removed `/scratch/xiaobo/23680/xca-8058097.53/working/protonate/xca-protomers.ism' removed `/scratch/xiaobo/23680/xca-8058097.53/working/protonate/xca-protonated-manual.ism' removed `/scratch/xiaobo/23680/xca-8058097.53/working/protonate/xca-protomers-expanded.ism' removed directory: `/scratch/xiaobo/23680/xca-8058097.53/working/protonate' removed `/scratch/xiaobo/23680/xca-8058097.53/working/input-smiles.ism'