diff --git a/modelling/pymod/_pipeline.py b/modelling/pymod/_pipeline.py
index 6f149369b31259b54dada119733bac167d7da50f..fdea48505c30f4bb49832cd1182c89babe04acd0 100644
--- a/modelling/pymod/_pipeline.py
+++ b/modelling/pymod/_pipeline.py
@@ -386,7 +386,9 @@ def CheckFinalModel(mhandle):
     ost.PopVerbosityLevel()
     # set bool props in model-residues
     atoms = [e.GetFirstAtom() for e in clash_info.GetClashList()]\
+          + [e.GetSecondAtom() for e in clash_info.GetClashList()]\
           + [e.GetFirstAtom() for e in stereo_info.GetBondViolationList()]\
+          + [e.GetSecondAtom() for e in stereo_info.GetBondViolationList()]\
           + [e.GetSecondAtom() for e in stereo_info.GetAngleViolationList()]
     for atomui in atoms:
         res = model_src.FindResidue(atomui.GetChainName(), atomui.GetResNum())