removed `/scratch/xiaobo/340083/xda-8058088.79/working/protonate/xda-protomers-expanded.ism' removed `/scratch/xiaobo/340083/xda-8058088.79/working/protonate/xda-protonated-manual.ism' removed `/scratch/xiaobo/340083/xda-8058088.79/working/protonate/xda-protomers.ism' removed directory: `/scratch/xiaobo/340083/xda-8058088.79/working/protonate' removed `/scratch/xiaobo/340083/xda-8058088.79/working/input-smiles.ism'