Thank you, Pavel. I am not clear about "model_based_outliers"; I searched phenix.refine documentation but did not find anything. Is it based on my structure model? I will look at the paper you suggested. By the way, "main.outliers_rejection=False" can also keep those model_based_outliers? http://www.phenix-online.org/documentation/refinement.htm did not mention this type of outliers: outliers_rejection= True Remove basic wilson outliers , extreme wilson outliers , and beamstop shadow outliers Thanks Rongjin = = = = = = = = On 2010-12-08 15:28:59 You wrote = = = = = = = = Rongjin, outliers detection and rejection was inspired by this paper R.Read, Acta Cryst. (1999). D55, 1759-1764. and the paper by R.Agarwal's (197?/198?) mentions this too. You can always turn this off using "main.outliers_rejection=False" if you believe it's necessary. It's probably the quality of your data that causes the amount of outliers you quote. Pavel. PS> FYI: I got your email sent off-list and I always get the emails sent to phenixbb, so there is no need to duplicate them. On 12/8/10 11:45 AM, [email protected] wrote: Hi All I have a question regarding reflection outliers detection in phenix.refine: in my input reflection file, there are 24432 reflections, but only 22769 of them were used in refinement. I checked the log file and saw 1663 outliers. (below if from the log) basic_wilson_outliers = 14 extreme_wilson_outliers = 18 beamstop_shadow_outliers = 0 model_based_outliers = 1657 total = 1663 What is the "model_based_outliers"? What causes so many reflections rejected and not used in the refinement? Thanks Rongjin _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb