In the Calculate Mutation Energy (Stability) protocol, under the Advanced parameters there is a parameter group called "Energy Terms Scaling Factors".  This group of parameters contains the scaling factors used to scale the different contributions to the mutation energy.
These are the empirical weight coefficients found to produce optimal results from the validation studies (with large sets of experimental data) conducted during the protocol development.

More details about the methodology and the prediction accuracy assessments are in the publication:
   Spassov, V.Z.; Yan, L.;  A pH-Dependent Computational Approach to the Effect of Mutations on Protein Stability. Journal of Computational Chemistry 2016, 37, 2573-2587.