[phenixbb] does phenix.refine ignore F-obs, SIGF-obs?
Pavel Afonine
PAfonine at lbl.gov
Thu Mar 11 13:34:12 PST 2010
Hi Scott,
phenix.refine removes only zero or strictly negative values. ONLY. NOthing else! It will not remove a reflection like Fobs=0.0001, regardless sigma.
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.03
means that this is what in your data file, but it does NOT mean it removed any positive Fobs.
Pavel.
PS> I'm not in a convenient place to look into it carefully, but if you send me the data I will have a look in a few days when I come back to Berkeley.
----- Original Message -----
From: Scott Classen <SClassen at lbl.gov>
Date: Thursday, March 11, 2010 4:27 pm
Subject: Re: [phenixbb] does phenix.refine ignore F-obs, SIGF-obs?
To: PHENIX user mailing list <phenixbb at phenix-online.org>
>
> Here are some excerpts from the phenix.refine log file:
>
> Resolution range: 44.4024 1.8604
> Completeness in resolution range: 0.995991
> Completeness with d_max=infinity: 0.995862
>
> Number of F-obs in resolution range: 92411
> Number of F-obs <= 0: 3322
> Refinement resolution range: d_max = 44.4024
> d_min = 1.8604
>
>
> Fobs statistics after all cutoffs applied:
>
> Miller array info: None
> Observation type: xray.amplitude
> Type of data: double, size=89089
> Type of sigmas: double, size=89089
> Number of Miller indices: 89089
> Anomalous flag: False
> Systematic absences: 0
> Centric reflections: 11672
> Resolution range: 44.4024 1.8604
> Completeness in resolution range: 0.960187
> Completeness with d_max=infinity: 0.960063
>
>
>
> This implies to me that phenix.refine is throwing out my very weak
> reflections. It appears that completeness goes from 99.6% to 96.0%
>
> Then further down in the log file I see:
>
> ============================== Outliers rejection
> =============================
> Distribution of F-obs values before outliers rejection:
> 0.126 - 28.714 : 65519
> 28.714 - 57.302 : 13850
> 57.302 - 85.890 : 5625
> 85.890 - 114.478 : 2515
> 114.478 - 143.066 : 991
> 143.066 - 171.654 : 393
> 171.654 - 200.242 : 128
> 200.242 - 228.830 : 49
> 228.830 - 257.418 : 12
> 257.418 - 286.006 : 7
>
> basic_wilson_outliers = 0
> extreme_wilson_outliers = 0
> beamstop_shadow_outliers = 0
> model_based_outliers = 1
> total = 1
>
> Distribution of F-obs values after outliers rejection:
> 0.126 - 28.714 : 65519
> 28.714 - 57.302 : 13850
> 57.302 - 85.890 : 5624
> 85.890 - 114.478 : 2515
> 114.478 - 143.066 : 991
> 143.066 - 171.654 : 393
> 171.654 - 200.242 : 128
> 200.242 - 228.830 : 49
> 228.830 - 257.418 : 12
> 257.418 - 286.006 : 7
>
>
> which makes it look like nothing is being rejected?
>
> So what is it?
>
> in the header of the resulting pdb file:
>
> REMARK 3 DATA USED IN REFINEMENT.
> REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.860
> REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.402
> REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.03
> REMARK 3 COMPLETENESS FOR RANGE (%) : 96.02
> REMARK 3 NUMBER OF REFLECTIONS : 89088
>
>
> which implies that indeed some reflections are being rejected.
>
> My hunch is that if F-obs = SIGF-obs then the reflection is rejected.
>
> Thanks,
> Scott
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