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
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