removed `/scratch/xiaobo/2794/xcl-8058115.64/working/protonate/xcl-protomers-expanded.ism' removed `/scratch/xiaobo/2794/xcl-8058115.64/working/protonate/xcl-protonated-manual.ism' removed `/scratch/xiaobo/2794/xcl-8058115.64/working/protonate/xcl-protomers.ism' removed directory: `/scratch/xiaobo/2794/xcl-8058115.64/working/protonate' removed `/scratch/xiaobo/2794/xcl-8058115.64/working/input-smiles.ism'