[phenixbb] inconsistent Rwork/Rfree in outputs

Michael Thompson miket at chem.ucla.edu
Tue Jul 9 10:07:27 PDT 2013


Hello All,

I am getting an output from phenix.refine that is somewhat confusing to me. I have a log file that seems to be reporting inconsistent values for the final Rwork and Rfree. The last line of my log file says:

Final R-work = 0.1815, R-free = 0.1912

However, when I check the pdb file from phenix.refine, I see:

REMARK Final: r_work = 0.1799 r_free = 0.1952 bonds = 0.012 angles = 1.315

In the log file, I get the following table, which seems to agree with what is in the pdb file.

 R-factors, x-ray target values and norm of gradient of x-ray target
 stage     r-work r-free  xray_target_w  xray_target_t
   0    :  0.1971 0.1916   1.408780e-01   1.965297e-01
   1_bss:  0.1971 0.1916   1.508155e-01   2.122150e-01
   1_ohs:  0.1971 0.1916   1.447084e-01   2.026856e-01
   1_xyz:  0.1928 0.2001   1.348543e-01   2.162596e-01
   1_adp:  0.1929 0.2134   1.006068e-01   1.652532e-01
   1_occ:  0.1928 0.2127   9.708801e-02   1.642701e-01
   2_bss:  0.1784 0.1978   1.001979e-01   1.536656e-01
   2_ohs:  0.1786 0.1982   1.146147e-01   1.876601e-01
   2_xyz:  0.1777 0.1959   1.187570e-01   1.899659e-01
   2_adp:  0.1952 0.2001   1.109064e-01   1.588435e-01
   2_occ:  0.1952 0.1995   1.059382e-01   1.580417e-01
   3_bss:  0.1831 0.1888   1.066004e-01   1.508888e-01
   3_ohs:  0.1833 0.1890   1.217008e-01   1.855605e-01
   3_xyz:  0.1824 0.1897   1.256200e-01   1.855714e-01
   3_adp:  0.1876 0.2039   1.027854e-01   1.533022e-01
   3_occ:  0.1877 0.2042   9.739524e-02   1.525993e-01
   4_bss:  0.1770 0.1931   9.830779e-02   1.515598e-01
   4_ohs:  0.1772 0.1933   1.132096e-01   1.824877e-01
   4_xyz:  0.1775 0.1933   1.179076e-01   1.860704e-01
   4_adp:  0.1911 0.2005   1.074584e-01   1.546149e-01
   4_occ:  0.1909 0.1997   1.023003e-01   1.530269e-01
   5_bss:  0.1805 0.1895   1.034638e-01   1.506407e-01
   5_ohs:  0.1807 0.1895   1.185810e-01   1.828381e-01
   5_xyz:  0.1803 0.1899   1.244219e-01   1.801964e-01
   5_adp:  0.1893 0.2019   1.072974e-01   1.503622e-01
   5_occ:  0.1893 0.2023   1.016701e-01   1.492730e-01
   6_bss:  0.1792 0.1915   1.021896e-01   1.490341e-01
   6_ohs:  0.1794 0.1915   1.174694e-01   1.798680e-01
   6_xyz:  0.1804 0.1926   1.224254e-01   1.830383e-01
   6_adp:  0.1952 0.2015   1.118187e-01   1.549205e-01
   6_occ:  0.1950 0.2017   1.063759e-01   1.538692e-01
   7_bss:  0.1842 0.1922   1.076805e-01   1.529198e-01
   7_ohs:  0.1845 0.1918   1.227818e-01   1.857086e-01
   7_xyz:  0.1846 0.1917   1.292627e-01   1.856928e-01
   7_adp:  0.1885 0.2042   1.071531e-01   1.532154e-01
   7_occ:  0.1885 0.2044   1.012764e-01   1.524448e-01
   7_bss:  0.1797 0.1952   1.353649e-01   1.556126e-01
   7_ohs:  0.1799 0.1952   1.353649e-01   1.556126e-01

I'm wondering why this last line of the log file isn't consistent with the other values that are being reported for R/Rfree? Which numbers should I believe?

Thanks,

Mike







-- 
Michael C. Thompson

Graduate Student

Biochemistry & Molecular Biology Division

Department of Chemistry & Biochemistry

University of California, Los Angeles

miket at chem.ucla.edu


More information about the phenixbb mailing list