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