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Dear Yi, it is very bad practice to refine an MR solution without looking at the map after MR first, especially at low resolution. The aim of refinement is to reduce R/ Rfree and it can do so by overfitting your data. This means that differences between the MR solution and your data become smoothed away, and you do want these differences in order to improve the model. So carry out the MR, then build and correct the model as much as possible before doing any refinement. Tim -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A On Thu, 3 Aug 2006, Yi Xue wrote: > *** For details on how to be removed from this list visit the *** > *** CCP4 home page http://www.ccp4.ac.uk *** > > > Dear all: > > > I have one dataset, diffracted to 3.2A. > It should be a protein-DNA complex. The protein structure has already > been solved. The DNA is a 23mer. > > I used phaser to do the molecular replacement, and it found a solution, > RFZ=7.2, TFZ=11.9, however, LLG is negative. > > I used the solution, did 20 cycles of restrained refinement, using > refmac. > > R decreased from 0.476 to 0.354 > Rfree decreased from 0.453 to 0.45. > > Since there is only trivial improvement for Rfree, so is it possibly a > right solution? > > thanks > Yi > >
