By default, ESHA does not calculate Calories based on the 4-4-9. ESHA software (The Food Processor or Genesis R&D) determines Calorie totals by adding up the Calories of the individual foods in a recipe or food list.
Genesis R&D has an additional optional feature which can be enabled for any given Recipe for US or Canadian Nutrition Facts labels. When in a Recipe, go to the Recipe tab of the ribbon and click the Edit Label button. Within, go to Nutrient Options and expand Calories. There, look to the settings for the Calorie Calculation Method (US and Canada).
Per the FDA regulations for U.S. foods, the sources of the individual foods can use one of six different methods for determining Calories for their food. The various foods and ingredients in your Recipes may incorporate more than one of the acceptable Calorie calculation methods. The ESHA Calorie totals reflect this.
The six methods for calculating Calories for Nutrition Facts panels as described in The Code of Federal Regulations (CFR) are: 4-4-9, Atwater factors, 4-4-9 minus insoluble fiber, specific food factors approved by the FDA, bomb calorimetry and using general factors for caloric value of sugar alcohols. These are explained in the CFR, section 101.9(c)(1)(i).