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:
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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