removed `/scratch/xiaobo/71991/xdc-8058115.81/working/protonate/xdc-protonated-manual.ism' removed `/scratch/xiaobo/71991/xdc-8058115.81/working/protonate/xdc-protomers-expanded.ism' removed `/scratch/xiaobo/71991/xdc-8058115.81/working/protonate/xdc-protomers.ism' removed directory: `/scratch/xiaobo/71991/xdc-8058115.81/working/protonate' removed `/scratch/xiaobo/71991/xdc-8058115.81/working/input-smiles.ism'