Note that Refmac will include the TLS contribution to the B-factors on the atom records if the keyword "TLSO ADDU" is given (of course, this is good for analysis and PDB submission, but not good for running subsequent Refmac runs since Refmac expects the atom records to contain the "residual" B-factors.)
Also, if the keyword TLSD WATERS INCLUDE is active, tlsanl may not give the correct result. Specifically, since this keyword assigns waters to the existing TLS groups, but does not include their assignment in the TLSOUT or PDB header sections describing the TLS groups, then tlsanl cannot add the TLS contribution to the waters and you end up with full B's on the protein atoms (described in the TLS cards) and residual B's on the waters. In this case, only the refmac TLSO ADDU option will be able to write the full-B for both the protein and water. In refmac 5.5 the default is TLSDetails WATERS INCLUDE You need to give the keyword TLSDetails WATERS EXCLUDE if you don't want your waters automatically assigned to TLS groups. Regards, Mitch -----Original Message----- From: CCP4 bulletin board [mailto:[email protected]] On Behalf Of Tim Gruene Sent: Tuesday, November 23, 2010 2:06 PM To: [email protected] Subject: Re: [ccp4bb] Low B-factors Dear Paula, I do not know about phenix, but the refmac5 output PDB file does not contain the contribution from the TLS refinement (not sure I get the terminology right). In order to get an idea of the average B-values, you should run tlsanl on the output of refmac5 with the keyword 'bresid true'. Tim On Tue, Nov 23, 2010 at 07:04:07PM +0000, Paula Salgado wrote: > Dear all > > I'm refining a 33kDa protein model and I have noticed that although all > other statistics seem fine, B factor values are quite low, with many around > 7-10A2 and average overall values as follows. > > Total number of atoms in chain A 2378 > Average B value for main chain A 10.684 > Average B value for side chain A 12.755 > Average B value for whole chain A 11.665 > > Average rms B for 312 main chain residues 0.748 > Average rms B for 273 side chain residues 1.777 > > These are values after anisotropic B refinement, with 1 TLS group in > refmac5. I get similar results if refinement is done without TLS (using > model + mtz before doing TLS refinement) and with > isotropic/overall/anisotropic B refinement and. Resetting B values to an > arbitrary high value (50 or 70) and rerunning refinement with all possible > options on/off also gives the same results. > > Using Phenix, after resetting B values before refinement to arbitrary > values and with anisotropic or isotropic refinement, with or without > occupancy refinement also gives similar results. > > As refinement of related molecules (but in different ligand bound states) > from similar quality crystals results in models with more realistic B > factors (as shown bellow), I strongly suspect that the B factors for this > protein have been over refined. However, I'm not sure what other refinement > settings to use to avoid this problem. > > Total number of atoms in chain A 2352 > Average B value for main chain A 20.651 > Average B value for side chain A 21.815 > Average B value for whole chain A 21.199 > > Any help and advice is most appreciated. > > Best regards > Paula > > > ======================================================== > > Dr Paula Salgado > > Division of Molecular Biosciences > Department of Life Sciences > Faculty of Natural Sciences > Biochemistry Building, 5th Floor > Imperial College London > South Kensington Campus > SW7 2AZ > London > > Tel: +44 (0)2075945464 > Fax: +44 (0)20 7594 3057 -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen phone: +49 (0)551 39 22149 GPG Key ID = A46BEE1A
