Hi Andrew, the ccp4 ANP.cif entry for C4'-C5' is 1.528A, but both the Phenix and Grade cif list 1.508A. The distance in 2JDI is 1.53, so if molprobity relies on one of the latter two sources, this might be the source of the flag. Also some shelxl dictionary lists 1.509A, so it's 3:1 for the flag being correct.
Well, this doesn't answer your actual question, but it may still be informative. Cheers, Tim On 09/15/2014 04:24 PM, Andrew Leslie wrote: > Does anyone know if Molprobity has recently changed the standard bond lengths > and angles that it uses ? > > Molprobity is reporting errors in the C4-C5 bond length and the C5-C4-N3 bond > angle (deviations of 8-10 sigma) for AMPPNP (monomer code ANP) for a new > structure refined with Refmac. I then tried Molprobity on a deposited PDB > structure that also contains AMPPNP and it reported the same errors. I am > sure that these errors were not reported when this structure (2JDI) was > deposited in 2007. > > This would suggest that the standard dictionary that Molprobity uses has > changed, but I cannot find any reference to this on the Molprobity pages. > > I would be very grateful if anyone can throw some light on this. > > Thanks, > > Andrew > -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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