diff --git a/modules/mol/alg/pymod/lddt.py b/modules/mol/alg/pymod/lddt.py
index 95a9a5af09f910454eda63231f29aab5c8e4b233..91419c91e5f40f2a9d5c1b53c3abcf9297986572 100644
--- a/modules/mol/alg/pymod/lddt.py
+++ b/modules/mol/alg/pymod/lddt.py
@@ -487,6 +487,7 @@ class lDDTScorer:
         for ch in model.chains:
             model_ch_name = ch.GetName()
             if model_ch_name not in chain_mapping:
+                current_model_res_idx += len(ch.residues)
                 continue # additional model chain which is not mapped
             target_ch_name = chain_mapping[model_ch_name]