[phenixbb] geometry_minimization makes molprobity score worse

James Holton jmholton at lbl.gov
Wed Jul 7 20:58:11 PDT 2021

Greetings all, and I hope this little observation helps improve things 

I did not expect this result, but there it is. My MolProbity score goes 
from 0.7 to 1.9 after a run of phenix.geometry_minimization

I started with an AMBER-minimized model (based on 1aho), and that got me 
my best MolProbity score so far (0.7). But, even with hydrogens and 
waters removed the geometry_minimization run increases the clashscore 
from 0 to 3.1 and Ramachandran favored drops from 98% to 88% with one 
residue reaching the outlier level.

Just for comparison, with refmac5 in "refi type ideal" mode I see the 
MolProbity rise to 1.13, but Clashscore remains zero, some Ramas go from 
favored to allowed, but none rise to the level of outliers.

Files and logs here:

I suspect this might have something to do with library values for 
main-chain bonds and angles?  They do seem to vary between programs. 
Phenix having the shortest CA-CA distance by up to 0.08 A. After running 
thorough minimization on a poly-A peptide I get:
bond   amber   refmac  phenix  shelxl Stryer
  C-N   1.330   1.339   1.331   1.325     1.32
  N-CA  1.462   1.482   1.455   1.454     1.47
CA-C   1.542   1.534   1.521   1.546     1.53
CA-CA  3.862   3.874   3.794   3.854

So, which one is "right" ?



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