[phenixbb] Is this a Phaser bug or am I misinterpreting ?

Phil Jeffrey pjeffrey at princeton.edu
Tue Dec 4 16:17:30 PST 2012


Phaser from CCP4 6.3.0 built via fink running on OSX 10.6.8 in 64-bit mode.

This is a snippet from a much larger run, ongoing.  In multiple 
instances the order of the LLG and the Z-score in the translation 
function are not in sync:  (42.16, 40.23, 40.18 vs 5.14, 5.24, 4.82) and 
looks like the Z-scores are still shown in the peak rank order before 
rescoring, while the LLGs are after rescoring.


    SET #5 of 6 TRIAL #60 of 115
    ----------------------------
    Search Euler =  263.0   82.1   85.7, Ensemble = ensemb3

    ANNOTATION:  RFZ=3.6 TFZ=3.8 PAK=0 LLG=26 LLG=30
    Known MR solutions
    SOLU SPAC C 1 2 1
    SOLU 6DIM ENSE ensemb3 EULER 30.6 65.7 246.9 FRAC 0.90 0.00 0.17 
BFAC -5.14

    Grid sampling: 0.825029 Angstroms

    Select peaks over 67.5% of top (i.e. 0.675*(top-mean)+mean)
    Top 360 translations before clustering will be rescored
    Calculating Likelihood for TF SET #5 of 6 TRIAL #60 of 115
    0% 
       100%
 
|=========================================================================| 
DONE

    Scoring 1 randomly sampled translations
    Generating Statistics for TF SET #5 of 6 TRIAL #60 of 115
    0% 100%
    |==| DONE


    Top Peaks With Clustering
    -------------------------
    #       Rank of the peak after rescoring search points
    (#)     Rank of the peak before rescoring search points
    LLG     Log-Likelihood Gain
    Z-Score Number of standard deviations of LLG above the mean
    FSS     Fast Search Score

    Select all peaks
    There were 159 peaks
    #     (#)   Frac X Frac Y Frac Z   LLG   Z-score Split #Group 
raw/top
    1     6      0.842  0.923  0.779  +42.16    5.14     0      2 
52.58/ 52.58
    2     3      0.369  0.865  0.553  +40.23    5.24    37      2 
53.18/ 53.18
    3     10     0.743  0.937  0.261  +40.18    4.82    48      2 
50.69/ 50.69
    #SITES = 159: OUTPUT TRUNCATED TO 3 SITES



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