Hi Andy:
Just be very careful of special pleading type arguments. I really
think this is trying to tell you something, along with the
Ramachandran plot. On a more practical level, the PDB will flag it
when you try to deposit it. There is something wrong.
It might be worth making a composite-omit map in CNS, and if you have
experimental phases, go back and look at the original MIR (or
whatever) map. Double-check the space group is right.
Do all that before you change any defaults.
It is very good by the way you are asking for feedback at this stage.
If it turns out there is a problem, it is much better to catch it
now. Also, if you do have to do something non-canonical during the
refinement, the burden is placed on the paper's authors to justify
why. So either way this will be time well spent.
Best of luck.
Bill
On Feb 6, 2009, at 8:13 AM, Andy Millston wrote:
Thank you for your responses.
Restrained refinement does a good job at refining most of the
structure except a small region with poor density. Every time I
refine it, it puts this region completely out of the map. It doesn't
have much effect on overall geometrical factors as its a very small
part of a relatively large molecule.
I am annoyed at the fact that Refmac doesn't seem to have much
respect for the electron density map while refining this region, and
all my attempts to keep the residues within the map go in vain. The
refined residues are still ok according to Fo-Fc map, but they're
completely out of the 2Fo-Fc map boundaries. Also, my model and the
refined model both look bad on Ramachandran plot. But I think its a
unique feature of the molecule, at least thats what the density
suggests. Also, packing score and quality value plot suggest that
there is nothing seriously wrong with my model.
As you've suggested I should try altering the restraints and see how
it goes.
Thank you.
Andy
