Merge pull request #1142 from RosettaCommons/dimaio/refine_apix
Checking in code that allows refinement of voxel spacing in electron density maps.
There are several integration test failures; all are expected as they either: a) refine with density (normalization of density values has changed a bit), b) report all scoreterms (one was deleted), or c) small numeric changes which are related to removing a scoreterm.