I use Refmac5 to refine my model. After the run, I check the model quality by Coot.
Here is the problem:
In Coot, the ligand - NAD, has bad geometry as indicated by a big red bar. While the geometry of NAD fit nicely with the electron density.
If I use refine tools (i.e. regularize Zone or real space refine zone), the geometry of NAD turns to perfec with bond, angle and so on. But the ligand slightly turn away from the electron density map.
If I run Refmac5 again with this modified model, the NAD turns back, fit nice to electron density, but gives red bar in coot geometry.
The Refinment Parameters in Refmac5 is set @ "use automatic weight" and "use experinmental sigmals to weight X-ray terms".
