BUSTER Output Interpretation


Examine the refine log file

  • Always capture the standard output of refine to a log file.
    • the normal way to do this is to use the > redirect symbol when starting refine
           % refine -p some.pdb -m other.mtz -d results.dir > refine.log
    • if you prefer it is also possible to use tee so you can see the output in the terminal while at the same capturing it too:
           % refine -p some.pdb -m other.mtz -d results.dir | tee refine.log
  • The refine.log file reports important information. It can be examined in an editor or with less or by using grep.
    • if the job fails it will contain an error message (often this points to additional information in separate log-files: make sure to always follow the information given in the ERROR messages)
    • if the refinement runs through, it is recommended to still look for lines containing the string "WARNING". WARNING messages can often be accepted, but for instance if you re-refine pdb entry 1udt with a grade dictionary for viagra a warning is generated:
            % grep WARNING 1udt_refine.log
WARNING: Have |delta/sigma| deviations > 5.0 sigma. Number of outliers for each term: 
WARNING:        12 bond lengths. Worst is    16.7 sigs     1.31 Angs A|1000:S10=O12 (VIA)
WARNING:        13 bond angles.  Worst is    16.5 sigs   105.07 degs A|1000:O11=S10=O12 (VIA)
WARNING:         2 idealD contacts. Worst     6.0 sigs     2.56 Angs A|677:SG=SG (CYS) symm: 1555=3556
WARNING:         1 Bcorrel.      Worst is     5.6 sigs    22.34 Angs**2 A|590:SD=CE (MET)
      • in this case the VIA residue has some unusual bond angles and bond lengths which can be fixed by refinement. More interestingly is the contact between atom SG of CYS A 677 and a symmetry copy of itself. Looking at the this atom in the final structure and map reveals that a disulfide bond is likely to have been formed.
    • of particular importance are WARNING messages at the end of the refinement. This is because refinement fails to remove them.

The output also reports "table 1" type information:

rms bond deviation should be in range 0.008 to 0.012 Å
rms angle deviation should be around 1.0 to 1.4 degrees
Rwork Rfree depends

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Page by Oliver Smart 07 Feb 2011. Any questions regarding our software or this wiki should be directed to buster-develop@globalphasing.com