I realize now I left out one key piece of information but I figured you probably assumed it anyways, that is that the water going in was ph'd at 7, and came out the soil at 5.0. But anyways yes 5.0 is low, when running water through the soil you can test the ph before and after to look at how it reacts with the soil. If it goes in at 7 and comes out at 5, that means your soil ph is far too low at 5 or perhaps even lower. Also yes, calcium does have something to do with it.

Do you grow in soil or hydro?