B 2640 LEU cc_start: 0.7710 (mt) cc_final: 0.7481 (mt) REVERT: B 2669 TYR cc_start: 0.8615 (t80) cc_final: 0.8244 (t80) REVERT: B 2685 PHE cc_start: 0.8605 (p90) cc_final: 0.8084 (p90) REVERT: B 2693 PHE cc_start: 0.8445 (t80) cc_final: 0.8242 (t80) REVERT: B 2722 LEU cc_start: 0.8311 (mt) cc_final: 0.8019 (mt) outliers start: 7 outliers final: 0 residues processed: 543 average time/residue: 0.0982 time to fit residues: 82.1303 Evaluate side-chains 405 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 45 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 ASN ** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 734 ASN A1170 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1922 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 GLN B2303 GLN B2615 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.117006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.095789 restraints weight = 34612.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100986 restraints weight = 23077.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.103742 restraints weight = 13644.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.105913 restraints weight = 9581.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.106294 restraints weight = 7915.101| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14120 Z= 0.153 Angle : 0.619 8.881 19094 Z= 0.327 Chirality : 0.040 0.220 2298 Planarity : 0.004 0.044 2351 Dihedral : 4.806 29.206 1819 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.32 % Allowed : 2.86 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.20), residues: 1683 helix: 1.80 (0.13), residues: 1403 sheet: None (None), residues: 0 loop : 0.18 (0.39), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 440 TYR 0.026 0.002 TYR A1927 PHE 0.026 0.002 PHE B1993 TRP 0.019 0.002 TRP A 9 HIS 0.013 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00329 (14120) covalent geometry : angle 0.61862 (19094) hydrogen bonds : bond 0.04524 ( 1042) hydrogen bonds : angle 4.38401 ( 3105) *********************** 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 496 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 491 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7825 (ttpt) REVERT: A 217 GLU cc_start: 0.8801 (tt0) cc_final: 0.8578 (tm-30) REVERT: A 231 PHE cc_start: 0.8256 (t80) cc_final: 0.7748 (t80) REVERT: A 303 LEU cc_start: 0.7655 (mt) cc_final: 0.7447 (mt) REVERT: A 344 LEU cc_start: 0.8386 (mt) cc_final: 0.8078 (tp) REVERT: A 383 CYS cc_start: 0.8476 (m) cc_final: 0.8202 (m) REVERT: A 524 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8518 (pt0) REVERT: A 540 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7319 (pm20) REVERT: A 543 GLN cc_start: 0.8394 (tp40) cc_final: 0.7940 (tm-30) REVERT: A 546 MET cc_start: 0.7714 (mtm) cc_final: 0.7275 (mtm) REVERT: A 604 LEU cc_start: 0.9018 (mt) cc_final: 0.8800 (mt) REVERT: A 687 LEU cc_start: 0.8952 (tp) cc_final: 0.8730 (tp) REVERT: A 691 LEU cc_start: 0.8444 (mt) cc_final: 0.8129 (mt) REVERT: A 711 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7661 (ttm170) REVERT: A 760 MET cc_start: 0.8487 (mtp) cc_final: 0.8140 (ptp) REVERT: A 775 GLU cc_start: 0.8328 (tt0) cc_final: 0.7354 (tm-30) REVERT: A 779 ASP cc_start: 0.8609 (m-30) cc_final: 0.8125 (m-30) REVERT: A 833 SER cc_start: 0.5730 (m) cc_final: 0.5173 (t) REVERT: A 836 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8449 (mt-10) REVERT: A 845 CYS cc_start: 0.9382 (m) cc_final: 0.8558 (p) REVERT: A 902 MET cc_start: 0.8410 (mtt) cc_final: 0.7999 (mtt) REVERT: A 924 GLU cc_start: 0.7758 (mm-30) cc_final: 0.6721 (mm-30) REVERT: A 964 THR cc_start: 0.9323 (t) cc_final: 0.8867 (t) REVERT: A 965 ILE cc_start: 0.8840 (mm) cc_final: 0.8471 (mm) REVERT: A 992 MET cc_start: 0.8917 (mmm) cc_final: 0.8608 (mmm) REVERT: A 998 TYR cc_start: 0.8721 (t80) cc_final: 0.8321 (t80) REVERT: A 1005 MET cc_start: 0.7968 (mtm) cc_final: 0.6666 (mpp) REVERT: A 1022 MET cc_start: 0.8658 (ptp) cc_final: 0.8379 (ptp) REVERT: A 1023 MET cc_start: 0.8286 (tpp) cc_final: 0.7678 (tpp) REVERT: A 1036 LYS cc_start: 0.9186 (tttt) cc_final: 0.8813 (ttpp) REVERT: A 1039 ASN cc_start: 0.9167 (m-40) cc_final: 0.8643 (m-40) REVERT: A 1042 VAL cc_start: 0.8553 (t) cc_final: 0.8232 (t) REVERT: A 1066 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7930 (ptm160) REVERT: A 1070 GLN cc_start: 0.8293 (tt0) cc_final: 0.7939 (tt0) REVERT: A 1096 MET cc_start: 0.8789 (tpp) cc_final: 0.8511 (tpp) REVERT: A 1099 LYS cc_start: 0.8793 (ptpt) cc_final: 0.8531 (pttt) REVERT: A 1105 LYS cc_start: 0.9169 (mppt) cc_final: 0.8923 (ptmt) REVERT: A 1170 HIS cc_start: 0.8146 (t-90) cc_final: 0.7914 (t70) REVERT: A 1848 LEU cc_start: 0.8799 (tp) cc_final: 0.8585 (tp) REVERT: A 1877 LEU cc_start: 0.9211 (mm) cc_final: 0.8896 (mm) REVERT: A 1878 CYS cc_start: 0.8649 (m) cc_final: 0.8379 (m) REVERT: A 1898 GLU cc_start: 0.8353 (mp0) cc_final: 0.7780 (mt-10) REVERT: A 1901 LEU cc_start: 0.9287 (mt) cc_final: 0.9040 (mt) REVERT: A 1902 THR cc_start: 0.8579 (m) cc_final: 0.8294 (p) REVERT: A 1904 GLU cc_start: 0.9384 (mp0) cc_final: 0.6756 (tt0) REVERT: A 1922 HIS cc_start: 0.7850 (t70) cc_final: 0.6862 (t70) REVERT: A 1926 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 1937 ARG cc_start: 0.8834 (mtt-85) cc_final: 0.8302 (ttp-110) REVERT: A 1960 MET cc_start: 0.8922 (ttp) cc_final: 0.8519 (tmm) REVERT: A 1964 GLU cc_start: 0.8293 (tp30) cc_final: 0.7799 (tp30) REVERT: A 1967 MET cc_start: 0.7994 (mmm) cc_final: 0.7497 (mmt) REVERT: B 1928 MET cc_start: 0.7764 (mmt) cc_final: 0.7508 (mmm) REVERT: B 1956 LYS cc_start: 0.8884 (mttt) cc_final: 0.8307 (mmmt) REVERT: B 1987 ASP cc_start: 0.8103 (m-30) cc_final: 0.7411 (t0) REVERT: B 1992 SER cc_start: 0.8975 (m) cc_final: 0.8680 (p) REVERT: B 2028 LYS cc_start: 0.8775 (mmtt) cc_final: 0.7936 (mmtt) REVERT: B 2107 ASN cc_start: 0.9036 (m-40) cc_final: 0.8770 (t0) REVERT: B 2120 PHE cc_start: 0.8534 (m-80) cc_final: 0.8324 (m-80) REVERT: B 2209 THR cc_start: 0.8563 (m) cc_final: 0.8308 (m) REVERT: B 2291 HIS cc_start: 0.8428 (m-70) cc_final: 0.8096 (m170) REVERT: B 2336 GLU cc_start: 0.7458 (pt0) cc_final: 0.6883 (pt0) REVERT: B 2346 LEU cc_start: 0.8869 (mt) cc_final: 0.8666 (mm) REVERT: B 2356 PHE cc_start: 0.6587 (t80) cc_final: 0.6298 (t80) REVERT: B 2359 LEU cc_start: 0.8887 (mt) cc_final: 0.8625 (mt) REVERT: B 2373 LEU cc_start: 0.8908 (mt) cc_final: 0.8593 (mt) REVERT: B 2375 LYS cc_start: 0.8471 (tttp) cc_final: 0.7757 (tttp) REVERT: B 2401 LYS cc_start: 0.8299 (tttt) cc_final: 0.7742 (mmmt) REVERT: B 2417 TYR cc_start: 0.8949 (m-80) cc_final: 0.8374 (m-10) REVERT: B 2418 LEU cc_start: 0.9085 (mt) cc_final: 0.8883 (mt) REVERT: B 2600 THR cc_start: 0.9447 (m) cc_final: 0.9235 (p) REVERT: B 2611 ASP cc_start: 0.7262 (m-30) cc_final: 0.7062 (t70) REVERT: B 2616 ARG cc_start: 0.6652 (ttt180) cc_final: 0.5881 (tmt170) REVERT: B 2721 TYR cc_start: 0.6103 (m-80) cc_final: 0.5793 (m-80) REVERT: B 2722 LEU cc_start: 0.8295 (mt) cc_final: 0.8081 (mt) outliers start: 5 outliers final: 0 residues processed: 491 average time/residue: 0.0953 time to fit residues: 72.0608 Evaluate side-chains 405 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 3 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 87 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 33 optimal weight: 0.0030 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- 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 ** A1033 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 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 ** 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 = 0.3707 r_free = 0.3707 target = 0.118691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.098129 restraints weight = 34128.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.101858 restraints weight = 21765.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.104596 restraints weight = 15085.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.106481 restraints weight = 11086.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.108066 restraints weight = 8603.019| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5185 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= 0.160 Angle : 0.619 11.234 19094 Z= 0.320 Chirality : 0.039 0.187 2298 Planarity : 0.004 0.046 2351 Dihedral : 4.728 26.959 1819 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.19 % Allowed : 1.97 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.20), residues: 1683 helix: 1.77 (0.13), residues: 1396 sheet: None (None), residues: 0 loop : 0.13 (0.38), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1137 TYR 0.026 0.002 TYR B1968 PHE 0.025 0.002 PHE A 741 TRP 0.033 0.002 TRP A 221 HIS 0.011 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00350 (14120) covalent geometry : angle 0.61924 (19094) hydrogen bonds : bond 0.04312 ( 1042) hydrogen bonds : angle 4.34506 ( 3105) *********************** 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 471 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 468 time to evaluate : 0.524 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 91 GLU cc_start: 0.8974 (pp20) cc_final: 0.8572 (pp20) REVERT: A 116 GLU cc_start: 0.6587 (mm-30) cc_final: 0.6256 (mm-30) REVERT: A 149 ASN cc_start: 0.8437 (t0) cc_final: 0.8116 (t0) REVERT: A 217 GLU cc_start: 0.8846 (tt0) cc_final: 0.8541 (tm-30) REVERT: A 222 ASN cc_start: 0.8497 (m-40) cc_final: 0.8256 (m-40) REVERT: A 250 PHE cc_start: 0.8354 (t80) cc_final: 0.7948 (t80) REVERT: A 303 LEU cc_start: 0.7833 (mt) cc_final: 0.7526 (mt) REVERT: A 344 LEU cc_start: 0.8450 (mt) cc_final: 0.8147 (tp) REVERT: A 496 MET cc_start: 0.7984 (mtp) cc_final: 0.7400 (mtp) REVERT: A 524 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8610 (pt0) REVERT: A 540 GLU cc_start: 0.7494 (mt-10) cc_final: 0.6973 (pm20) REVERT: A 543 GLN cc_start: 0.8433 (tp40) cc_final: 0.8069 (pp30) REVERT: A 546 MET cc_start: 0.7489 (mtm) cc_final: 0.7077 (mtm) REVERT: A 691 LEU cc_start: 0.8558 (mt) cc_final: 0.8306 (mp) REVERT: A 695 LEU cc_start: 0.8239 (mt) cc_final: 0.7990 (mt) REVERT: A 707 MET cc_start: 0.8413 (ttm) cc_final: 0.7906 (tmm) REVERT: A 760 MET cc_start: 0.8431 (mtp) cc_final: 0.8224 (ptp) REVERT: A 775 GLU cc_start: 0.8349 (tt0) cc_final: 0.7197 (tm-30) REVERT: A 779 ASP cc_start: 0.8663 (m-30) cc_final: 0.8145 (m-30) REVERT: A 833 SER cc_start: 0.5741 (m) cc_final: 0.5093 (t) REVERT: A 836 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8507 (mt-10) REVERT: A 902 MET cc_start: 0.8428 (mtt) cc_final: 0.8069 (mtt) REVERT: A 924 GLU cc_start: 0.7792 (mm-30) cc_final: 0.6691 (mm-30) REVERT: A 964 THR cc_start: 0.9264 (t) cc_final: 0.8888 (t) REVERT: A 965 ILE cc_start: 0.8914 (mm) cc_final: 0.8563 (mm) REVERT: A 992 MET cc_start: 0.9004 (mmm) cc_final: 0.8542 (mmm) REVERT: A 998 TYR cc_start: 0.8648 (t80) cc_final: 0.8311 (t80) REVERT: A 1005 MET cc_start: 0.7923 (mtm) cc_final: 0.6623 (mpp) REVERT: A 1022 MET cc_start: 0.8720 (ptp) cc_final: 0.8434 (ptp) REVERT: A 1023 MET cc_start: 0.8363 (tpp) cc_final: 0.7775 (tpp) REVERT: A 1039 ASN cc_start: 0.9206 (m-40) cc_final: 0.8681 (m-40) REVERT: A 1066 ARG cc_start: 0.8412 (ttm-80) cc_final: 0.8188 (ptm160) REVERT: A 1105 LYS cc_start: 0.9139 (mppt) cc_final: 0.8889 (ptmt) REVERT: A 1170 HIS cc_start: 0.8205 (t-90) cc_final: 0.8000 (t70) REVERT: A 1839 LEU cc_start: 0.8648 (tp) cc_final: 0.8441 (tp) REVERT: A 1877 LEU cc_start: 0.9256 (mm) cc_final: 0.8849 (mm) REVERT: A 1878 CYS cc_start: 0.8704 (m) cc_final: 0.8377 (m) REVERT: A 1880 PRO cc_start: 0.8685 (Cg_endo) cc_final: 0.8021 (Cg_exo) REVERT: A 1898 GLU cc_start: 0.8407 (mp0) cc_final: 0.7949 (mt-10) REVERT: A 1904 GLU cc_start: 0.9371 (mp0) cc_final: 0.6901 (tt0) REVERT: A 1925 LEU cc_start: 0.8884 (mt) cc_final: 0.8609 (mt) REVERT: A 1937 ARG cc_start: 0.8822 (mtt-85) cc_final: 0.8254 (ttp-110) REVERT: A 1960 MET cc_start: 0.8969 (ttp) cc_final: 0.8546 (tmm) REVERT: A 1964 GLU cc_start: 0.8461 (tp30) cc_final: 0.8201 (tp30) REVERT: A 1967 MET cc_start: 0.7921 (mmm) cc_final: 0.7521 (mmt) REVERT: B 1956 LYS cc_start: 0.8897 (mttt) cc_final: 0.8460 (mtpt) REVERT: B 1987 ASP cc_start: 0.7932 (m-30) cc_final: 0.7399 (t0) REVERT: B 2028 LYS cc_start: 0.8643 (mmtt) cc_final: 0.7803 (mmtt) REVERT: B 2178 LEU cc_start: 0.8598 (mm) cc_final: 0.8123 (mm) REVERT: B 2209 THR cc_start: 0.8786 (m) cc_final: 0.8536 (m) REVERT: B 2291 HIS cc_start: 0.8691 (m-70) cc_final: 0.8235 (m170) REVERT: B 2306 GLU cc_start: 0.5154 (mp0) cc_final: 0.4771 (mp0) REVERT: B 2333 LYS cc_start: 0.7262 (mttt) cc_final: 0.6403 (mptt) REVERT: B 2353 MET cc_start: 0.8224 (mmm) cc_final: 0.7799 (mmm) REVERT: B 2359 LEU cc_start: 0.9170 (mt) cc_final: 0.8527 (mt) REVERT: B 2373 LEU cc_start: 0.8979 (mt) cc_final: 0.8676 (mt) REVERT: B 2401 LYS cc_start: 0.8338 (tttt) cc_final: 0.7867 (mmmm) REVERT: B 2417 TYR cc_start: 0.8922 (m-80) cc_final: 0.8561 (m-10) REVERT: B 2418 LEU cc_start: 0.9174 (mt) cc_final: 0.8950 (mt) REVERT: B 2613 PHE cc_start: 0.7248 (t80) cc_final: 0.7041 (t80) REVERT: B 2616 ARG cc_start: 0.6668 (ttt180) cc_final: 0.6119 (tmt170) REVERT: B 2685 PHE cc_start: 0.8767 (p90) cc_final: 0.8402 (p90) outliers start: 3 outliers final: 0 residues processed: 469 average time/residue: 0.1003 time to fit residues: 72.3940 Evaluate side-chains 382 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 4 optimal weight: 8.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 92 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 GLN A 67 ASN A 531 GLN A 537 HIS A 608 ASN A 912 GLN ** A1163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B2021 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2051 HIS B2107 ASN ** B2303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B2676 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.115217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094001 restraints weight = 34860.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.097631 restraints weight = 22741.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.100305 restraints weight = 16034.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.102257 restraints weight = 12037.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.103785 restraints weight = 9458.184| |-----------------------------------------------------------------------------| r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14120 Z= 0.210 Angle : 0.684 9.056 19094 Z= 0.353 Chirality : 0.040 0.201 2298 Planarity : 0.004 0.051 2351 Dihedral : 4.870 26.283 1819 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.06 % Allowed : 2.67 % Favored : 97.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.92 (0.20), residues: 1683 helix: 1.54 (0.13), residues: 1381 sheet: None (None), residues: 0 loop : 0.27 (0.38), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B2343 TYR 0.037 0.003 TYR A 433 PHE 0.028 0.002 PHE B1993 TRP 0.021 0.002 TRP B2296 HIS 0.008 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00454 (14120) covalent geometry : angle 0.68424 (19094) hydrogen bonds : bond 0.04543 ( 1042) hydrogen bonds : angle 4.56867 ( 3105) *********************** 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 439 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 438 time to evaluate : 0.523 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 8 GLU cc_start: 0.5561 (mp0) cc_final: 0.4406 (tp30) REVERT: A 50 LYS cc_start: 0.8117 (mmtt) cc_final: 0.7820 (ttpt) REVERT: A 91 GLU cc_start: 0.8904 (pp20) cc_final: 0.8511 (pp20) REVERT: A 116 GLU cc_start: 0.6466 (mm-30) cc_final: 0.6188 (mt-10) REVERT: A 149 ASN cc_start: 0.8460 (t0) cc_final: 0.7993 (t0) REVERT: A 217 GLU cc_start: 0.8755 (tt0) cc_final: 0.8492 (tm-30) REVERT: A 303 LEU cc_start: 0.7914 (mt) cc_final: 0.7498 (mt) REVERT: A 344 LEU cc_start: 0.8594 (mt) cc_final: 0.8382 (tp) REVERT: A 524 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8036 (tp30) REVERT: A 540 GLU cc_start: 0.7503 (mt-10) cc_final: 0.6886 (pm20) REVERT: A 543 GLN cc_start: 0.8508 (tp40) cc_final: 0.8104 (pp30) REVERT: A 546 MET cc_start: 0.7506 (mtm) cc_final: 0.7065 (mtm) REVERT: A 573 ILE cc_start: 0.8350 (tp) cc_final: 0.7938 (tp) REVERT: A 577 MET cc_start: 0.8814 (ttm) cc_final: 0.8432 (tmm) REVERT: A 687 LEU cc_start: 0.8925 (tp) cc_final: 0.8680 (tt) REVERT: A 691 LEU cc_start: 0.8701 (mt) cc_final: 0.8355 (mt) REVERT: A 707 MET cc_start: 0.8371 (ttm) cc_final: 0.7999 (tmm) REVERT: A 833 SER cc_start: 0.5838 (m) cc_final: 0.4974 (t) REVERT: A 836 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8405 (mt-10) REVERT: A 902 MET cc_start: 0.8568 (mtt) cc_final: 0.8314 (mtt) REVERT: A 964 THR cc_start: 0.9321 (t) cc_final: 0.8998 (t) REVERT: A 965 ILE cc_start: 0.8935 (mm) cc_final: 0.8633 (mm) REVERT: A 992 MET cc_start: 0.8861 (mmm) cc_final: 0.8598 (mmm) REVERT: A 998 TYR cc_start: 0.8710 (t80) cc_final: 0.8322 (t80) REVERT: A 1005 MET cc_start: 0.8072 (mtm) cc_final: 0.6599 (mpp) REVERT: A 1022 MET cc_start: 0.8814 (ptp) cc_final: 0.7840 (ptp) REVERT: A 1023 MET cc_start: 0.7701 (tpp) cc_final: 0.7274 (tpp) REVERT: A 1039 ASN cc_start: 0.9277 (m-40) cc_final: 0.8951 (m-40) REVERT: A 1066 ARG cc_start: 0.8511 (ttm-80) cc_final: 0.8029 (ptm160) REVERT: A 1877 LEU cc_start: 0.9115 (mm) cc_final: 0.8887 (mm) REVERT: A 1880 PRO cc_start: 0.8739 (Cg_endo) cc_final: 0.8063 (Cg_exo) REVERT: A 1904 GLU cc_start: 0.9336 (mp0) cc_final: 0.7085 (tt0) REVERT: A 1926 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7284 (mt-10) REVERT: A 1937 ARG cc_start: 0.8858 (mtt-85) cc_final: 0.8317 (ttm-80) REVERT: A 1947 ARG cc_start: 0.8702 (ttt-90) cc_final: 0.8300 (ttm110) REVERT: A 1960 MET cc_start: 0.8941 (ttp) cc_final: 0.8511 (tmm) REVERT: A 1961 THR cc_start: 0.8091 (m) cc_final: 0.7261 (m) REVERT: A 1964 GLU cc_start: 0.8577 (tp30) cc_final: 0.8072 (tp30) REVERT: A 1967 MET cc_start: 0.7806 (mmm) cc_final: 0.7594 (mmt) REVERT: B 1910 ILE cc_start: 0.8468 (mm) cc_final: 0.8238 (mm) REVERT: B 1956 LYS cc_start: 0.8962 (mttt) cc_final: 0.8518 (mtpt) REVERT: B 1986 LEU cc_start: 0.9205 (mt) cc_final: 0.8997 (mt) REVERT: B 1987 ASP cc_start: 0.7782 (m-30) cc_final: 0.7417 (t0) REVERT: B 2021 ASN cc_start: 0.7875 (t0) cc_final: 0.7488 (p0) REVERT: B 2028 LYS cc_start: 0.8621 (mmtt) cc_final: 0.7809 (mmtt) REVERT: B 2209 THR cc_start: 0.8780 (m) cc_final: 0.8556 (m) REVERT: B 2291 HIS cc_start: 0.8510 (m-70) cc_final: 0.8157 (m170) REVERT: B 2333 LYS cc_start: 0.7340 (mttt) cc_final: 0.6557 (mptt) REVERT: B 2353 MET cc_start: 0.8251 (mmm) cc_final: 0.8009 (mmm) REVERT: B 2359 LEU cc_start: 0.9139 (mt) cc_final: 0.8736 (mt) REVERT: B 2370 VAL cc_start: 0.9014 (t) cc_final: 0.8768 (t) REVERT: B 2400 ASN cc_start: 0.8597 (m110) cc_final: 0.7892 (p0) REVERT: B 2401 LYS cc_start: 0.8377 (tttt) cc_final: 0.7762 (mmmm) REVERT: B 2417 TYR cc_start: 0.8908 (m-80) cc_final: 0.8690 (m-10) REVERT: B 2418 LEU cc_start: 0.9261 (mt) cc_final: 0.9009 (mt) REVERT: B 2616 ARG cc_start: 0.6786 (ttt180) cc_final: 0.6305 (tmt170) REVERT: B 2685 PHE cc_start: 0.9016 (p90) cc_final: 0.8251 (p90) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 0.0990 time to fit residues: 67.2155 Evaluate side-chains 374 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 173 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 162 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- 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 ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2021 ASN B2107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.117914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.096871 restraints weight = 34384.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.100592 restraints weight = 22252.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.103317 restraints weight = 15650.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.105378 restraints weight = 11643.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.106837 restraints weight = 9068.522| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14120 Z= 0.153 Angle : 0.620 9.137 19094 Z= 0.320 Chirality : 0.039 0.213 2298 Planarity : 0.004 0.046 2351 Dihedral : 4.683 23.833 1819 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.20), residues: 1683 helix: 1.63 (0.13), residues: 1389 sheet: None (None), residues: 0 loop : 0.12 (0.39), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1137 TYR 0.026 0.002 TYR A1927 PHE 0.034 0.002 PHE A 250 TRP 0.036 0.002 TRP A 221 HIS 0.012 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00340 (14120) covalent geometry : angle 0.61985 (19094) hydrogen bonds : bond 0.04211 ( 1042) hydrogen bonds : angle 4.39068 ( 3105) *********************** 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 458 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 0.489 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: 0.5740 (mp0) cc_final: 0.4653 (tp30) REVERT: A 41 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8816 (mm-30) REVERT: A 50 LYS cc_start: 0.8127 (mmtt) cc_final: 0.7868 (ttpt) REVERT: A 91 GLU cc_start: 0.8872 (pp20) cc_final: 0.8375 (pp20) REVERT: A 116 GLU cc_start: 0.6404 (mm-30) cc_final: 0.6125 (mm-30) REVERT: A 217 GLU cc_start: 0.8692 (tt0) cc_final: 0.8421 (tm-30) REVERT: A 303 LEU cc_start: 0.7788 (mt) cc_final: 0.7520 (mt) REVERT: A 496 MET cc_start: 0.8051 (mtp) cc_final: 0.7696 (mtp) REVERT: A 524 GLU cc_start: 0.8903 (mt-10) cc_final: 0.8046 (tp30) REVERT: A 533 VAL cc_start: 0.8189 (t) cc_final: 0.7985 (t) REVERT: A 540 GLU cc_start: 0.7441 (mt-10) cc_final: 0.6905 (pm20) REVERT: A 543 GLN cc_start: 0.8560 (tp40) cc_final: 0.8157 (pp30) REVERT: A 546 MET cc_start: 0.7482 (mtm) cc_final: 0.7048 (mtm) REVERT: A 573 ILE cc_start: 0.8311 (tp) cc_final: 0.7772 (tp) REVERT: A 577 MET cc_start: 0.8844 (ttm) cc_final: 0.8437 (tmm) REVERT: A 707 MET cc_start: 0.8535 (ttm) cc_final: 0.8092 (tmm) REVERT: A 735 TYR cc_start: 0.7595 (t80) cc_final: 0.6287 (m-10) REVERT: A 739 MET cc_start: 0.7323 (tpt) cc_final: 0.6993 (mtm) REVERT: A 841 THR cc_start: 0.9208 (m) cc_final: 0.8924 (p) REVERT: A 902 MET cc_start: 0.8581 (mtt) cc_final: 0.8303 (mtt) REVERT: A 964 THR cc_start: 0.9302 (t) cc_final: 0.8989 (t) REVERT: A 965 ILE cc_start: 0.8937 (mm) cc_final: 0.8620 (mm) REVERT: A 992 MET cc_start: 0.8869 (mmm) cc_final: 0.8640 (mmm) REVERT: A 998 TYR cc_start: 0.8633 (t80) cc_final: 0.8313 (t80) REVERT: A 1005 MET cc_start: 0.8246 (mtm) cc_final: 0.6722 (mpp) REVERT: A 1012 LYS cc_start: 0.8405 (mttt) cc_final: 0.7798 (mmtp) REVERT: A 1022 MET cc_start: 0.8757 (ptp) cc_final: 0.7720 (ptp) REVERT: A 1023 MET cc_start: 0.7606 (tpp) cc_final: 0.7110 (tpp) REVERT: A 1039 ASN cc_start: 0.9271 (m-40) cc_final: 0.8930 (m-40) REVERT: A 1066 ARG cc_start: 0.8426 (ttm-80) cc_final: 0.8061 (ptm160) REVERT: A 1070 GLN cc_start: 0.8305 (tt0) cc_final: 0.8039 (tt0) REVERT: A 1167 LEU cc_start: 0.9093 (mt) cc_final: 0.8883 (mt) REVERT: A 1171 LYS cc_start: 0.8010 (tmmt) cc_final: 0.7781 (tmtt) REVERT: A 1880 PRO cc_start: 0.8681 (Cg_endo) cc_final: 0.8190 (Cg_exo) REVERT: A 1898 GLU cc_start: 0.8496 (mp0) cc_final: 0.8078 (mt-10) REVERT: A 1904 GLU cc_start: 0.9336 (mp0) cc_final: 0.7011 (tt0) REVERT: A 1921 LYS cc_start: 0.7595 (mttt) cc_final: 0.7056 (mttm) REVERT: A 1925 LEU cc_start: 0.8815 (mt) cc_final: 0.8513 (mt) REVERT: A 1926 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7040 (mt-10) REVERT: A 1937 ARG cc_start: 0.8653 (mtt-85) cc_final: 0.8139 (ttm-80) REVERT: A 1947 ARG cc_start: 0.8717 (ttt-90) cc_final: 0.8287 (ttm110) REVERT: A 1960 MET cc_start: 0.8942 (ttp) cc_final: 0.8495 (tmm) REVERT: A 1961 THR cc_start: 0.8140 (m) cc_final: 0.7371 (m) REVERT: A 1964 GLU cc_start: 0.8326 (tp30) cc_final: 0.7895 (tp30) REVERT: A 1967 MET cc_start: 0.7762 (mmm) cc_final: 0.7358 (mmt) REVERT: A 2008 GLU cc_start: 0.7333 (pp20) cc_final: 0.6890 (pt0) REVERT: B 1922 HIS cc_start: 0.7569 (m-70) cc_final: 0.7323 (m-70) REVERT: B 1928 MET cc_start: 0.8078 (mmt) cc_final: 0.6851 (mmt) REVERT: B 1956 LYS cc_start: 0.8865 (mttt) cc_final: 0.8042 (tptm) REVERT: B 1986 LEU cc_start: 0.9171 (mt) cc_final: 0.8971 (mt) REVERT: B 1987 ASP cc_start: 0.7723 (m-30) cc_final: 0.7369 (t0) REVERT: B 2021 ASN cc_start: 0.7876 (t160) cc_final: 0.7615 (p0) REVERT: B 2028 LYS cc_start: 0.8610 (mmtt) cc_final: 0.7801 (mmtt) REVERT: B 2120 PHE cc_start: 0.8134 (m-80) cc_final: 0.7857 (m-80) REVERT: B 2209 THR cc_start: 0.8760 (m) cc_final: 0.8483 (m) REVERT: B 2291 HIS cc_start: 0.8671 (m-70) cc_final: 0.8137 (m170) REVERT: B 2306 GLU cc_start: 0.5677 (mp0) cc_final: 0.5034 (mp0) REVERT: B 2333 LYS cc_start: 0.7479 (mttt) cc_final: 0.6682 (mptt) REVERT: B 2347 GLU cc_start: 0.8036 (tp30) cc_final: 0.6764 (tt0) REVERT: B 2353 MET cc_start: 0.8069 (mmm) cc_final: 0.7776 (mmm) REVERT: B 2359 LEU cc_start: 0.9115 (mt) cc_final: 0.8791 (mt) REVERT: B 2373 LEU cc_start: 0.8992 (mt) cc_final: 0.8773 (mt) REVERT: B 2377 TYR cc_start: 0.7979 (m-80) cc_final: 0.7500 (m-80) REVERT: B 2401 LYS cc_start: 0.8269 (tttt) cc_final: 0.7914 (mmmm) REVERT: B 2417 TYR cc_start: 0.8916 (m-80) cc_final: 0.8595 (m-10) REVERT: B 2418 LEU cc_start: 0.9233 (mt) cc_final: 0.9018 (mt) REVERT: B 2423 THR cc_start: 0.8073 (p) cc_final: 0.7485 (p) REVERT: B 2616 ARG cc_start: 0.6632 (ttt180) cc_final: 0.6059 (tmt170) REVERT: B 2685 PHE cc_start: 0.8918 (p90) cc_final: 0.8395 (p90) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 0.0961 time to fit residues: 68.6051 Evaluate side-chains 389 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 8.9990 chunk 148 optimal weight: 0.6980 chunk 154 optimal weight: 0.0020 chunk 163 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 101 optimal weight: 10.0000 chunk 128 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 412 ASN A 435 HIS A 531 GLN ** A 553 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1163 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1972 GLN B1882 ASN B2021 ASN B2107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.120333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.099310 restraints weight = 33690.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.103119 restraints weight = 21792.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.105960 restraints weight = 15262.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.108040 restraints weight = 11265.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.109499 restraints weight = 8706.807| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14120 Z= 0.139 Angle : 0.628 13.915 19094 Z= 0.318 Chirality : 0.039 0.183 2298 Planarity : 0.003 0.045 2351 Dihedral : 4.580 22.206 1819 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.06 % Allowed : 1.53 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.13 (0.20), residues: 1683 helix: 1.71 (0.13), residues: 1391 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2378 TYR 0.029 0.002 TYR A1927 PHE 0.070 0.002 PHE B1993 TRP 0.021 0.002 TRP A 777 HIS 0.010 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00312 (14120) covalent geometry : angle 0.62846 (19094) hydrogen bonds : bond 0.04020 ( 1042) hydrogen bonds : angle 4.34208 ( 3105) *********************** 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 467 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 466 time to evaluate : 0.507 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: 0.5497 (mp0) cc_final: 0.4506 (tp30) REVERT: A 41 GLU cc_start: 0.9365 (mt-10) cc_final: 0.8846 (mm-30) REVERT: A 91 GLU cc_start: 0.8763 (pp20) cc_final: 0.8482 (pp20) REVERT: A 116 GLU cc_start: 0.6302 (mm-30) cc_final: 0.6038 (mm-30) REVERT: A 149 ASN cc_start: 0.8207 (OUTLIER) cc_final: 0.7824 (t0) REVERT: A 183 ILE cc_start: 0.9186 (pt) cc_final: 0.8730 (tp) REVERT: A 217 GLU cc_start: 0.8676 (tt0) cc_final: 0.8435 (tm-30) REVERT: A 356 LEU cc_start: 0.8199 (tp) cc_final: 0.7853 (pp) REVERT: A 493 LEU cc_start: 0.8929 (tp) cc_final: 0.8702 (tp) REVERT: A 496 MET cc_start: 0.8180 (mtp) cc_final: 0.7477 (mtp) REVERT: A 524 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8155 (tp30) REVERT: A 533 VAL cc_start: 0.8178 (t) cc_final: 0.7967 (t) REVERT: A 540 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6872 (pm20) REVERT: A 543 GLN cc_start: 0.8449 (tp40) cc_final: 0.8102 (pp30) REVERT: A 546 MET cc_start: 0.7474 (mtm) cc_final: 0.7170 (mtm) REVERT: A 707 MET cc_start: 0.8624 (ttm) cc_final: 0.8207 (ttp) REVERT: A 711 ARG cc_start: 0.7598 (ttp-110) cc_final: 0.6821 (mtm-85) REVERT: A 735 TYR cc_start: 0.7123 (t80) cc_final: 0.5904 (m-10) REVERT: A 739 MET cc_start: 0.7077 (tpt) cc_final: 0.6850 (mtm) REVERT: A 766 ILE cc_start: 0.8467 (mt) cc_final: 0.8219 (mt) REVERT: A 775 GLU cc_start: 0.8141 (tt0) cc_final: 0.7085 (tm-30) REVERT: A 779 ASP cc_start: 0.8604 (m-30) cc_final: 0.7548 (m-30) REVERT: A 836 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8714 (mt-10) REVERT: A 837 TRP cc_start: 0.8656 (t60) cc_final: 0.8417 (t60) REVERT: A 845 CYS cc_start: 0.9285 (m) cc_final: 0.8508 (p) REVERT: A 902 MET cc_start: 0.8538 (mtt) cc_final: 0.8307 (mtt) REVERT: A 924 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7349 (mm-30) REVERT: A 960 PHE cc_start: 0.8892 (t80) cc_final: 0.8680 (t80) REVERT: A 964 THR cc_start: 0.9233 (t) cc_final: 0.8835 (t) REVERT: A 965 ILE cc_start: 0.8887 (mm) cc_final: 0.8482 (mm) REVERT: A 992 MET cc_start: 0.8763 (mmm) cc_final: 0.8443 (mmm) REVERT: A 998 TYR cc_start: 0.8510 (t80) cc_final: 0.8236 (t80) REVERT: A 1005 MET cc_start: 0.8155 (mtm) cc_final: 0.6512 (mpp) REVERT: A 1012 LYS cc_start: 0.8443 (mttt) cc_final: 0.7829 (mmtp) REVERT: A 1022 MET cc_start: 0.8660 (ptp) cc_final: 0.7625 (ptp) REVERT: A 1023 MET cc_start: 0.7583 (tpp) cc_final: 0.7099 (tpp) REVERT: A 1039 ASN cc_start: 0.9343 (m-40) cc_final: 0.8912 (m-40) REVERT: A 1066 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8051 (ptm160) REVERT: A 1070 GLN cc_start: 0.8333 (tt0) cc_final: 0.8052 (tt0) REVERT: A 1171 LYS cc_start: 0.7987 (tmmt) cc_final: 0.7700 (tmtt) REVERT: A 1880 PRO cc_start: 0.8550 (Cg_endo) cc_final: 0.8275 (Cg_exo) REVERT: A 1904 GLU cc_start: 0.9166 (mp0) cc_final: 0.6865 (tt0) REVERT: A 1921 LYS cc_start: 0.7549 (mttt) cc_final: 0.7026 (mttm) REVERT: A 1925 LEU cc_start: 0.8793 (mt) cc_final: 0.8570 (mt) REVERT: A 1926 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7261 (mt-10) REVERT: A 1937 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.8037 (ttm-80) REVERT: A 1951 THR cc_start: 0.7991 (m) cc_final: 0.7766 (p) REVERT: A 1960 MET cc_start: 0.8829 (ttp) cc_final: 0.8512 (tmm) REVERT: A 1961 THR cc_start: 0.8011 (m) cc_final: 0.7657 (p) REVERT: A 1967 MET cc_start: 0.7629 (mmm) cc_final: 0.6946 (mmt) REVERT: A 2008 GLU cc_start: 0.7129 (pp20) cc_final: 0.6653 (pt0) REVERT: B 1910 ILE cc_start: 0.8180 (mm) cc_final: 0.7232 (mm) REVERT: B 1922 HIS cc_start: 0.7396 (m-70) cc_final: 0.7062 (m-70) REVERT: B 1925 LEU cc_start: 0.8707 (mt) cc_final: 0.8029 (pp) REVERT: B 1928 MET cc_start: 0.8538 (mmt) cc_final: 0.7939 (mmt) REVERT: B 1956 LYS cc_start: 0.8734 (mttt) cc_final: 0.7963 (tptm) REVERT: B 1967 MET cc_start: 0.8543 (mmt) cc_final: 0.7717 (mmt) REVERT: B 1986 LEU cc_start: 0.9169 (mt) cc_final: 0.8873 (mt) REVERT: B 2028 LYS cc_start: 0.8531 (mmtt) cc_final: 0.7844 (mmtt) REVERT: B 2120 PHE cc_start: 0.7938 (m-80) cc_final: 0.7704 (m-80) REVERT: B 2140 PHE cc_start: 0.8463 (m-80) cc_final: 0.8220 (m-80) REVERT: B 2143 LEU cc_start: 0.9022 (mt) cc_final: 0.8816 (mt) REVERT: B 2180 SER cc_start: 0.8690 (m) cc_final: 0.7748 (t) REVERT: B 2184 VAL cc_start: 0.8252 (t) cc_final: 0.7917 (t) REVERT: B 2209 THR cc_start: 0.8655 (m) cc_final: 0.8424 (m) REVERT: B 2218 GLN cc_start: 0.7087 (mm-40) cc_final: 0.6871 (mp10) REVERT: B 2291 HIS cc_start: 0.8620 (m-70) cc_final: 0.8247 (m170) REVERT: B 2303 GLN cc_start: 0.8039 (tt0) cc_final: 0.7523 (tm-30) REVERT: B 2306 GLU cc_start: 0.5522 (mp0) cc_final: 0.4965 (mp0) REVERT: B 2333 LYS cc_start: 0.7475 (mttt) cc_final: 0.6646 (mptt) REVERT: B 2340 MET cc_start: 0.6900 (mmm) cc_final: 0.6181 (mmm) REVERT: B 2347 GLU cc_start: 0.7989 (tp30) cc_final: 0.6778 (tt0) REVERT: B 2359 LEU cc_start: 0.9140 (mt) cc_final: 0.8790 (mt) REVERT: B 2377 TYR cc_start: 0.7902 (m-80) cc_final: 0.7363 (m-80) REVERT: B 2417 TYR cc_start: 0.8876 (m-80) cc_final: 0.8510 (m-10) REVERT: B 2418 LEU cc_start: 0.9180 (mt) cc_final: 0.8973 (mt) REVERT: B 2423 THR cc_start: 0.8237 (p) cc_final: 0.7740 (p) REVERT: B 2616 ARG cc_start: 0.6728 (ttt180) cc_final: 0.5940 (tmt170) REVERT: B 2618 LEU cc_start: 0.8674 (mm) cc_final: 0.8419 (mm) REVERT: B 2685 PHE cc_start: 0.8710 (p90) cc_final: 0.8217 (p90) outliers start: 1 outliers final: 0 residues processed: 466 average time/residue: 0.0974 time to fit residues: 70.6717 Evaluate side-chains 398 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 397 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 91 optimal weight: 0.9990 chunk 167 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 149 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 ASN A 412 ASN A 501 HIS A 531 GLN A 781 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1966 GLN B1835 ASN B2107 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.121246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.100112 restraints weight = 33972.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.103906 restraints weight = 22070.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.106601 restraints weight = 15509.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.108663 restraints weight = 11579.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.110112 restraints weight = 9037.525| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.6468 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= 0.147 Angle : 0.660 20.495 19094 Z= 0.328 Chirality : 0.039 0.245 2298 Planarity : 0.003 0.045 2351 Dihedral : 4.596 21.541 1819 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.06 % Allowed : 1.08 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.20), residues: 1683 helix: 1.64 (0.13), residues: 1382 sheet: None (None), residues: 0 loop : 0.30 (0.39), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.037 0.002 TYR A 408 PHE 0.065 0.002 PHE A1107 TRP 0.021 0.002 TRP A 9 HIS 0.009 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00336 (14120) covalent geometry : angle 0.65993 (19094) hydrogen bonds : bond 0.04078 ( 1042) hydrogen bonds : angle 4.39384 ( 3105) *********************** 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 453 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 0.533 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: 0.5601 (mp0) cc_final: 0.4364 (tp30) REVERT: A 41 GLU cc_start: 0.9397 (mt-10) cc_final: 0.8834 (mm-30) REVERT: A 91 GLU cc_start: 0.8788 (pp20) cc_final: 0.8534 (pp20) REVERT: A 116 GLU cc_start: 0.6285 (mm-30) cc_final: 0.6057 (mt-10) REVERT: A 183 ILE cc_start: 0.9156 (pt) cc_final: 0.8706 (tp) REVERT: A 217 GLU cc_start: 0.8686 (tt0) cc_final: 0.8438 (tm-30) REVERT: A 384 PHE cc_start: 0.8616 (t80) cc_final: 0.8329 (t80) REVERT: A 442 MET cc_start: 0.8584 (ttm) cc_final: 0.8337 (tpp) REVERT: A 493 LEU cc_start: 0.8894 (tp) cc_final: 0.8683 (tp) REVERT: A 496 MET cc_start: 0.8231 (mtp) cc_final: 0.7241 (mtp) REVERT: A 524 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8223 (tp30) REVERT: A 533 VAL cc_start: 0.8154 (t) cc_final: 0.7942 (t) REVERT: A 540 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6866 (pm20) REVERT: A 543 GLN cc_start: 0.8450 (tp40) cc_final: 0.8106 (pp30) REVERT: A 546 MET cc_start: 0.7473 (mtm) cc_final: 0.7152 (mtm) REVERT: A 604 LEU cc_start: 0.9030 (mt) cc_final: 0.8719 (mt) REVERT: A 608 ASN cc_start: 0.8420 (m110) cc_final: 0.6793 (m110) REVERT: A 707 MET cc_start: 0.8689 (ttm) cc_final: 0.8190 (ttp) REVERT: A 711 ARG cc_start: 0.7640 (ttp-110) cc_final: 0.6912 (mtm-85) REVERT: A 766 ILE cc_start: 0.8577 (mt) cc_final: 0.8370 (mt) REVERT: A 773 ASN cc_start: 0.8026 (m-40) cc_final: 0.7690 (m-40) REVERT: A 775 GLU cc_start: 0.8195 (tt0) cc_final: 0.6805 (tm-30) REVERT: A 779 ASP cc_start: 0.8637 (m-30) cc_final: 0.7173 (m-30) REVERT: A 836 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8642 (mt-10) REVERT: A 845 CYS cc_start: 0.9370 (m) cc_final: 0.8640 (p) REVERT: A 902 MET cc_start: 0.8545 (mtt) cc_final: 0.8336 (mtt) REVERT: A 964 THR cc_start: 0.9213 (t) cc_final: 0.8799 (t) REVERT: A 965 ILE cc_start: 0.8895 (mm) cc_final: 0.8383 (mm) REVERT: A 992 MET cc_start: 0.8711 (mmm) cc_final: 0.8482 (mmm) REVERT: A 998 TYR cc_start: 0.8542 (t80) cc_final: 0.8186 (t80) REVERT: A 1005 MET cc_start: 0.8190 (mtm) cc_final: 0.6745 (mpp) REVERT: A 1012 LYS cc_start: 0.8375 (mttt) cc_final: 0.7806 (mmtp) REVERT: A 1022 MET cc_start: 0.8720 (ptp) cc_final: 0.7673 (ptp) REVERT: A 1023 MET cc_start: 0.7652 (tpp) cc_final: 0.7138 (tpp) REVERT: A 1039 ASN cc_start: 0.9408 (m-40) cc_final: 0.8927 (m-40) REVERT: A 1066 ARG cc_start: 0.8411 (ttm-80) cc_final: 0.8046 (ptm160) REVERT: A 1070 GLN cc_start: 0.8293 (tt0) cc_final: 0.7991 (tt0) REVERT: A 1106 TYR cc_start: 0.7881 (m-80) cc_final: 0.7553 (m-80) REVERT: A 1162 MET cc_start: 0.8061 (pmm) cc_final: 0.7828 (pmm) REVERT: A 1171 LYS cc_start: 0.7911 (tmmt) cc_final: 0.7634 (tmtt) REVERT: A 1883 ASN cc_start: 0.8519 (t0) cc_final: 0.8250 (t0) REVERT: A 1901 LEU cc_start: 0.9377 (mt) cc_final: 0.9173 (mt) REVERT: A 1904 GLU cc_start: 0.9193 (mp0) cc_final: 0.6978 (tt0) REVERT: A 1921 LYS cc_start: 0.7467 (mttt) cc_final: 0.7051 (mttm) REVERT: A 1925 LEU cc_start: 0.8718 (mt) cc_final: 0.8487 (mt) REVERT: A 1926 GLU cc_start: 0.7821 (mm-30) cc_final: 0.6994 (mt-10) REVERT: A 1927 TYR cc_start: 0.8033 (p90) cc_final: 0.7713 (p90) REVERT: A 1937 ARG cc_start: 0.8479 (mtt-85) cc_final: 0.7813 (ttp-110) REVERT: A 1961 THR cc_start: 0.8261 (m) cc_final: 0.7222 (m) REVERT: A 2008 GLU cc_start: 0.7192 (pp20) cc_final: 0.6874 (pt0) REVERT: B 1892 LYS cc_start: 0.8772 (ptmt) cc_final: 0.8268 (mttp) REVERT: B 1894 LEU cc_start: 0.8926 (mt) cc_final: 0.8673 (mt) REVERT: B 1898 GLU cc_start: 0.6484 (pm20) cc_final: 0.6255 (pm20) REVERT: B 1910 ILE cc_start: 0.8143 (mm) cc_final: 0.7227 (mm) REVERT: B 1922 HIS cc_start: 0.7444 (m-70) cc_final: 0.7054 (m-70) REVERT: B 1925 LEU cc_start: 0.8694 (mt) cc_final: 0.8254 (pp) REVERT: B 1928 MET cc_start: 0.8574 (mmt) cc_final: 0.7853 (mmt) REVERT: B 1956 LYS cc_start: 0.8749 (mttt) cc_final: 0.8010 (tptm) REVERT: B 1986 LEU cc_start: 0.9012 (mt) cc_final: 0.8806 (mp) REVERT: B 2028 LYS cc_start: 0.8096 (mmtt) cc_final: 0.7842 (mmtt) REVERT: B 2120 PHE cc_start: 0.7977 (m-80) cc_final: 0.7717 (m-80) REVERT: B 2140 PHE cc_start: 0.8608 (m-80) cc_final: 0.8308 (m-80) REVERT: B 2180 SER cc_start: 0.8539 (m) cc_final: 0.7604 (t) REVERT: B 2184 VAL cc_start: 0.8287 (t) cc_final: 0.7968 (t) REVERT: B 2205 LEU cc_start: 0.7919 (tt) cc_final: 0.7431 (pt) REVERT: B 2209 THR cc_start: 0.8683 (m) cc_final: 0.8462 (m) REVERT: B 2218 GLN cc_start: 0.7137 (mm-40) cc_final: 0.6862 (mp10) REVERT: B 2291 HIS cc_start: 0.8574 (m-70) cc_final: 0.8217 (m170) REVERT: B 2303 GLN cc_start: 0.8175 (tt0) cc_final: 0.7478 (tm-30) REVERT: B 2306 GLU cc_start: 0.5539 (mp0) cc_final: 0.4968 (mp0) REVERT: B 2333 LYS cc_start: 0.7466 (mttt) cc_final: 0.6611 (mptt) REVERT: B 2340 MET cc_start: 0.7118 (mmm) cc_final: 0.6440 (mmm) REVERT: B 2347 GLU cc_start: 0.7991 (tp30) cc_final: 0.6834 (tt0) REVERT: B 2359 LEU cc_start: 0.9193 (mt) cc_final: 0.8809 (mt) REVERT: B 2417 TYR cc_start: 0.8879 (m-80) cc_final: 0.8574 (m-10) REVERT: B 2418 LEU cc_start: 0.9148 (mt) cc_final: 0.8915 (mt) REVERT: B 2616 ARG cc_start: 0.6698 (ttt180) cc_final: 0.5898 (tmt170) REVERT: B 2618 LEU cc_start: 0.8627 (mm) cc_final: 0.8336 (mm) REVERT: B 2685 PHE cc_start: 0.8738 (p90) cc_final: 0.8304 (p90) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.0997 time to fit residues: 70.6829 Evaluate side-chains 387 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 132 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 173 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 531 GLN A 773 ASN A 835 GLN A 982 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1972 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN ** B1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1972 GLN B2107 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.122077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100852 restraints weight = 33942.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.104656 restraints weight = 22037.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.107442 restraints weight = 15465.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.109394 restraints weight = 11510.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.110934 restraints weight = 9029.856| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.6687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14120 Z= 0.145 Angle : 0.657 10.907 19094 Z= 0.332 Chirality : 0.040 0.198 2298 Planarity : 0.004 0.045 2351 Dihedral : 4.611 25.077 1819 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.06 % Allowed : 0.76 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.20), residues: 1683 helix: 1.61 (0.13), residues: 1390 sheet: None (None), residues: 0 loop : -0.03 (0.38), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.037 0.002 TYR A 408 PHE 0.058 0.002 PHE B1993 TRP 0.039 0.002 TRP B1931 HIS 0.007 0.001 HIS A1922 Details of bonding type rmsd covalent geometry : bond 0.00325 (14120) covalent geometry : angle 0.65660 (19094) hydrogen bonds : bond 0.04091 ( 1042) hydrogen bonds : angle 4.37654 ( 3105) *********************** 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 461 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 0.511 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: 0.5594 (mp0) cc_final: 0.4382 (tp30) REVERT: A 41 GLU cc_start: 0.9373 (mt-10) cc_final: 0.8847 (mm-30) REVERT: A 116 GLU cc_start: 0.6268 (mm-30) cc_final: 0.6003 (mm-30) REVERT: A 149 ASN cc_start: 0.8209 (t0) cc_final: 0.7897 (t0) REVERT: A 183 ILE cc_start: 0.9093 (pt) cc_final: 0.8670 (tp) REVERT: A 184 ASN cc_start: 0.8311 (t0) cc_final: 0.8101 (t0) REVERT: A 217 GLU cc_start: 0.8681 (tt0) cc_final: 0.8410 (tm-30) REVERT: A 384 PHE cc_start: 0.8506 (t80) cc_final: 0.8290 (t80) REVERT: A 442 MET cc_start: 0.8545 (ttm) cc_final: 0.8329 (tpp) REVERT: A 493 LEU cc_start: 0.8890 (tp) cc_final: 0.8667 (tp) REVERT: A 496 MET cc_start: 0.8237 (mtp) cc_final: 0.7225 (mtp) REVERT: A 524 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8148 (tp30) REVERT: A 540 GLU cc_start: 0.7524 (mt-10) cc_final: 0.6969 (pm20) REVERT: A 543 GLN cc_start: 0.8441 (tp40) cc_final: 0.8150 (pp30) REVERT: A 546 MET cc_start: 0.7443 (mtm) cc_final: 0.7162 (mtm) REVERT: A 609 LYS cc_start: 0.7817 (mttt) cc_final: 0.7207 (tttm) REVERT: A 695 LEU cc_start: 0.8297 (mt) cc_final: 0.8084 (mt) REVERT: A 707 MET cc_start: 0.8684 (ttm) cc_final: 0.8184 (ttp) REVERT: A 711 ARG cc_start: 0.7612 (ttp-110) cc_final: 0.6878 (mtm-85) REVERT: A 773 ASN cc_start: 0.7734 (m110) cc_final: 0.7390 (m110) REVERT: A 775 GLU cc_start: 0.8233 (tt0) cc_final: 0.7214 (tm-30) REVERT: A 779 ASP cc_start: 0.8568 (m-30) cc_final: 0.7144 (m-30) REVERT: A 835 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7922 (tp-100) REVERT: A 836 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8613 (mt-10) REVERT: A 845 CYS cc_start: 0.9335 (m) cc_final: 0.8589 (p) REVERT: A 902 MET cc_start: 0.8506 (mtt) cc_final: 0.8301 (mtt) REVERT: A 964 THR cc_start: 0.9207 (t) cc_final: 0.8878 (t) REVERT: A 965 ILE cc_start: 0.8878 (mm) cc_final: 0.8434 (mm) REVERT: A 988 ILE cc_start: 0.8655 (pt) cc_final: 0.8281 (pt) REVERT: A 992 MET cc_start: 0.8725 (mmm) cc_final: 0.8432 (mmm) REVERT: A 998 TYR cc_start: 0.8511 (t80) cc_final: 0.8192 (t80) REVERT: A 1005 MET cc_start: 0.8226 (mtm) cc_final: 0.6748 (mpp) REVERT: A 1012 LYS cc_start: 0.8422 (mttt) cc_final: 0.7861 (mmtp) REVERT: A 1022 MET cc_start: 0.8745 (ptp) cc_final: 0.7652 (ptp) REVERT: A 1023 MET cc_start: 0.7682 (tpp) cc_final: 0.7086 (tpp) REVERT: A 1039 ASN cc_start: 0.9413 (m-40) cc_final: 0.8920 (m-40) REVERT: A 1066 ARG cc_start: 0.8437 (ttm-80) cc_final: 0.8101 (ptm160) REVERT: A 1070 GLN cc_start: 0.8293 (tt0) cc_final: 0.7991 (tt0) REVERT: A 1146 VAL cc_start: 0.8787 (t) cc_final: 0.8567 (t) REVERT: A 1149 MET cc_start: 0.8704 (ptm) cc_final: 0.8001 (ttt) REVERT: A 1162 MET cc_start: 0.7708 (pmm) cc_final: 0.7465 (pmm) REVERT: A 1171 LYS cc_start: 0.7906 (tmmt) cc_final: 0.7674 (tmtt) REVERT: A 1904 GLU cc_start: 0.9168 (mp0) cc_final: 0.6883 (tt0) REVERT: A 1921 LYS cc_start: 0.7364 (mttt) cc_final: 0.7004 (mttm) REVERT: A 1925 LEU cc_start: 0.8769 (mt) cc_final: 0.8480 (mt) REVERT: A 1926 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7025 (mt-10) REVERT: A 1927 TYR cc_start: 0.7935 (p90) cc_final: 0.7634 (p90) REVERT: A 1937 ARG cc_start: 0.8440 (mtt-85) cc_final: 0.7822 (ttp-110) REVERT: A 1961 THR cc_start: 0.7965 (m) cc_final: 0.7286 (m) REVERT: A 2008 GLU cc_start: 0.7231 (pp20) cc_final: 0.6806 (pt0) REVERT: B 1885 LEU cc_start: 0.8994 (tp) cc_final: 0.8511 (pp) REVERT: B 1894 LEU cc_start: 0.9105 (mt) cc_final: 0.8718 (mt) REVERT: B 1910 ILE cc_start: 0.8042 (mm) cc_final: 0.7143 (mm) REVERT: B 1919 GLU cc_start: 0.8405 (mp0) cc_final: 0.7686 (mp0) REVERT: B 1922 HIS cc_start: 0.7429 (m-70) cc_final: 0.7111 (m-70) REVERT: B 1928 MET cc_start: 0.8546 (mmt) cc_final: 0.7799 (mmt) REVERT: B 1947 ARG cc_start: 0.9116 (ptm-80) cc_final: 0.8836 (mtt180) REVERT: B 1956 LYS cc_start: 0.8717 (mttt) cc_final: 0.7980 (tptm) REVERT: B 1986 LEU cc_start: 0.8975 (mt) cc_final: 0.8767 (mp) REVERT: B 2010 MET cc_start: 0.8516 (mmm) cc_final: 0.7920 (tmm) REVERT: B 2028 LYS cc_start: 0.8095 (mmtt) cc_final: 0.7867 (mmtt) REVERT: B 2060 LEU cc_start: 0.8795 (mt) cc_final: 0.8571 (mt) REVERT: B 2083 PHE cc_start: 0.8131 (m-10) cc_final: 0.7638 (m-80) REVERT: B 2140 PHE cc_start: 0.8437 (m-80) cc_final: 0.8222 (m-80) REVERT: B 2180 SER cc_start: 0.8706 (m) cc_final: 0.7911 (t) REVERT: B 2184 VAL cc_start: 0.8296 (t) cc_final: 0.8019 (t) REVERT: B 2205 LEU cc_start: 0.7919 (tt) cc_final: 0.7506 (pt) REVERT: B 2209 THR cc_start: 0.8571 (m) cc_final: 0.8238 (m) REVERT: B 2210 GLU cc_start: 0.8360 (tt0) cc_final: 0.8107 (pt0) REVERT: B 2218 GLN cc_start: 0.7200 (mm-40) cc_final: 0.6867 (mp10) REVERT: B 2291 HIS cc_start: 0.8573 (m-70) cc_final: 0.8221 (m170) REVERT: B 2303 GLN cc_start: 0.8177 (tt0) cc_final: 0.7532 (tm-30) REVERT: B 2306 GLU cc_start: 0.5532 (mp0) cc_final: 0.4918 (mp0) REVERT: B 2333 LYS cc_start: 0.7227 (mttt) cc_final: 0.6405 (mptt) REVERT: B 2340 MET cc_start: 0.7135 (mmm) cc_final: 0.6378 (mmm) REVERT: B 2347 GLU cc_start: 0.8029 (tp30) cc_final: 0.6838 (tt0) REVERT: B 2359 LEU cc_start: 0.9191 (mt) cc_final: 0.8689 (mt) REVERT: B 2373 LEU cc_start: 0.9015 (mt) cc_final: 0.8798 (mt) REVERT: B 2417 TYR cc_start: 0.8865 (m-80) cc_final: 0.8568 (m-10) REVERT: B 2418 LEU cc_start: 0.9082 (mt) cc_final: 0.8856 (mt) REVERT: B 2616 ARG cc_start: 0.6700 (ttt180) cc_final: 0.5946 (tmt170) REVERT: B 2685 PHE cc_start: 0.8693 (p90) cc_final: 0.8275 (p90) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.0972 time to fit residues: 69.9796 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 : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 93 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 165 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN A 501 HIS ** A1835 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1882 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1835 ASN B2107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.119853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.098733 restraints weight = 34068.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.102480 restraints weight = 22235.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.105228 restraints weight = 15704.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.107188 restraints weight = 11751.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.108789 restraints weight = 9263.750| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14120 Z= 0.148 Angle : 0.655 9.161 19094 Z= 0.336 Chirality : 0.040 0.203 2298 Planarity : 0.004 0.044 2351 Dihedral : 4.603 22.452 1819 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.06 % Allowed : 0.38 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.20), residues: 1683 helix: 1.62 (0.13), residues: 1384 sheet: None (None), residues: 0 loop : 0.19 (0.39), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 156 TYR 0.035 0.002 TYR A 408 PHE 0.038 0.002 PHE B1993 TRP 0.029 0.002 TRP B1931 HIS 0.007 0.001 HIS B1922 Details of bonding type rmsd covalent geometry : bond 0.00330 (14120) covalent geometry : angle 0.65528 (19094) hydrogen bonds : bond 0.04120 ( 1042) hydrogen bonds : angle 4.42577 ( 3105) ********************** 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 444 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 443 time to evaluate : 0.544 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: 0.5610 (mp0) cc_final: 0.4393 (tp30) REVERT: A 41 GLU cc_start: 0.9370 (mt-10) cc_final: 0.8842 (mm-30) REVERT: A 58 LEU cc_start: 0.8129 (mt) cc_final: 0.7920 (mt) REVERT: A 116 GLU cc_start: 0.6154 (mm-30) cc_final: 0.5910 (mm-30) REVERT: A 183 ILE cc_start: 0.9106 (pt) cc_final: 0.8680 (tp) REVERT: A 184 ASN cc_start: 0.8319 (t0) cc_final: 0.8113 (t0) REVERT: A 217 GLU cc_start: 0.8769 (tt0) cc_final: 0.8475 (tm-30) REVERT: A 356 LEU cc_start: 0.8208 (tp) cc_final: 0.7989 (pp) REVERT: A 496 MET cc_start: 0.8234 (mtp) cc_final: 0.7647 (mtp) REVERT: A 524 GLU cc_start: 0.8882 (mt-10) cc_final: 0.8244 (tp30) REVERT: A 540 GLU cc_start: 0.7606 (mt-10) cc_final: 0.6980 (pm20) REVERT: A 543 GLN cc_start: 0.8449 (tp40) cc_final: 0.8143 (pp30) REVERT: A 546 MET cc_start: 0.7487 (mtm) cc_final: 0.7204 (mtm) REVERT: A 604 LEU cc_start: 0.9012 (mt) cc_final: 0.8743 (mt) REVERT: A 608 ASN cc_start: 0.8339 (m110) cc_final: 0.6794 (m110) REVERT: A 609 LYS cc_start: 0.7819 (mttt) cc_final: 0.7424 (tttm) REVERT: A 695 LEU cc_start: 0.8285 (mt) cc_final: 0.8065 (mt) REVERT: A 707 MET cc_start: 0.8692 (ttm) cc_final: 0.8182 (ttp) REVERT: A 711 ARG cc_start: 0.7584 (ttp-110) cc_final: 0.6909 (mtm-85) REVERT: A 773 ASN cc_start: 0.7478 (m110) cc_final: 0.7178 (m110) REVERT: A 775 GLU cc_start: 0.8149 (tt0) cc_final: 0.7127 (tm-30) REVERT: A 779 ASP cc_start: 0.8625 (m-30) cc_final: 0.7160 (m-30) REVERT: A 845 CYS cc_start: 0.9258 (m) cc_final: 0.8419 (p) REVERT: A 902 MET cc_start: 0.8515 (mtt) cc_final: 0.8301 (mtt) REVERT: A 964 THR cc_start: 0.9204 (t) cc_final: 0.8837 (t) REVERT: A 965 ILE cc_start: 0.8969 (mm) cc_final: 0.8670 (mm) REVERT: A 998 TYR cc_start: 0.8529 (t80) cc_final: 0.8185 (t80) REVERT: A 1005 MET cc_start: 0.8224 (mtm) cc_final: 0.6773 (mpp) REVERT: A 1022 MET cc_start: 0.8766 (ptp) cc_final: 0.7755 (ptp) REVERT: A 1023 MET cc_start: 0.7683 (tpp) cc_final: 0.7091 (tpp) REVERT: A 1039 ASN cc_start: 0.9412 (m-40) cc_final: 0.8922 (m-40) REVERT: A 1066 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8096 (ptm160) REVERT: A 1070 GLN cc_start: 0.8280 (tt0) cc_final: 0.7994 (tt0) REVERT: A 1146 VAL cc_start: 0.8868 (t) cc_final: 0.8662 (t) REVERT: A 1149 MET cc_start: 0.8713 (ptm) cc_final: 0.8063 (ttt) REVERT: A 1162 MET cc_start: 0.7691 (pmm) cc_final: 0.7445 (pmm) REVERT: A 1171 LYS cc_start: 0.7844 (tmmt) cc_final: 0.7568 (tttt) REVERT: A 1921 LYS cc_start: 0.7449 (mttt) cc_final: 0.7175 (mttp) REVERT: A 1925 LEU cc_start: 0.8699 (mt) cc_final: 0.8467 (mt) REVERT: A 1926 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7183 (mt-10) REVERT: A 1937 ARG cc_start: 0.8422 (mtt-85) cc_final: 0.7838 (ttm-80) REVERT: A 1961 THR cc_start: 0.7939 (m) cc_final: 0.7252 (m) REVERT: A 2008 GLU cc_start: 0.7233 (pp20) cc_final: 0.6800 (pt0) REVERT: B 1885 LEU cc_start: 0.8976 (tp) cc_final: 0.8503 (pp) REVERT: B 1910 ILE cc_start: 0.8028 (mm) cc_final: 0.7069 (mm) REVERT: B 1919 GLU cc_start: 0.8499 (mp0) cc_final: 0.7830 (mp0) REVERT: B 1925 LEU cc_start: 0.8694 (mt) cc_final: 0.8048 (pp) REVERT: B 1928 MET cc_start: 0.8559 (mmt) cc_final: 0.7875 (mmt) REVERT: B 1932 LEU cc_start: 0.8836 (mt) cc_final: 0.8634 (mt) REVERT: B 1947 ARG cc_start: 0.9108 (ptm-80) cc_final: 0.8860 (mtt180) REVERT: B 1956 LYS cc_start: 0.8737 (mttt) cc_final: 0.8007 (tptm) REVERT: B 1967 MET cc_start: 0.8773 (mmt) cc_final: 0.7799 (mmt) REVERT: B 1986 LEU cc_start: 0.8982 (mt) cc_final: 0.8778 (mp) REVERT: B 2010 MET cc_start: 0.8556 (mmm) cc_final: 0.7601 (tmm) REVERT: B 2028 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7889 (mmtt) REVERT: B 2056 ASP cc_start: 0.8456 (t0) cc_final: 0.8173 (t0) REVERT: B 2083 PHE cc_start: 0.8185 (m-10) cc_final: 0.7644 (m-80) REVERT: B 2205 LEU cc_start: 0.7849 (tt) cc_final: 0.7421 (pt) REVERT: B 2209 THR cc_start: 0.8635 (m) cc_final: 0.8326 (m) REVERT: B 2210 GLU cc_start: 0.8388 (tt0) cc_final: 0.8134 (pt0) REVERT: B 2218 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6737 (mp10) REVERT: B 2291 HIS cc_start: 0.8566 (m-70) cc_final: 0.8219 (m170) REVERT: B 2303 GLN cc_start: 0.8128 (tt0) cc_final: 0.7649 (tm-30) REVERT: B 2306 GLU cc_start: 0.5555 (mp0) cc_final: 0.4940 (mp0) REVERT: B 2333 LYS cc_start: 0.7220 (mttt) cc_final: 0.6447 (mptt) REVERT: B 2340 MET cc_start: 0.7124 (mmm) cc_final: 0.6380 (mmm) REVERT: B 2347 GLU cc_start: 0.8080 (tp30) cc_final: 0.6801 (tt0) REVERT: B 2359 LEU cc_start: 0.9215 (mt) cc_final: 0.8705 (mt) REVERT: B 2373 LEU cc_start: 0.9004 (mt) cc_final: 0.8798 (mt) REVERT: B 2401 LYS cc_start: 0.8195 (tttt) cc_final: 0.7944 (mmmm) REVERT: B 2417 TYR cc_start: 0.8828 (m-80) cc_final: 0.8563 (m-10) REVERT: B 2418 LEU cc_start: 0.9138 (mt) cc_final: 0.8898 (mt) REVERT: B 2616 ARG cc_start: 0.6706 (ttt180) cc_final: 0.5976 (tmt170) REVERT: B 2685 PHE cc_start: 0.8735 (p90) cc_final: 0.8388 (p90) outliers start: 1 outliers final: 0 residues processed: 444 average time/residue: 0.0984 time to fit residues: 67.9150 Evaluate side-chains 385 residues out of total 1571 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 124 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 171 optimal weight: 0.2980 chunk 149 optimal weight: 0.6980 chunk 76 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN A 222 ASN A 501 HIS ** 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** B2107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099652 restraints weight = 34400.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.103512 restraints weight = 22359.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106292 restraints weight = 15661.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.108371 restraints weight = 11627.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.109863 restraints weight = 9058.823| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.6982 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= 0.146 Angle : 0.669 12.626 19094 Z= 0.341 Chirality : 0.040 0.184 2298 Planarity : 0.004 0.045 2351 Dihedral : 4.593 22.130 1819 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.06 % Allowed : 0.25 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.20), residues: 1683 helix: 1.61 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : 0.00 (0.39), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.034 0.002 TYR A 408 PHE 0.042 0.002 PHE A1107 TRP 0.038 0.002 TRP B1976 HIS 0.010 0.001 HIS B2051 Details of bonding type rmsd covalent geometry : bond 0.00325 (14120) covalent geometry : angle 0.66873 (19094) hydrogen bonds : bond 0.04097 ( 1042) hydrogen bonds : angle 4.42003 ( 3105) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2308.84 seconds wall clock time: 40 minutes 56.26 seconds (2456.26 seconds total)