To elucidate the relationship between factors resolved by the positive matrix factorization (PMF) receptor model and actual emission sources and to refine the PMF modeling strategy, speciated PM2.5 (particulate matter with aerodynamic diameter < 2.5 microm) data generated from a state-of-the-art chemical transport model for two rural sites in the eastern United States are subjected to PMF analysis. In addition to chi2 and R2 used to infer the quality of fitting, the interpretability of PMF factors with respect to known primary and secondary sources is evaluated using a root mean square difference analysis. For the most part, factors are found to represent imperfect combinations of sources, and the optimal number of factors should be just adequate to explain the input data (e.g., R2 > 0.95). Retaining more factors in the model does not help resolve minor sources, unless temporal resolution of the data is increased, thus allowing more information to be used by the model. If guided with a priori knowledge of source markers and/or special events, rotation of factors leads to more interpretable PMF factors. The choice of uncertainty weighting coefficients greatly influences the PMF modeling results, but it cannot usually be determined for simulated or real-world data. A simple test is recommended to check whether the weighting coefficients are suitable. However, uncertainties in the data divert PMF solutions even when the optimal weighting coefficients and number of factors are in place.