[phenixbb] Re: phenixbb Digest, Vol 232, Issue 13 (out of office)

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13.4.25 20:51 >>>

Send phenixbb mailing list submissions to [email protected] To subscribe or unsubscribe via email, send a message with subject or body 'help' to [email protected] You can reach the person managing the list at [email protected] When replying, please edit your Subject line so it is more specific than "Re: Contents of phenixbb digest..." Today's Topics: 1. Re: Question about geometry outliers in RealSpaceRefine (Pavel Afonine) 2. Re: DEN restraints and ECHT disorder models (Tom Burnley - STFC UKRI) ---------------------------------------------------------------------- Message: 1 Date: Fri, 11 Apr 2025 11:47:11 -0700 From: Pavel Afonine Subject: [phenixbb] Re: Question about geometry outliers in RealSpaceRefine To: Kevin M Jude , "[email protected]" Message-ID: <[email protected]> Content-Type: multipart/alternative; boundary="------------YozFq5Oyt0xmhpmEfOqMdIo0" Hi Kevin, could you please send me the file (off list)? Thanks! Pavel On 4/11/25 09:34, Kevin M Jude wrote:

After a recent RealSpaceRefine run, the Geometry Restraints tab in the gui reports that I have two bond angle outliers > 4 sigma, but only lists one of them:

D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2

So I check the logfile for the job and see:

Bond angle restraints: 12582

Sorted by residual:

angle pdb=" N MET D 180 "

pdb=" CA MET D 180 "

pdb=" CB MET D 180 "

ideal model delta sigma weight residual

114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01

angle pdb=" CA LEU B 79 "

pdb=" CB LEU B 79 "

pdb=" CG LEU B 79 "

ideal model delta sigma weight residual

116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01

angle pdb=" C ASP B 333 "

pdb=" N SER B 334 "

pdb=" CA SER B 334 "

ideal model delta sigma weight residual

122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00

angle pdb=" C GLN D 167 "

pdb=" N ARG D 168 "

pdb=" CA ARG D 168 "

ideal model delta sigma weight residual

121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00

angle pdb=" C ASP B 163 "

pdb=" N THR B 164 "

pdb=" CA THR B 164 "

ideal model delta sigma weight residual

123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00

ValidationCryoEM returns identical results except the gui says only one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only the outlier at //B/Leu79/, which does have the largest sigma in the above log.

My questions are:

1. Why does the gui report two 4-sigma outliers but only show one? 2. Why do the sigmas in the log file not correspond to the sigmas in the gui?

Best wishes

Kevin

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Kevin Jude, PhD

Structural Biology Research Specialist, Garcia Lab

Howard Hughes Medical Institute

Stanford University School of Medicine

Beckman B177, 279 Campus Drive, Stanford CA 94305

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