[modeller_usage] question about basic modelling

Hi,

I am a new MODELLER user. I am trying to duplicate a result in literature using v8.1 of MODELLER, and am trying to use 1H8C.pdb as template to model 1D3Z.pdb structure. I followed the basic outline of the scripts in the tutorial (and attached the scripts I used). At the end of modelling, the homology model I obtain is about 9A cRMSD from the target structure, whereas in the literature an earlier version of MODELLER (v6.2) was used to achieve a closer structure to the template (1.9A cRMSD). I was wondering whether there is any simple step I may be missing.

Thanks,

--Serkan