Try looking at the differences in completeness when you run CCP4's Truncate with TRUNCATE YES and TRUNCATE NO. The former option alters the intensity distribution such that most of the weak data are set to small positive values. Depending on phenix.refine's current policies this may alter how many reflections are included in refinement. Another way to see this is to look at the range of values for Imean data in the MTZ file using something like Mtzdump - if the completeness reported by Mtzdump is what you expect, but the range of values includes negative intensities that might be the source of your problem. Negative intensities can be a significant proportion of data for anisotropic diffraction. BTW: you're posting on Phenixbb for CCP4 programs. Better to ask this question in CCP4bb if the above doesn't answer it. Phil Jeffrey Princeton ________________________________________ From: [email protected] [[email protected]] on behalf of [email protected] [[email protected]] Sent: Saturday, July 07, 2012 12:24 AM To: PHENIX user mailing list Subject: [phenixbb] a question on completeness Hi all, I have one question on completeness. The output from SCALA give the completeness of about 97 to 99%, but after TRUNCATE, the completeness becomes only 90%. I tried to refine my model against intensity or amplitude. They show different completeness too. I guess some reflections are deleted during the truncation, but i could not see the corresponding information in the log file. Does anybody have any experience on what cause the difference in completeness? Thanks in advance! Fengyun _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb