diff --git a/gpu/modal_app.py b/gpu/modal_app.py
index 36b09af..6831902 100644
--- a/gpu/modal_app.py
+++ b/gpu/modal_app.py
@@ -127,7 +127,8 @@ def build_boltz_yaml(protein_seq: str, ligand_smiles: str, cofactor_ccds: list[s
 # max_containers caps parallel fan-out (cost control). The download race that corrupts the
 # checkpoint only happens on a COLD volume; once weights are cached+committed (Phase 1 did this),
 # parallel containers just reload them, so a screen can safely run ~10-wide.
-@app.function(gpu="L4", image=image, volumes={WEIGHTS: weights}, timeout=1800)
+# Long timeout: the public ColabFold MSA server queues and can take 20-40+ min for one query.
+@app.function(gpu="L4", image=image, volumes={WEIGHTS: weights}, timeout=4200)
 def cache_msa(label: str, protein_seq: str, ligand_smiles: str, cofactor_ccds: list[str]) -> str:
     """Compute the target's MSA ONCE (via the server) and cache the a3m on the Volume.