removed `/scratch/xiaobo/353693/xcq-8058115.69/working/protonate/xcq-protomers.ism' removed `/scratch/xiaobo/353693/xcq-8058115.69/working/protonate/xcq-protomers-expanded.ism' removed `/scratch/xiaobo/353693/xcq-8058115.69/working/protonate/xcq-protonated-manual.ism' removed directory: `/scratch/xiaobo/353693/xcq-8058115.69/working/protonate' removed `/scratch/xiaobo/353693/xcq-8058115.69/working/input-smiles.ism'