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Using the "master mtz file" (as you call it) is the safe thing to do. If you use the previous refmac output file, you have to careful the right structure factor columns are selected. They should be non-modified by the previous refmac run, otherwise you are refining both the data and the model. Mark J van Raaij Lab 20B Dpto de Estructura de Macromoleculas Centro Nacional de Biotecnologia - CSIC c/Darwin 3 E-28049 Madrid, Spain tel. (+34) 91 585 4616 http://www.cnb.csic.es/~mjvanraaij On 1 Jul 2014, at 14:35, Dilip Badjugar wrote: > Dear CCP4bb users and Refinement experts, > > As input for (n+1)st run of refmac, should I use as input reflection file the output produced by refmac in the nth run? Currently I have been giving the master mtz file as input for all runs. > > I would appreciate the clarification from the community. > > Thanking you > > Dilip Badgujar > Graduate Student > ACTREC > > >