[phenixbb] Clashes problem

[Simon Kolstoe]

Dear Phenix community,

I am using phenix.refine version 2007_08_18_1856 to refine a 2.65A  
structure (with individual_sites, group_adp, TLS & NCS,  
wxc_scale=0.1). After refinement I am running the pdb file through the  
Molprobity server. Molprobity gives a clash score of 33.78 indicating  
the number of steric clashes (within 0.4A) per 1000 atoms.

I am slightly concerned that a refinement program seems happy to allow  
such clashes. Is this a problem with the version of phenix.refine I am  
running, or is there a more obvious explanation that I have missed?

Thanks,

Simon