Juliana,
I think if you compare otherwise equivalent refinement runs in phenix.refine
with
refinement.input.xray_data.outliers_rejection=True (the default)
and
refinement.input.xray_data.outliers_rejection=False
then this will tell you if there's any meaningful difference in the refinement
statistics (or map). This doesn't mean you have to use phenix.refine on your
structure beyond that point, just that this is likely the cleanest comparison
that I can think of.
Phil Jeffrey
Princeton
________________________________
From: CCP4 bulletin board [CCP4BB@JISCMAIL.AC.UK] on behalf of Juliana Ferreira
de Oliveira [juliana.olive...@lnbio.cnpem.br]
Sent: Wednesday, March 29, 2017 9:54 AM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Large number of outliers in the dataset
Hello,
I have one dataset at 2.3 Å (probably it can be better, I/σ = 2.1 and CC1/2 =
0.779, the summary data is below), but when I perform Xtriage analysis it says
that “There are a large number of outliers in the data”. The space group is
P212121. When I refine the MR solution the Rfree stops around 30% and it
doesn´t decrease (in fact if I continue refining it starts to increase).
The Wilson plot graph is not fitting very well between 2.3 and 2.6 Å:
[cid:image001.jpg@01D2A87A.D704ACD0]
So I decided to cut the data at 2.6A and Xtriage analysis doesn’t notify about
outliers anymore. I could refine the MR solution very well, the final Rwork is
0.2427 and Rfree = 0.2730 and validation on Phenix results in a good structure.
I run Zanuda to confirm the space group and it says that the space group
assignment seems to be correct.
Do you think that I can improve my structure and solve it at 2.3 Å or better?
Or I can finish it with 2.6 Å? To publish at 2.6 Å I need to justify the
resolution cut, right? What should I say?
Thank you for your help!
Regards,
Juliana
Summary data:
Overall InnerShell OuterShell
Low resolution limit 51.51 51.51
2.42
High resolution limit 2.30 7.27
2.30
Rmerge 0.147 0.054
0.487
Rmerge in top intensity bin 0.080 -
-
Rmeas (within I+/I-) 0.155 0.057
0.516
Rmeas (all I+ & I-) 0.155 0.057
0.516
Rpim (within I+/I-) 0.048 0.017
0.164
Rpim (all I+ & I-) 0.048 0.017
0.164
Fractional partial bias -0.006 -0.003
0.146
Total number of observations 83988 2907
11885
Total number unique 8145 307
1167
Mean((I)/sd(I)) 9.3 23.9
2.1
Mn(I) half-set correlation CC(1/2) 0.991 0.998
0.779
Completeness 99.9 99.5
100.0
Multiplicity 10.3 9.5
10.2
Average unit cell: 37.57 51.51 88.75 90.00 90.00 90.00
Space group: P212121
Average mosaicity: 1.90
Juliana Ferreira de Oliveira
Brazilian Laboratory of Biosciences - LNBio
Brazilian Center for Research in Energy and Materials - CNPEM
Campinas-SP, Brazil
