I was running refinement from an mtz file from sigmaa in ccp4 with an appropriate FreeR flag designated in the MTZ file. phenix.refine worked fine and seemed to exclude the test reflections, but I wanted to know what these commands do.

Don't! :-)

r_free_flags { file_name = "S19_sigmaa1.mtz" label = "FreeR_flag" test_flag_value = 0 --> don't know what this means? disable_suitability_test = False --> implications of this?

phenix.refine is designed to figure everything out automatically. You will have to specify file_name and label only if you have multiple R-free-flag arrays in the reflection files you give to phenix.refine, which is very unusual. phenix.refine does some sanity checks to determine if arrays that "look like" R-free-flag arrays are actually suitable for refinement, and reject them if "it doesn't think so". It will then tell you that you can override the sanity checks by setting disable_suitability_test to True. Again, this is very unusual. The test_flag_value could potentially be important. phenix.refine analyses the putative R-free-flag array(s) to guess if they came from CNS, where 0 usually means work set, 1 free set, or CCP4, which mostly uses values from 0 to 19, 0 is the default free set in REFMAC. Therefore, roughly, if phenix.refine "thinks" it is a CNS R-free-flag array it assigns test_flag_value=1, or 0 if it "thinks" it is a CCP4 array. Only if you used REFMAC before for refinement, and only if you manually instructed REFMAC to use a value different from 0 for the free set, will you have to manually tell phenix.refine about it, e.g. via r_free_flags.test_flag_value=19. If you are interested in more details, inspect the script iotbx/iotbx/reflection_file_utils.py, which does all the guesswork. Look for "get_r_free_flags_scores".