MUSCLE manual
BALIBASE sets are not globally alignable, and many do not have known structures
This figure shows two sets from BALIBASE v3 with annotations from SWISS-PROT. These proteins have radically different domain organizations, with only a small locally alignable region in the SH2 domain. MUSCLE was not designed to align this type of data, and in my opinion it is not reasonable to use these alignments as a test of accuracy.

None of these proteins have solved structures.