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anneal.inp CNS falling R's but odd geometry

Kim Peaslee kawp at Dartmouth.EDU
Mon Apr 25 12:01:53 EST 2005

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 
Thank you so much,


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