In this study, the conventional two-step nitrification model was extended with complete ammonia oxidation (comammox) and heterotrophic & nitrification on soluble microbial products. The data for model calibration/validation were collected at four long-tern washout experiments when the solid retention time (SRT) and hydraulic retention time (HRT) were progressively reduced from 4 d to 1 d, with mixed liquor suspended solids (MISS) of approximately 2000 mg/L at the start of each trial. A new calibration protocol was proposed by including a systematic calculation of the initial biomass concentrations and microbial relationships as the calibration targets. Moreover, the impact assessment of initial biomass concentrations (X) and maximum growth rates (p) for ammonia-oxidizing bacteria (AOB), nitrite-oxidizing bacteria (NOB), comammox Nunospira, and heterotrophs on the calibration accuracy were investigated using the response surface methodology (RSM). The RSM results revealed the strongest interaction of X-AOB and mu(AOB )on the model calibration accuracy. All the examined model efficiency measures confirmed that the extended model was accurately calibrated and validated. The estimated p values were as follows: mu(AOB) = 0.38 +/- 0.005 d(-1), mu(NOB) = 0.20 +/- 0.01 d(-1), mu(CMX) = 0.20 +/- 0.01 d(-1), mu(HET) = 1.0 +/- 0.03 d(-1). For comparison, when using the conventional model, mu(NOB) and mu(AOB) increased respectively by 26 and 15 % (mu(AOB) = 0.48 +/- 0.02 d(-1) and mu(NOB) = 0.23 +/- 0.005 d(-1)). This study provides better understanding of the effects of the initial biomass composition and the accompanying processes (comammox and heterotrophic denitrification) on modeling two-step nitrification.