In your case the likely cause of noise is insufficient atmosphere samples. Although you do have fairly high sample settings (128 for atmosphere), your lighting is quite dramatic and complex and so higher settings may be necessary to eliminate grain. You can try 256 but I wouldn't bother trying higher than that - the render time will be very high. I would also *reduce* the quality/samples of the clouds, perhaps to 2 or so, since the majority of noise is actually coming from the atmosphere. So you can essentially trade render time on clouds for atmosphere and it should have a greater effect.
If 256 atmosphere samples fails to resolve it I would instead look at post processing with a noise removal tool of some kind, for example Noise Ninja or Neat Image. At a certain point the increased render time needed to eliminate noise entirely is no longer worth it and the results such post processing tools can give you are essentially as good, as long as the noise isn't too severe.
- Oshyan
