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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