I am almost done repeating fix-rotamers run. First time it gave a way
worse validation results then before running phenix without
fix_rotamers=true.
This method behaves very poorly at low resolution - I ran some tests recently on a variety of 3.0-4.5A structures solved by molecular replacement, and while the rotamer fitting usually decreased the R-factor, it always made the clashscore much worse. I wouldn't bother using it if you have worse than 3.0A data.
Model pdb contained the model
identical to the control run but with added H atoms. I have not add H to the
ADP molecules since I did not know how to write a correct CIF file for it.
If you use phenix.ready_set, it will handle the ADP molecules.
Interestingly in previous release
version the same refinement runs produced:
without H clashscore = 77.580195/cbeta
=8
with H clashscore = 119.729960/cbeta=330
We increased the weight on the nonbonded restraints 5x in the last few releases - this always improves the clashscore and Ramachandran statistics at low resolution, although it doesn't change the R-factors very much. Still, 12% is an awful lot of Ramachandran outliers, even at that resolution. If you're willing to experiment a little, try adding "ncs.type=torsion" to the parameters (without hydrogens) and let us know what happens.
-Nat