"Nagura" translates to "Correcting" in Japanese and hence we have a "correcting stone". A Nagura stone is effectively a smaller waterstone, used to condition medium to fine grit waterstones during use.
Using a Nagura stone wears away hard particles or contamination in the waterstone, such as metal from sharpening. It will also help remove high spots in the process. However, it is primarily used to create a slurry of cutting sediment, particularly in finer grit stones, that improves performance in sharpening and achieves a highly polished edge.
A very light rubbing is enough, as the honing paste should not be too thick.