1, Processing data with XDS (or HKL2000 for some of the datasets)
2,Molecule replacement with phaser.
3,Check and modify the structure residue by residue with COOT,
4,phenix.refine with the following command line:

Step 3 is probably redundant - you can usually go straight to refinement, and afterwards the maps will be much clearer and easier to correct manually. Add the rigid_body strategy if you're worried about the overall orientation of domains, and fix_rotamers=True to correct individual residues.

-Nat