diff --git a/predict_bindingsites.py b/predict_bindingsites.py
index 7ff5236..ae07725 100644
--- a/predict_bindingsites.py
+++ b/predict_bindingsites.py
@@ -661,9 +661,16 @@ def predict_interface_residues(
                         chimera.annotate_pdb_file(pdb_file_locations[i], csv_file, annotated_pdb_file, output_script=True, mini=mini, maxi=maxi)
 
     if output_format == 'dictionary':
-        query_dictionary_predictions = [PDB_processing.make_values_dictionary(query_residue_id,query_prediction) for query_residue_id,query_prediction in zip(query_residue_ids,query_predictions)]
+        if ((isinstance(layer, list)) | (isinstance(layer, tuple)) | (not aggregate_models)):
+            query_dictionary_predictions = [PDB_processing.make_values_dictionary(query_residue_ids[k], [query_predictions[l][k] for l in range(len(query_predictions))])
+                                            for k in range(len(query_residue_ids))]
+        else:
+            query_dictionary_predictions = [PDB_processing.make_values_dictionary(query_residue_id,query_prediction) for query_residue_id,query_prediction in zip(query_residue_ids,query_predictions)]
         return query_pdbs,query_names,query_dictionary_predictions
     else:
+        if ((isinstance(layer, list)) | (isinstance(layer, tuple)) | (not aggregate_models)):
+            query_predictions = [
+                [query_predictions[i][j] for i in range(len(query_predictions))] for j in range(len(query_predictions[0]))]
         return query_pdbs,query_names,query_predictions, query_residue_ids, query_sequences
 
 
diff --git a/predict_features.py b/predict_features.py
index 8f3befe..fcd8a9e 100644
--- a/predict_features.py
+++ b/predict_features.py
@@ -63,6 +63,7 @@ def predict_features(list_queries,layer='SCAN_filter_activity_aa',
     )
     if output_format == 'numpy':
         query_pdbs, query_names, query_features, query_residue_ids, query_sequences = query_outputs
+
         if return_one:
             query_pdbs = query_pdbs[0]
             query_names = query_names[0]
@@ -106,7 +107,7 @@ if __name__ == '__main__':
 
 
     if output_format == 'dictionary':
-        list_names, list_dictionary_features = predict_features(['1a3x_A','1brs_A'],layer=layer,model=model,output_format=output_format)
+        list_names, list_dictionary_features = predict_features(['1a3x_A','1brs_A'],layer=layer,model=model,output_format=output_format,permissive=True)
         print('Dictionary format: Dictionary with residue ids as key and features as items.')
         for k in range(2):
             print('Query',list_names[k])
@@ -117,7 +118,7 @@ if __name__ == '__main__':
                 else:
                     print('AA',key, 'Features:',item[:5],'Feature shape',item.shape)
     elif output_format == 'numpy':
-        list_names, list_features, list_residue_ids = predict_features(['1a3x_A','1brs_A'],layer=layer,model=model,output_format='numpy')
+        list_names,list_features, list_residue_ids = predict_features(['1a3x_A','1brs_A'],layer=layer,model=model,output_format='numpy',permissive=True)
         print('Numpy format: Numpy arrays with residue ids as key and features as items.')
         for k in range(2):
             print('Query',list_names[k])