Dear x-plor users,
I'm refining a structure of a complex at 2.6 A resolution. The enzyme
is complexed with NAD and an inhibitor. And one can see clearly the
molecule of NAD+ in Fo-Fc maps without any problem.
In order to avoid problems with "O". I renamed the atoms in the NAD+
molecule to my own ones (like C1, C2, .. N1, N2... O1, O2... etc)
and change the corresponding xplor topology.nad file.
Then I divide the molecule in several pieces to fit easier the molecule
into the density.
Do model building and assemble the pieces to a single regular NAD+
molecule, finally do some positional refinement cycles (150 steps), it
usually refines the molecule away from the electron density.(??? I wonder
why?)
When I do group b-factor refinement of the NAD+ molecule, the value
gets about 100 A2? If I try individual b-factor refinement -only for
the NAD+ molecule- some atoms get as well 100 A2 as b-factor.
Could someone give me a hint?
Cheers,
JB
