refmac and DNA bond angles

From: Gregory Bowman
Date: 15 September 2011 00:10

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

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From: Gregory Bowman

OK, I updated ccp4 to 6.2.0 (and refmac to 5.6.0117) and now the angles coming out close to the ideal values. Also, I see now the the "MODRES" in the pdb header from before was tell future refmac runs to rename those residues - which confused the newer refmac version as it thought the DT (renamed Td) were somehow "DY". By just deleting these MODRES lines it was fine.

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