When pruning the collection set before rebuild, only freed space is taken into account when selecting these regions (i.e. gc-efficiency).

This can cause G1 selecting extremely bad to evacuate regions (with low efficiency), which in turn then can cause pause time spikes, particularly in combination with grouping.

One option is to improve the gc efficiency calculation by using more information, like number of incoming references calculated during marking, so improve the selection.

Another option is to select more regions to build the remembered sets for and prune later again.