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Looking at the plots, the main thing I noticed is that the quantity CALRMSTRANS seems to be different in most tests, AG, Muons, Bkg.
I dowloaded the merit files for the allGamma, and compared the merit variable called Cal1TransRms... and they are identical, see plot attached.
I am a bit curious, where does the CALRMSTRANS variable of the systests come from ?
Is that the trans rms of each cluster (not just the first one) before
normalization by the energy, as the units suggests ?
...and why would it be different ?

For other variables in the BackGndMixDC2, the differences seem really small to me, small enough to be ignored... unless someone is willing to dig into the code obviously.

Cheers,
Johan