Dear CCP4 bulletin board
I am trying to solve structure with molecular-replacement. I have got good solution using Phaser. The refined structure fits well to electron density
and appears reasonable in terms of geometry, ramachandran, rotamers
etc. The problem I experience is that there are very many clashes and
MolProbity check gives a score of 34th percentile and when I refine, the
Rfree does not go below 30% for under 2A resolution. I tried
reprocessing in different space group (from P212121 to P21) and also got
a MR solution. In P21 number of clashes was reduced but still very high
and Rfree was slightly reduced but the gap between Rfree and R was still
high. I am not sure what this means and how I can sort out the problem
of so many clashes? Any suggestions would be helpful and
appreciated
regards
Careina