removed `/scratch/xiaobo/36058/xaf-8058115.6/working/protonate/xaf-protomers-expanded.ism' removed `/scratch/xiaobo/36058/xaf-8058115.6/working/protonate/xaf-protonated-manual.ism' removed `/scratch/xiaobo/36058/xaf-8058115.6/working/protonate/xaf-protomers.ism' removed directory: `/scratch/xiaobo/36058/xaf-8058115.6/working/protonate' removed `/scratch/xiaobo/36058/xaf-8058115.6/working/input-smiles.ism'