Hi Dale,
1) Why you specify reflection MTZ file twice in phenix.refine script?
I put the mtz in twice because if I put it in once phenix.refine complains that I have no free R flags. It seems to want one file with the amplitudes and another with the flags. Since I have both in the same file I put that file on the line twice and phenix.refine finds everything it needs.
phenix.refine looks for free-R flags in your main data file (1M50-2.mtz). Optionally you can provide a separate file containing free-R flags (I have to write about this in the manual). However, if your 1M50-2.mtz contains free-R flags then you don't need to give it twice. So clearly something is wrong at this step and we need to find out what is wrong before doing anything else. Could you send the result of the command "phenix.mtz.dump 1M50-2.mtz" to see what's inside of your data file? Or I can debug it myself if you send me the data and model.
If the MD5 hash of the test set depends on the resolution then certainly I could be in trouble.
No. It must always use the original files before any processing.
Does the resolution limit affect the MD5 hash of the test set?
No. If it does then it is a very bad bug. I will play with this myself later tonight.
3) Does this work:
(...)
I'll try these but it will take a bit of time.
Don't run it until completion. Just make sure it passed through the processing step. Pavel.