diff --git a/frustratometer/classes/AWSEM.py b/frustratometer/classes/AWSEM.py
index 770f4ad..a25290c 100644
--- a/frustratometer/classes/AWSEM.py
+++ b/frustratometer/classes/AWSEM.py
@@ -341,7 +341,7 @@ def compute_configurational_energies(self):
 
         # decoy_data_columns=['decoy_i','i_resno','j_resno','ires_type','jres_type','aa1','aa2','rij','rho_i','rho_j','water_energy','burial_energy_i','burial_energy_j','electrostatic_energy','total_energies']
         # decoy_data=[]
-        configurational_energies=np.zeros((n,n))
+        configurational_energies=np.full((n,n), np.nan) # masked pairs will be left as nan
         for c in range(n_contacts):
             n1=indices1[c]
             n2=indices2[c]
@@ -366,4 +366,4 @@ def compute_configurational_energies(self):
     
     def configurational_frustration(self,aa_freq=None, correction=0, n_decoys=4000):
         mean_decoy_energy, std_decoy_energy = self.compute_configurational_decoy_statistics(n_decoys=n_decoys,aa_freq=aa_freq)
-        return -(self.compute_configurational_energies()-mean_decoy_energy)/(std_decoy_energy+correction)
\ No newline at end of file
+        return -(self.compute_configurational_energies()-mean_decoy_energy)/(std_decoy_energy+correction)