[phenixbb] does phenix.refine ignore F-obs, SIGF-obs?
Scott Classen
SClassen at lbl.gov
Thu Mar 11 13:26:51 PST 2010
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
More information about the phenixbb
mailing list