Could it be that you reserved 10% of your data for Rfree and are looking at the completeness for the work set? Do you have an I/sigma(I) cutoff that is high? If not, it might help to post the some of the Phenix output, e.g., the table with the completeness data along with the resolution limits, etc. Best - MM

On Feb 3, 2010, at 10:42 PM, J. Fleming wrote:

Hi,
 
  I'm having a problem using phenix.refine with my x-ray data.  My completeness is always 89% when it should be 99%.  My data was originally processed with CCP4i.  I found an old post (see below) with a potential fix that doesn't work for me.  I've tried changing the 'Anomalous flag: True' to 'Anomalous flag: False'  but my completeness is still 89%.  I've clicked through a variety of other setting in the GUI that I thought would help but no luck. Does anyone have any ideas?   

Thanks in advance,
Jon


----- Original Message -----
From: "Ralf W. Grosse-Kunstleve" <rwgk at cci.lbl.gov>
To: phenixbb at phenix-online.org
Sent: Monday, December 15, 2008 12:59:12 PM GMT -05:00 US/Canada Eastern
Subject: Re: [phenixbb] Completeness issue by phenix

Hi YoungJin,

I suspect phenix.refine decided your mtz file contains anomalous data
when you actually have non-anomalous data. Could you look in the
phenix.refine output for something like this:

================================== X-ray data =================================

F-obs:
1yjp.mtz:FOBS_X,SIGFOBS_X

R-free flags:
1yjp.mtz:R-free-flags

Miller array info: 1yjp.mtz:FOBS_X,SIGFOBS_X
Observation type: xray.amplitude
Type of data: double, size=495
Type of sigmas: double, size=495
Number of Miller indices: 495
Anomalous flag: False
^^^^^
in particular here

If you see "Anomalous flag: True" try adding this to the phenix.refine
command line:

xray_data.force_anomalous_flag_to_be_equal_to=False

Let me know if this doesn't help.
If it does help, I'd be interested to know how the .mtz file was
generated.

Ralf

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