HI,
I have a few questions about the use of anneal.inp from CNS. I am
refining a model placed by MR which accounts for 35% of the total
scattering and have resultion limit of 3A. I have 4 molecules in the
assymetric unit and am using strict NCS. When I run anneal.inp, I have
a nice drop in both R and Rfree (4+%) but when I load up the resultant
pdb in O to check it out, I notice that some helices are a bit tweaked.
If I run model_stats.inp I find that there are a few improper bond
angles and such. My question is this, can I trust the dropping R as to
my progress and is the 'bad' geometry just an artifact of refining
against an average structure as with strict NCS? Should I somehow
tighten up the rmsd's allowed in anneal and if so how do I do that? If
I am not to trust the falling R's what is my clue that something is not
right?
Thank you so much,
Kim
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