diff --git a/tree/iqtree.cpp b/tree/iqtree.cpp
index b431cdb9e..7757a146a 100644
--- a/tree/iqtree.cpp
+++ b/tree/iqtree.cpp
@@ -2723,7 +2723,10 @@ void IQTree::refineBootTrees() {
             boot_tree->constraintTree.readConstraint(constraintTree);
         }
 
+        // set likelihood kernel
         boot_tree->setParams(params);
+        boot_tree->setLikelihoodKernel(sse);
+        boot_tree->setNumThreads(num_threads);
 
         // 2019-06-03: bug fix setting part_info properly
         if (boot_tree->isSuperTree())
@@ -2738,11 +2741,6 @@ void IQTree::refineBootTrees() {
         else
             boot_tree->getModelFactory()->restoreCheckpoint();
 
-        // set likelihood kernel
-        boot_tree->setParams(params);
-        boot_tree->setLikelihoodKernel(sse);
-        boot_tree->setNumThreads(num_threads);
-
         // load the current ufboot tree
         // 2019-02-06: fix crash with -sp and -bnni
         if (isSuperTree())