I'm unsure what you're trying here. Relief is the amount of forward bow, as in, the direction the headstock is pulled with string tension applied, relative to the straight line of the string. If you have too much relief, surely you need to apply back-bow?
Either way, as you're trying to manipulate the wood into a shape here, make sure you do it with the truss rod fully slack. The truss rod is (usually) a tool to counteract the pull of the strings. If there's no string tension, there shouldn't be any truss rod tension either. The nut shouldn't be putting any tension into the rod so it shouldn't be making contact with anything.