If several models are calculated for the same target, the ``best'' model can be selected by picking the model with the lowest value of the MODELLER objective function, which is reported in the second line of the model PDB file. The value of the objective function in MODELLER is not an absolute measure in the sense that it can only be used to rank models calculated from the same alignment.
Once a final model is selected, there are many ways to assess it (Section 2.5). In this example, PROSAII [45] is used to evaluate the model fold and PROCHECK [69] is used to check the model's stereochemistry. Before any external evaluation of the model, one should check the log file from the modeling run for runtime errors (`model.log') and restraint violations (see the MODELLER manual for details [72]). Both PROSAII and PROCHECK confirm that a reasonable model was obtained, with a Z-score comparable to that of the template (-10.53 and -12.69 for the model and the template, respectively). However, the PROSAII energy profile indicates an error in the long active site loop between residues 90 and 100 (Figure 4). This loop interacts with region 220-250, that forms the other half of the active site. This latter part is well resolved in the template and probably correctly modeled in the target structure, but due to the unfavourable non-bonded interactions with the 90-100 region, it is also reported to be in error by PROSA. In general, an error indicated by PROSAII is not neccessarily an actual error, especially if it highlights an active site or a protein-protein interface. However, in this case, the same active site loops have a better profile in the template structure, which strengthens the assessment that the model is probably incorrect in the active site region.