[phenixbb] reflection outliers detection in phenix.refine

[Pavel Afonine]

  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, guanrj at foxmail.com 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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