[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


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