I'm running into some geometry problems with my DNA model after refinement with refmac (version 5.5.0109), and would appreciate any feedback.
The problem is that the angles for many of the glycosidic bonds are 2 to 4 degrees off of the ideal values, and so are several standard deviations outside what's expected. Our data (from MR) is ~2 Å, and the density is well defined for the DNA. I was thinking that perhaps refmac was not recognizing my DNA and so just taking the poor geometry from one model and enforcing it for the next, but in the log file it does not indicate that a new molecule has been found, and I do not feed in a cif file from previous runs. Another indication that refmac recognizes the DNA bases is that it says it is renaming them. The DNA bases are named DA, DC, DT, DG, and the header of the output pdb file says: MODRES DC B 1 Cd RENAME MODRES DC B 2 Cd RENAME MODRES DA B 3 Ad RENAME MODRES DT B 4 Td RENAME (etc...) In the output, strangely (to me), it is actually not renaming them. That is, it is keeping the "DC" etc names. In coot, I'm measuring the glycosidic bond (O4'-C1'-N9) to be 104.6, whereas in AD.cif, it is listed as 108.4. The bond lengths are fine, and there are no distortions of the protein model. Thanks, Greg
