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[ccp4bb]: Jumping between refinement programs..

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Dear all,
Would anyone have suggestions about what is going on here:

I have bene refining my model with CNS, but as the unit cell is 
very large i thouhgt i might use ARP to add the rest of the waters
--then i thought refine it a bit more with CNS, the R-factors 
at the at the beginning of the CNS conjugate gradient 
minimisation (with max. likelyhood target) very OK 
- better than i expected and better than what ARP/Refmac
statistics gave me  --but the refinement  allways starts
going upwards 'R-factorwise' in CNS
--so the initial R-free is 2 % lower than the end value no matter 
what --Any suggestions for an explanations other than that its  a bad 
idea to jump between refinement programs..??
've tried altering the ncs-restrians and the xray/geometry 

I am just puzzled with the fact that the inital R-factors are allways 
the lowest!! Based only on R-factors (and geometry) one could take 
the model after ARP and say thats a done model -- its just that when 
one tries to refine it it tha doeasnt work. I have never had this 
kind of a problem with using diffrent refinement programs -- but it 
raises interestinn questions..

Thanks for comments,
Tommi Kajander
Institute for biotechnology
Structural biology/cultivator building
P.O. Box 56
00014 University of Helsinki