Q: I multiplied protein, fat and carbohydrate values by 4-9-4 (449) but my energy value is different, why?

A: There are a few ways to calculate Calories for a food item.  For example Atwater system, Lab or Database Analysis, 449 calculation, and then the values can also be rounded and recorded for a food.  Since the manufacturer and other sources of food data can use any of these methods for analysis and since a diet or recipe will have a mixture of these foods which have used various different allowable methods for calculating Calories, there can be differences when you use the 449 method in your diet or recipe.  

Per USDA here is an explanation about the difference when calculating with 449 formula.  

Calorie values are based on the Atwater system for determining energy values. The factors used in the calculation of energy in the database are given in the food description file of the USDA National Nutrient Database for Standard Reference, Release. The basis and derivation of these factors are described in:

Merrill, A.L. and Watt, B.K. 1973. Energy Value of Foods...Basis and Derivation. Agriculture Handbook No. 74. U.S. Government Printing Office. Washington, DC. 105p.

The Atwater system uses specific energy factors which have been determined for basic food commodities. These specific factors take into account the physiological availability of the energy from these foods. The more general factors of 4-9-4 were developed from the specific calorie factors determined by Professor Atwater and associates. 

For multi-ingredient foods which are listed by brand name, calorie values generally reflect industry practices of calculating calories from 4-9-4 kcal/g for protein, fat, and carbohydrate, respectively, or from 449 minus insoluble fiber. The latter method is frequently used for high-fiber foods because insoluble fiber is considered to provide no physiological energy.

If the user is using a MFR food, rounding may play a part in calorie difference as well.