Hi This may be totally out of date, but in the past the PDB used Refmac to calculate the validation maps, and this caused RSZ problems for certain structures refined with phenix (certain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 ZjQcmQRYFpfptBannerStart This Message Is From a New External Sender You have not previously corresponded with this sender. Please exercise caution when opening links or attachments included in this message. ZjQcmQRYFpfptBannerEnd 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] ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [jiscmail.ac.uk]<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DEB2xdhGk8K7R9q6NQrEtVcZjK7T4ah3OPKcZgBYyU2TibpgOHqilLVafXVtRJZlPMsOiyZ7VH9lYmgKrB_EkJXebvIDqSX_yA$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 [jiscmail.ac.uk]<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!PDiH4ENfjr2_Jw!DEB2xdhGk8K7R9q6NQrEtVcZjK7T4ah3OPKcZgBYyU2TibpgOHqilLVafXVtRJZlPMsOiyZ7VH9lYmgKrB_EkJXebvIDqSX_yA$> ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
