Another difference between the TNT and REFI standard geometry formats is that the REFI format does not allow the definition of planes and chiral centers. This ommission does not mean that you will not have planar groups and proper chiral centers if you use REFI. These quantities can be enforced by a judicious use of torsion angles.
Imagine a benzene ring. In TNT you would state that the six carbon atoms are in a common plane. In REFI format you would specify that all the torsion angles are equal to zero. Both methods get the job done. Converting from one to the other is a problem.
If you have four atoms, which form a torsion angle, and all lie in a plane the torsion angle might be zero degrees or it might be 180 degrees. There is no way to tell if all you know about is the plane. The TNT format converter will hazard a guess but will warn you that there is a problem. The messages will be discussed later.
You can also define chirality with torsion angles. TNT will perform this conversion without bothering you.
Your biggest problem will be undefined torsion angles. The general recommendation of the authors of TNT is to leave torsion angles unrestrained during refinement. Because the angles would not be used often people simply don't define them. REFI will not allow you to get away with such laziness. You don't have to define the torsion angles for every set of four atoms - just a subset which is almost impossible to predict. The simplest way to define these angles is to attempt the conversion and read the messages. The converted will list all the undefined, but required, angles.