I believe the default in scalepack2mtz in ccp4i is Anomalous on. That clearly explains your observations.
You should consider Ralf's point that the data might have been converted to mtz with separate Friedel pairs, even though it was scaled initially as not.
Engin
----- Original Message -----
From: "Rupert Russell"
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 _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
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