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 [email protected]
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
participants (2)
-
Michael Thompson -
Pavel Afonine