DDG_monomer ΔΔG question

I read the  paper Role of conformational sampling in computing mutation-induced changes in protein structure and stability (Kellogg etal.2011),

and  set the flags as row 3 , 13 and 16, and some questions comfuses me.

The paper shows  the predicted ΔΔG of row 3 is the mean of the mutant energies subtracted by the mean of the wildtype energies.

while that of row 13 and row 16 are defined as the difference between the mutant and wildtype mean of the lowest 3 energy models out of 50.

But I  check the log and .out file , the predicted ΔΔG of  row 3, row 13 and row 16 all are seem defined as the difference between the mutant and wildtype mean of the lowest 3 energy models out of 50.

Why it cause?

Thanks!~