Hi Kevin,

could you please send me the file (off list)?

Thanks!
Pavel

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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