Use this guide to upgrade the RAM in your 2009 model Mac Pro (quad-core) to a maximum of 48GB (16GB x3). Note, although this machine has 4 memory sockets, it can't utilise any more than 48GB of RAM.
According to this post on the macrumors forum, MacPro4,1 models with a 'W' or 'E' series CPU can only utilise up to 48GB on quad-core models (single cpu) and 96GB on 8-core models (dual cpu). Those with an 'X' series CPU, which is the 8-core 2.66GHz or 8-core 2.93GHz models, can utilise up to 128GB of RAM. (16GB x8).
If you try installing 64GB (16GB x4) then the memory in the fourth socket won't be recognised.