Index: src/main/java/org/biojava3/ronn/ORonn.java
===================================================================
--- src/main/java/org/biojava3/ronn/ORonn.java	(revision 9674)
+++ src/main/java/org/biojava3/ronn/ORonn.java	(working copy)
@@ -102,7 +102,9 @@
 		timer = new Timer(TimeUnit.MILLISECONDS);
 	}
 
-	synchronized void writeResults(final float[] meanScores, final char[] seqs) {
+	void writeResults(final float[] meanScores, final char[] seqs) {
+		synchronized (out)
+		{
 		out.println(">" + sequence.getId());
 		if (layout == ResultLayout.VERTICAL) {
 			for (int i = 0; i < meanScores.length; i++) {
@@ -124,6 +126,7 @@
 		}
 		out.println();
 		out.flush();
+		}
 	}
 
 	static boolean isValidSequence(final FastaSequence fsequence) {