diff --git a/alphapulldown/predict_structure.py b/alphapulldown/predict_structure.py
index 2abbc6ad..965b59b0 100644
--- a/alphapulldown/predict_structure.py
+++ b/alphapulldown/predict_structure.py
@@ -13,6 +13,7 @@
 from alphafold.relax import relax
 import numpy as np
 from alphapulldown.utils import get_run_alphafold
+import jax.numpy as jnp
 
 
 run_af = get_run_alphafold()
@@ -24,6 +25,15 @@
 
 ModelsToRelax = run_af.ModelsToRelax
 
+def _jnp_to_np(output):
+  """Recursively changes jax arrays to numpy arrays."""
+  for k, v in output.items():
+    if isinstance(v, dict):
+      output[k] = _jnp_to_np(v)
+    elif isinstance(v, jnp.ndarray):
+      output[k] = np.array(v)
+  return output
+
 def get_score_from_result_pkl(pkl_path):
     """Get the score from the model result pkl file"""
 
@@ -176,9 +186,12 @@ def predict(
         plddt = prediction_result["plddt"]
         ranking_confidences[model_name] = prediction_result["ranking_confidence"]
 
+        # Remove jax dependency from results.
+        np_prediction_result = _jnp_to_np(dict(prediction_result))
+
         result_output_path = os.path.join(output_dir, f"result_{model_name}.pkl")
         with open(result_output_path, "wb") as f:
-            pickle.dump(prediction_result, f, protocol=4)
+            pickle.dump(np_prediction_result, f, protocol=4)
 
         plddt_b_factors = np.repeat(
             plddt[:, None], residue_constants.atom_type_num, axis=-1