In general, accuracy of homology modelling decreases with lower levels of pairwise sequence identity between your sequence U and the target structure. Furthermore, successful applications of homology modelling may be hampered by two other difficulties. Avoid over-interpreting the details of the model. The main purpose of homology modelling is to translate a given alignment into more intuitive 3D images. Such images often look temptingly 'real'.
Homology modelling tends to yield sketches of structure rather than accurate co-ordinates.
Guessing details about protein function is such a difficult task that any null hypothesis may help to guide experiments. This may result in over-interpretations of the level of homology suggested by the sequence alignment and the level of accuracy of the resulting model. In practice, modelling often strikes a balance between users pushing for more interpretations and models pin-pointing the limitations of the methods. One problem of homology modelling for lower levels of pairwise sequence identity is to get the alignment between your sequence U and the template structure T correct. But even if the alignment were correct, a principle limitation is that T and U just do NOT have identical 3D structures.