So the 'right' answer here would be for you to use a
diff tool of some kind (WinDiff, or just the diff command in a Unix-like environment). That would show you the exact added lines. (Although, trying this myself does not produce very clear results...)
However, I know from running
reduce on PDB files that it's added a few things:
- The "USER MOD" lines, there's one on the first line and a large block just before the ATOM records
- The hydrogen atoms, of course, needed for correct H-bond calculations
As some commenters have pointed out, this should really be in the paper or other documentation for the tool.