removed `/scratch/xiaobo/97666/xcr-8058088.70/working/protonate/xcr-protonated-manual.ism' removed `/scratch/xiaobo/97666/xcr-8058088.70/working/protonate/xcr-protomers.ism' removed `/scratch/xiaobo/97666/xcr-8058088.70/working/protonate/xcr-protomers-expanded.ism' removed directory: `/scratch/xiaobo/97666/xcr-8058088.70/working/protonate' removed `/scratch/xiaobo/97666/xcr-8058088.70/working/input-smiles.ism'