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Hi Graeme, in a data set with just below 800,000 independent reflections I use 1 % for freeR which is still impressive 8,000. xia2 would have assigned 40,000 for freeR at 5 %. I think this is way too much. Often we collect many data sets of the same project to find the better data. We do use default xia2 FreeR assignments at this stage, and after locating the best data set we can not go back and reassign FreeR, as the new set will be biased towards the model. Referees/editors however query cases when over 5,000 reflections were used for cross-validation. Misha ________________________________________ From: CCP4 bulletin board [[log in to unmask]] on behalf of Pavel Afonine [[log in to unmask]] Sent: Tuesday, June 2, 2015 3:10 PM To: [log in to unmask] Subject: Re: [ccp4bb] How many is too many free reflections? Hi Graeme, free reflections are used for two purposes, at least: cross-validation (calculation of Rfree) and ML parameters estimation (sigmaa or alpha/beta). For the latter it is important that each relatively thin resolution bin (sufficiently thin so that alpha/beta can be considered constants in it) receives no less than 50 reflections absolute min; in Phenix we found that ~150 per bin is sufficient and this is what's used by default. Pavel On Tue, Jun 2, 2015 at 3:26 AM, Graeme Winter <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Folks Had a vague comment handed my way that "xia2 assigns too many free reflections" - I have a feeling that by default it makes a free set of 5% which was OK back in the day (like I/sig(I) = 2 was OK) but maybe seems excessive now. This was particularly in the case of high resolution data where you have a lot of reflections, so 5% could be several thousand which would be more than you need to just check Rfree seems OK. Since I really don't know what is the right # reflections to assign to a free set thought I would ask here - what do you think? Essentially I need to assign a minimum %age or minimum # - the lower of the two presumably? Any comments welcome! Thanks & best wishes Graeme