removed `/scratch/xiaobo/382291/xcy-8058088.77/working/protonate/xcy-protomers-expanded.ism' removed `/scratch/xiaobo/382291/xcy-8058088.77/working/protonate/xcy-protonated-manual.ism' removed `/scratch/xiaobo/382291/xcy-8058088.77/working/protonate/xcy-protomers.ism' removed directory: `/scratch/xiaobo/382291/xcy-8058088.77/working/protonate' removed `/scratch/xiaobo/382291/xcy-8058088.77/working/input-smiles.ism'