The stereo chemical quality of the predicted models and accuracy of the protein model was evaluated after the refinement process using Ramachandran Map calculations computed with the PROCHECK program. The assessment of the predicted models generated by modeller was shown in Figure 2. The main chain parameters plotted are Ramachandran plot quality, peptide bond planarity, Bad nonbonded interactions, main chain hydrogen bond energy, C-alpha chirality and over-all G factor. In the Ramachandran plot analysis, the residues were classified according to its regions in the quadrangle. The red regions in the graph indicate the most allowed regions whereas the yellow regions represent allowed regions. Glycine is represented by triangles and other residues are represented by squares. The result revealed that the modeled structure for APX, DHAR, PHGPX and 2CPS has 96.2%, 80.0%, 95.0% and 91.5% residue respectively in allowed region. The distribution of the main chain bond lengths and bond angles were found to be within the limits for these proteins. Such figures assigned by Ramachandran plot represent a good quality of the predicted models.