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suggestions on refinement

Balaji Bhyravbhatla bbhyravbhatla at hotmail.com
Fri Dec 31 03:42:53 EST 1999

Dear All,
I have a molecular replacement solution with initial  R's between 38 and
I have been trying to refine this model against our dataset but am not
having much
luck.  This is what happens when I do either minimize or annealing:

REMARK coordinates from minimization refinement
REMARK refinement resolution: 100.0 - 3.0 A
REMARK starting r= 0.3815 free_r= 0.4102    <<<<<<<<<<<< Look <<<<<<<<
REMARK final    r= 0.4971 free_r= 0.6025        <<<<<<<<<<<<Look
REMARK rmsd bonds= 0.020111  rmsd angles=  4.89617
REMARK wa= 9.39831
REMARK target= mlf cycles= 10 steps= 50
REMARK sg= P2(1) a= 26.37 b= 26.91 c= 101.92 alpha= 90 beta= 89.98
gamma= 90

This is after a round of just minimization. When I do annealing it is
even worse!!! and the
r-factor jumps up to the high 50's and free_r is in the low 60's!! I
have also changed reso
limits and no improvement.
I have done several rounds of annealing and have not gotten anywhere!!
Rigid body has stabilized it
at ~37-38% and I am not seeing any improvements there at all. I have
also tried bfactor
refinement but that has not done much good either. Water picking has
also not pushed the
Can anyone suggest what I need to monitor to find the cause? Or may be
another way of
pushing the refinement??  Or just plain suggestions are welcome so that
I know I am not
missing something!!

I have tried the ccp4 set also a bit (arp, refmac etc.) but no
improvements there either.


PS: Happy millenium to all!

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