Hi am using the same exact mtz data file from CCP4 uniquefy for two  refinements in phenix.
I did one round of refinement in phenix 1.3 and then used the output pdb of that refinement and input into the next round of refinement . Only I switched versions to phenix version 1.4.

Most other things weere the same including the resolution cutoff used and the input mtz.
But phenix tells me that the md5checksums dont match.

i am very sure its the same input mtz and identical data resolution ( both cases  specifying refinement.input.xray_data.high_resolution=3.0)

Could this message of mismatched checksums be an error due to chaging versions midtsream . I certainly dont want to be trampling on my Rfree reflections but apart from copying files to a new directory for the next round and changing phenix versions I have changed little else

Thanks for your help in advance

hari