No paper has been published describing ProFit itself since it is simply a convenient program (I hope) to let you use a standard fitting algorithm; consequently, it is a little difficult to reference. The exact wording is up to you and dependent on the context, but I suggest something similar to:
Fitting was performed using the McLachlan algorithm (McLachlan, A.D.,
1982 ``Rapid Comparison of Protein Structres'', Acta Cryst A38,
871-873) as implemented in the program ProFit (Martin, A.C.R.,
http://www.bioinf.org.uk/software/profit/)