Consider including more information with the --verbose flag

[dennisbrookner]

Currently, the --verbose flag results in the phenix.refine (and SCALEIT) logs being printed out to the terminal. It has been suggested that this flag should also provide additional useful debugging information from the actual python portion of the algorithm. I think this would be nice to implement at some point; it would require a lot of small code changes and some careful thinking about what should be included.