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Hi Jimson,
The foll. are not clear to me from your description - as what stage of
refinement you refer to (initial, later?), what is the resolution? what
% of data is allotted towards your free R set?
I also notice that your Rfac and Rfree are identical. Hmmm...?
Also, does the Rfree value alone increase (with no concomitant increase
in Rfac.)? How large is the increase (give nos.)?
Ensure that you are using the same freeR set between programs.
You write that the Rfree goes up after two cycles of refinement. How
many cycles of positional refinement are you doing in CNS. It is not
uncommon for the Rfree/Rfac values to increase slightly in the initial
cycles followed by a drop through subsequent cycles. Look at your
logfile to make sure this is not the case.
It is also not uncommon for starting Rfree/Rfac values to be slightly
higher when switching to CNS from other programs.
Hope that helps.
Raji
Raji Edayathumangalam
Postdoctoral Associate
The Rockefeller University
Box 224. 1230 York Avenue
New York, NY 10021
Jimson Wong wrote:
Hello all
I am trying to do positional refinement on a model of a protein & DNA
complex using minimize.inp from CNS. The problem I am having is that
after 2 cycles of automatic position refinement the Rfree would start
to go up. This happens almost everytime I try to use minimize.inp to
do positional refinement. Through labourous manual rebuilding and
with the help of DM solvent flipping + NCS averaging map the Rfree and
Rfactor are both 0.271 at the moment, with only 200 water molecules
along with 680 residues. I could add more water molecules to drive
down the Rfree, but I really would l like to be able to use
minimize.inp to refine the position of the molecules and so far I
cannot do that for some reason. I have made sure that there were no
clashes between non-covalently linked atoms and that their distances
are not closer than 2.2A.
Would any experienced CNS users know what it means when the Rfree
starts to go up when one uses minimize.inp?
Jimson
