I have a few questions about phenix.refine and I couldn't find the answer in the manual.

1)  How to generate the ligand library in phenix.refine?

2) Can phenix.refine calculate an OMIT COMPOSITE map?

3) When I used ML as the target, I couldn't find the output of LLG or similar number in the log file.  How do I know the refinement is converged?

Thanks.

Jianghai