Question about geometry outliers in RealSpaceRefine
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 -- 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
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
--
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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participants (2)
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Kevin M Jude -
Pavel Afonine