[phenixbb] inconsistent Rwork/Rfree in outputs

[Pavel Afonine]

Hi Michael,

I just tried myself and I'm getting consistent numbers. Can you send me 
all inputs necessary to reproduce this (data, model, cif for ligands if 
any, and .eff file)? Obviously, final numbers must be consistent no 
matter where you get them from (end of log file, or PDB file header, etc).

Pavel

On 7/9/13 10:07 AM, Michael Thompson wrote:
> 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
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