[modeller_usage] Question about alignment.check()

Hello,

I have a question about the alignment.check() command (more precisely check_structure_structure). After using this command I get a log which contains many large distances between equivalent pairs of templates. For example, one line of the log looks like this:

ALN_POS TMPL1 TMPL2 RID1 RID2 NAM1 NAM2 DIST ---------------------------------------------------- 21 1 2 39 43 I G 14.905

Using the superimposed templates and a visualisation program (pymol), the measured distance between the mentioned pairs is only 0,6 A. The problem is the same for other pairs. I've checked the alignment pir file many times and there are no errors in it, the sequences are aligned correctly. How can this be explained?

Best regards,

Mat