bDNA
CELL 24.87 40.39 66.2 INCLUDE /usr/local/tnt/data/symmetry/p212121.dat FO 1bna.hkl RESOLUTION 2.3 SET BSOL 150 INCLUDE bdna.seq EXCLUDE H|25:O H|86:O EXCLUDE H|54:O H|86:O EXCLUDE H|62:O H|77:O EXCLUDE H|63:O H|77:O NOTE Define NCS symmetry for only the core. There are NOTE significant differences at the ends. It is probably NOTE not good to restrain this, just monitor it. CLUSTER BDNA RESIDUES 4 - 9 CHAINS A B CONSTANT OCC WEIGHT RFACTOR 0.03 NCS 0 WEIGHT BOND 0.8 ANGLE 1.3 TORSION 0 PSEUDOROTATION 0 WEIGHT TRIGONAL 2 PLANE 5 CONTACT 10 BCORREL 0
This TNT control file varies the position and temperature factor of each
atom in the model. A number of problems arise with this refinement.
First, the quality of the diffraction data is low. This results in a
failure to properly scale the observed and calculated data without forcing
the parameter 
equal to 150.
Second, a large number of bad contacts are discovered between various water molecules. EXCLUDE statements were entered to cause TNT to ignore the worst. Before beginning a serious refinement these water molecules should be examined manually and corrected. (The water molecules in the original PDB file are unsupported by the density map. I would remove them all, refine the DNA, and build back those whose density returned. I have done this and very few return.)
There are two chains in the asymmetric unit which are chemically identical. Therefore a CLUSTER statement has been added to describe the noncrystallographic symmetry. However the similarity of the two chains is poor. Either the current model is incorrect or the ncs does not hold. Since we doubt the ncs we set the weight for the NCS term to zero. The only effect of the CLUSTER statement is that it allows the use of the ncs command to monitor the similarity of the two chains.
You may have noticed that the weight for the B correlation restraint has been set to zero in spite of the poor quality of the diffraction data. This is done because a library for temperature factor correlations in nucleic acids does not exist at this time. You cannot use the BCORREL restraints with DNA or RNA.
All the files required to perform refinement on this example are supplied in $refroot/tnt/doc/examples/bdna.