TM-score only compare the common regions where both model and PDB structure have
avaliable coordinates. The common regions are decided by the residue sequence number (Column 23-26
in PDB format).
It is user's responsibility to keep the equivalence of compared residues in both pdb files.
You can also apply http://zhanglab.ccmb.med.umich.edu/TM-align/TM-align
to compare the two structures. TM-align is designed to ignor the residue order numbers
and generate best alignment based on the structural similarity.