[phenixbb] model_vs_data

Pavel Afonine pafonine at lbl.gov
Wed Jan 25 11:42:54 PST 2012

Hi Karolina,

> Information extracted from PDB file header:
>      program_name    : REFMAC
>      year            : None
>      r_work          : 0.15793
>      r_free          : 0.19845
>      high_resolution : 1.45
>      low_resolution  : 36.92
>      sigma_cutoff    : None
>      matthews_coeff  : None
>      solvent_cont    : None
>      TLS             : False (number of groups: 0)

this is exactly what phenix.model_vs_data extracted from the header of 
input PDB file.

>    After applying resolution and sigma cutoffs:
>      n_refl_cutoff : 26357
>      r_work_cutoff : 0.1450
>      r_free_cutoff : 0.1687

These numbers are actually calculated by phenix.model_vs_data (after 
applying all resolution and sigma cutoffs, if any were reported in input 
PDB file header). These numbers may be lower than resorted ones for a 
number of reasons, among which these are the most likely ones:

1) account for twinning (if any present);
2) better bulk-solvent and overall (anisotropic) scaling used in Phenix;
3) rejection of Fobs outliers.

>   When I do refinement in phenix I get practically the same
> results that Refmac produces.

What I wrote above is based on the amount of information you sent us. If 
you send me the input data and model files then I will be able to look 
into the details and explain what's causing the difference.


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