sentence: Protein structure superimpositions were performed with VMD ( Humphrey et al. 1996 ) , and structural quality assessments were carried out using RAMPAGE ( Lovell et al. 2003 ) , QMEAN ( Benkert et al. 2009 ) , WHATCHECK ( Hooft et al. 1996 ) , PROCHECK ( Laskowski et al. 1993 ) , and MOLPROBITY ( Chen et al. 2010 ) .