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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