removed `/scratch/xiaobo/343839/xcg-8058088.59/working/protonate/xcg-protonated-manual.ism' removed `/scratch/xiaobo/343839/xcg-8058088.59/working/protonate/xcg-protomers.ism' removed `/scratch/xiaobo/343839/xcg-8058088.59/working/protonate/xcg-protomers-expanded.ism' removed directory: `/scratch/xiaobo/343839/xcg-8058088.59/working/protonate' removed `/scratch/xiaobo/343839/xcg-8058088.59/working/input-smiles.ism'