  We report improved frequency ratio measurement with $^{87}$Sr and $^{171}$Yb
optical lattice clocks at the National Metrology Institute of Japan (NMIJ). The
$^{87}$Sr optical lattice clock is enhanced with several major modifications
and is re-evaluated with a reduced uncertainty of $1.1\times10^{-16}$. We
employed a $^{171}$Yb optical lattice clock with an uncertainty of
$4\times10^{-16}$ that was developed for contributing to International Atomic
Time (TAI). The measurement result is $\nu_{\mathrm{Yb}}/\nu_{\mathrm{Sr}}$ =
1.207 507 039 343 338 58(49)$_{\mathrm{sys}}$(6)$_{\mathrm{stat}}$ with a
fractional uncertainty of $4.1\times10^{-16}$, which is 3.4 times smaller than
our previous measurement result.
