diff --git a/src/clm/commands/write_structural_prior_CV.py b/src/clm/commands/write_structural_prior_CV.py
index e5c1b855..62d7e7e6 100644
--- a/src/clm/commands/write_structural_prior_CV.py
+++ b/src/clm/commands/write_structural_prior_CV.py
@@ -261,8 +261,6 @@ def write_structural_prior_CV(
         )
     ]
 
-    gen = gen.drop(invalid_idx)
-
     n_candidates = len(candidates)
     n_invalid = len(invalid_idx)
 
@@ -277,6 +275,8 @@ def write_structural_prior_CV(
             f"Examples: {examples}"
         )
 
+    gen = gen.drop(invalid_idx)
+
     inputs = {"model": gen.assign(source="model")}
 
     if pubchem_file: