Thanks so much for the suggestions. They are really helpful! A few questions relative to Phenix. Is there a way to check with Phenix the thin resolution shells? I created Free Rs in Phenix using the thin resolution shells options but removed the 2000 limit and instead used 5%. Maybe I over-did it relative to your reply. Just wondering how to check each of these thin shells. Alternatively, does Phenix ensure one has an adequate number of test reflections in each "thin shell" if this option is set? If so, what should I used for the maximum number of reflections and/or %?

There isn't a good way to check the shells in the GUI - but all of the pieces are there, and I've been meaning to add some utilities for examining reflection files anyway. For now, on the command line, run this:

iotbx.r_free_flags_accumulation data.mtz

and it will print out something like this:

Number of work/free reflections by resolution:

work free %free

bin 1: 135.8135 - 4.3073 [7861/7861] 7663 198 2.5%

bin 2: 4.3073 - 3.4187 [7682/7682] 7484 198 2.6%

bin 3: 3.4187 - 2.9866 [7645/7645] 7444 201 2.6%

bin 4: 2.9866 - 2.7135 [7605/7605] 7406 199 2.6%

bin 5: 2.7135 - 2.5190 [7593/7593] 7395 198 2.6%

bin 6: 2.5190 - 2.3704 [7618/7618] 7416 202 2.7%

bin 7: 2.3704 - 2.2517 [7535/7535] 7337 198 2.6%

bin 8: 2.2517 - 2.1537 [7573/7573] 7374 199 2.6%

bin 9: 2.1537 - 2.0708 [7556/7556] 7354 202 2.7%

bin 10: 2.0708 - 1.9993 [7547/7547] 7348 199 2.6%

overall 74221 1994 2.6%

This is a real example, using the default settings in the reflection file editor (20 thin shells for the test set). It looks much better than what I had originally done with this dataset five years ago using a different program, where the last shell had only 0.2% of reflections flagged. However, the code that does this isn't particularly sophisticated, so I would recommend double-checking the output for your data. I don't think you're going to do any harm by sticking with 5% and removing the absolute limit.

-Nat