diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
index 93e118ce0..87572b804 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyExactAFCalculationModel.java
@@ -224,12 +224,16 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
         indexesToACset.put(zeroSet.ACcounts, zeroSet);
 
         // keep processing while we have AC conformations that need to be calculated
-        double maxLog10L = Double.NEGATIVE_INFINITY;
+        MaxLikelihoodSeen maxLikelihoodSeen = new MaxLikelihoodSeen();
         while ( !ACqueue.isEmpty() ) {
             // compute log10Likelihoods
             final ExactACset ACset = ACqueue.remove();
-            final double log10LofKs = calculateACConformationAndUpdateQueue(ACset, newPool, originalPool, newGL, log10AlleleFrequencyPriors, originalPloidy, newGLPloidy, result, maxLog10L, ACqueue, indexesToACset);
-            maxLog10L = Math.max(maxLog10L, log10LofKs);
+            final double log10LofKs = calculateACConformationAndUpdateQueue(ACset, newPool, originalPool, newGL, log10AlleleFrequencyPriors, originalPloidy, newGLPloidy, result, maxLikelihoodSeen, ACqueue, indexesToACset);
+
+            // adjust max likelihood seen if needed
+            if ( log10LofKs > maxLikelihoodSeen.maxLog10L )
+                maxLikelihoodSeen.update(log10LofKs, ACset.ACcounts);
+
             // clean up memory
             indexesToACset.remove(ACset.ACcounts);
             if ( VERBOSE )
@@ -250,7 +254,7 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
      * @param originalPloidy             Total ploidy of original combined pool
      * @param newGLPloidy                Ploidy of GL vector
      * @param result                     AFResult object
-     * @param maxLog10L                  max likelihood observed so far
+     * @param maxLikelihoodSeen          max likelihood observed so far
      * @param ACqueue                    Queue of conformations to compute
      * @param indexesToACset             AC indices of objects in queue
      * @return                           max log likelihood
@@ -263,7 +267,7 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
                                                                 final int originalPloidy,
                                                                 final int newGLPloidy,
                                                                 final AlleleFrequencyCalculationResult result,
-                                                                final double  maxLog10L,
+                                                                final MaxLikelihoodSeen maxLikelihoodSeen,
                                                                 final LinkedList<ExactACset> ACqueue,
                                                                 final HashMap<ExactACcounts, ExactACset> indexesToACset) {
 
@@ -277,9 +281,9 @@ public class GeneralPloidyExactAFCalculationModel extends AlleleFrequencyCalcula
         if (!Double.isInfinite(log10LofK))
             newPool.add(set);
 
-        if ( log10LofK < maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY ) {
+        if ( log10LofK < maxLikelihoodSeen.maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY && maxLikelihoodSeen.isLowerAC(set.ACcounts) ) {
             if ( VERBOSE )
-                System.out.printf(" *** breaking early set=%s log10L=%.2f maxLog10L=%.2f%n", set.ACcounts, log10LofK, maxLog10L);
+                System.out.printf(" *** breaking early set=%s log10L=%.2f maxLog10L=%.2f%n", set.ACcounts, log10LofK, maxLikelihoodSeen.maxLog10L);
             return log10LofK;
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
index 08a333486..569cd7072 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationModel.java
@@ -204,4 +204,28 @@ public abstract class AlleleFrequencyCalculationModel implements Cloneable {
             return (obj instanceof ExactACset) && ACcounts.equals(((ExactACset)obj).ACcounts);
         }
     }
+
+    protected static final class MaxLikelihoodSeen {
+        double maxLog10L = Double.NEGATIVE_INFINITY;
+        ExactACcounts ACs = null;
+
+        public MaxLikelihoodSeen() {}
+
+        public void update(final double maxLog10L, final ExactACcounts ACs) {
+            this.maxLog10L = maxLog10L;
+            this.ACs = ACs;
+        }
+
+        // returns true iff all ACs in this object are less than or equal to their corresponding ACs in the provided set
+        public boolean isLowerAC(final ExactACcounts otherACs) {
+            final int[] myACcounts = this.ACs.getCounts();
+            final int[] otherACcounts = otherACs.getCounts();
+
+            for ( int i = 0; i < myACcounts.length; i++ ) {
+                if ( myACcounts[i] > otherACcounts[i] )
+                    return false;
+            }
+            return true;
+        }
+    }
 }
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
index 77a39afc2..ba7f0f622 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ExactAFCalculationModel.java
@@ -68,7 +68,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
 
     private static final int PL_INDEX_OF_HOM_REF = 0;
-    private static final List<Allele> chooseMostLikelyAlternateAlleles(VariantContext vc, int numAllelesToChoose) {
+    private static List<Allele> chooseMostLikelyAlternateAlleles(VariantContext vc, int numAllelesToChoose) {
         final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
         final LikelihoodSum[] likelihoodSums = new LikelihoodSum[numOriginalAltAlleles];
         for ( int i = 0; i < numOriginalAltAlleles; i++ )
@@ -132,14 +132,15 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         indexesToACset.put(zeroSet.ACcounts, zeroSet);
 
         // keep processing while we have AC conformations that need to be calculated
-        double maxLog10L = Double.NEGATIVE_INFINITY;
+        MaxLikelihoodSeen maxLikelihoodSeen = new MaxLikelihoodSeen();
         while ( !ACqueue.isEmpty() ) {
             // compute log10Likelihoods
             final ExactACset set = ACqueue.remove();
-            final double log10LofKs = calculateAlleleCountConformation(set, genotypeLikelihoods, maxLog10L, numChr, ACqueue, indexesToACset, log10AlleleFrequencyPriors, result);
+            final double log10LofKs = calculateAlleleCountConformation(set, genotypeLikelihoods, maxLikelihoodSeen, numChr, ACqueue, indexesToACset, log10AlleleFrequencyPriors, result);
 
             // adjust max likelihood seen if needed
-            maxLog10L = Math.max(maxLog10L, log10LofKs);
+            if ( log10LofKs > maxLikelihoodSeen.maxLog10L )
+                maxLikelihoodSeen.update(log10LofKs, set.ACcounts);
 
             // clean up memory
             indexesToACset.remove(set.ACcounts);
@@ -160,7 +161,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
 
     private static double calculateAlleleCountConformation(final ExactACset set,
                                                            final ArrayList<double[]> genotypeLikelihoods,
-                                                           final double maxLog10L,
+                                                           final MaxLikelihoodSeen maxLikelihoodSeen,
                                                            final int numChr,
                                                            final LinkedList<ExactACset> ACqueue,
                                                            final HashMap<ExactACcounts, ExactACset> indexesToACset,
@@ -176,7 +177,7 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
         final double log10LofK = set.log10Likelihoods[set.log10Likelihoods.length-1];
 
         // can we abort early because the log10Likelihoods are so small?
-        if ( log10LofK < maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY ) {
+        if ( log10LofK < maxLikelihoodSeen.maxLog10L - MAX_LOG10_ERROR_TO_STOP_EARLY && maxLikelihoodSeen.isLowerAC(set.ACcounts) ) {
             //if ( DEBUG )
             //    System.out.printf(" *** breaking early set=%s log10L=%.2f maxLog10L=%.2f%n", set.ACcounts, log10LofK, maxLog10L);
             return log10LofK;