If you have tried all of the other things suggested by others (especially beam-center and direction of rotation), you can try the keyword 'weak level' in indexing box (see page 29 on HKL manual http://hkl-xray.com/sites/default/files/manual_online.pdf or http://www.hkl-xray.com/denzo-keywords-alphabetical-order).
This has solved that very problem for me more than once. You will need to play with the value for your data try weak level 2, 5, 20, etc...
I assume you don't have the darkest spots in the world, right?
____________________________________________
Joseph M. Watts, Ph.D.
Syngenta Biotechnology, Inc.
3054 E. Cornwallis Road
Durham, North Carolina. 27709
USA
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