Hi

This may be totally out of date,  but in the past the PDB used Refmac  to 
calculate the validation maps, and this caused RSZ problems for certain 
structures refined with phenix (certain resolution ranges use of TLS If I 
remember rightly).
I think the RSZ outlier score can also be affected by an atypical distribution 
between strongly resolved regions and weaker more flexible regions.

I would just inspect your outliers (starting with a selection with the highest 
Z score) and use some bias-detection techniques to see if this high score is 
really reflective of errors in your model building.  Composite omit maps are 
good for this,  but you can also do quick things like setting residues to 
occupancy of 0 and refining.

Also, any discrepancies between the validation maps calculated by the PDB, and 
your own refinements will be minimized if your data is strong.
Perhaps have a look at paired refinement to see if your data needs truncating a 
little, I think it can be run easily through PDB REDO.

Best wishes

Matthew.

________________________________
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Pavel Afonine 
<pafon...@gmail.com>
Sent: 29 January 2025 16:18
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] Reduces the RSRZ outliers in the wwPDB validation report

Hi, It’s hard to comment on this without knowing the resolution. A general rule 
of thumb is: an outlier is a statistical outlier, meaning it is not necessarily 
wrong but unlikely. If you can justify it based on the experimental data, just 
leave
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Hi,

It’s hard to comment on this without knowing the resolution. A general rule of 
thumb is: an outlier is a statistical outlier, meaning it is not necessarily 
wrong but unlikely. If you can justify it based on the experimental data, just 
leave it alone.

This, in turn, means that at low resolution, it’s hard to justify outliers 
based on the data, so your goal should be to have none. At high resolution, 
however, you do expect valid outliers.

Pavel

On Wed, Jan 29, 2025 at 7:43 AM 白雪慧 
<zb20193020...@cau.edu.cn<mailto:zb20193020...@cau.edu.cn>> wrote:

  Happy New Year, everyone.

  Recently, I have encountered some problems when submitting PDB, and I have 
seen some discussions about these problems before.

Meanwhile, I still want to ask how to reduce the RSRZ outliers in the wwPDB 
validation report, is there any good way to reduce the RSRZ outliers

in the WWPDB Validation report? I enclose my alidation report.

[cid:ii_194b2d70574cb971f161]

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