It seems that you probably use the default option
INTERVAL=EIGENFREQUENCY
Abaqus calculates the responce for each eigenfrequency and 498 points in between (in your case- 1Hz, next 498 points, first eigenfrequncy, next 498 points, second eigenfrequency etc.).
You should use INTERVAL=RANGE to...
You could try with substructures, see below Abaqus Analysis user's manual:
10.1.1 Using substructures
...
Comparison with component mode synthesis
The component mode synthesis method (also known as the Craig-Bampton method) has been developed to permit the structure to be subdivided into...