[phenixbb] Weighting in phenix.real_space_refine

Oliver Clarke olibclarke at gmail.com
Tue Sep 13 08:12:14 PDT 2016

Hi Pavel,
So how do I interpret the weights in the output? For example, with a structure I am refining at the moment, I have the following:

"Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 30 optimal weight:   10.0000
   chunk 16 optimal weight:    9.9990
   chunk 10 optimal weight:    9.9990
   chunk 20 optimal weight:    9.9990
   chunk 16 optimal weight:    9.9990
   chunk 31 optimal weight:    0.0040
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:   10.0000
   chunk 23 optimal weight:    0.8980
   overall best weight:    9.4279”

Is low tight and high loose, as for phenix.refine? And are there any prospects for the future of varying weights across the structure? Often in EM we will have  large regions at good resolution, say <4Å, and other regions which while well defined are at lower resolution, say 6Å - applying the same weights to both regions doesn’t seem ideal.

Would your suggested strategy at the moment be to split the structure domain-by-domain, refine domains separately and then recombine?


(Also, there seems to be a very minor bug in the output model stats - “Dist moved from start” changes, but “Dist moved from previous” is always 0.000.

Model statistics:
   Map CC (whole unit cell):  0.662
   Map CC (around atoms):     0.773
   rmsd (bonds):              0.01
   rmsd (angles):             1.04
   Dist. moved from start:    0.060
   Dist. moved from previous: 0.000
   All-atom clashscore        4.47
   Ramachandran plot:
     outliers:                0.27  %
     allowed:                 12.24 %
     favored:                 87.49 %
   Rotamer outliers:          0.54 %
   C-beta deviations:         4)

> On Sep 13, 2016, at 11:01 AM, Pavel Afonine <pafonine at lbl.gov> wrote:
> Hi Oliver,
>> So just to be sure - the average weight obtained with the randomly selected fragments is used for the entire model?
> correct.
> Pavel

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