figure shows this transformation explicitly. If the overlap matrices are not averaged over replicas there are more instances of results that do not reach the threshold of 0.03, these all occur for the complex leg of the MCL1 target simulations. Half of these low overlap cases are for the OpenMM protocol and 7 out of 8 of the cases are for transformations substantially similar to l12-l35 see; figure for representative examples of such transformations. Without averaging over replicas the value of the overlap averaged over all instances failing to reach the 0.03 threshold is 0.02. If the same entries of the overlap are matrices are averaged over all replicas this value increases to 0.05. Despite lower overlap in some cases this does not manifest itself materially in any significant differences between the TI and FEP results for these transformations. To show this conclusively, table 4 exhibits the difference in ∆G results in the low overlap MCL1 case for the complex leg.