removed `/scratch/xiaobo/9784/xdk-8058115.89/working/protonate/xdk-protomers.ism' removed `/scratch/xiaobo/9784/xdk-8058115.89/working/protonate/xdk-protomers-expanded.ism' removed `/scratch/xiaobo/9784/xdk-8058115.89/working/protonate/xdk-protonated-manual.ism' removed directory: `/scratch/xiaobo/9784/xdk-8058115.89/working/protonate' removed `/scratch/xiaobo/9784/xdk-8058115.89/working/input-smiles.ism'