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
