The TNT control file will require a lot of work. The starting file created by from_pdb will contain only the most basic information. It will contain the cell constants, INCLUDE the sequence file, and a first guess for the weights to use in refinement. A complete control file must contain much more. You must edit this file to reflect the space group, supply the name of the structure factor file and resolution limits, and include any special statements required to define unusual chemical groups or situations.
Chapter describes many of the statements you can use in this file.
As you progress with your refinement you will edit this file many times. As it stands, the prototype results in a stereochemically restrained refinement of the positions and temperature factors of your atoms, with torsion angles restraints turned off. (I don't believe in torsion angle restraints. They are better used to validate the final model.)