[phenixbb] phenix.refine Ile peptide bond breaks
PAfonine at lbl.gov
Wed May 6 20:57:06 PDT 2009
sorry for the problem! From what you describe I can't really see what is
wrong... So let's approach it this way:
- Are you using the latest version of PHENIX (or at least not older than
a few months)? If not, please get the latest:
and try the refinement again.
- It is nearly impossible to tell what is wrong without actually looking
at the PDB file. Could you please send me the PDB file? Also, I will
need the exact command and parameters file (if you use one) that you use
to run refinement. At this point I don't need the data, since I can
simulate it given the PDB file. Please indicate the bonds that get broken.
I will look into this problem once I get the file and the command.
On 5/6/09 6:07 PM, SIPPEL,KATHERINE H wrote:
> Hi all,
> I've got a 2.1 angstrom structure that I am refining. The space
> group is P212121. The structure is a dimer which I am refining
> without NCS restraints. Each monomer has 333 residues and one
> ligand, there are 33 Ile residues in each monomer. The first
> couple of rounds of refinement I had no problems, but during the
> third round phenix started breaking the main chain at the peptide
> bond and the side chain between CA and CB on some of the Ile
> residues. Specifically there are two breaks in chain A and four
> breaks in chain B, with two additional residues in chain B
> breaking only the CA-CB bond. Only one of the breaks is between
> the same residue in both chains.
> I'll be boring and run through my refinement process. This is the
> first time I've used phenix for anything but AutoSol and it is
> very likely that I have messed something up. Feel free to correct
> anything else I've done wrong along the way.
> Round 1, I rigid body refined chain A and B independently,
> performed simulated annealing, and refined individual coordinates.
> In COOT I manually refined and removed some bad loops. A few of
> the Ile were deleted but none of the problem ones
> Round 2, I refined individual_sites and individual_adp and turned
> off simulated annealing. In COOT I rebuilt some of the loops and
> fitted the ligand into the density. I generated a .cif file in
> Round 3, I refined the same as round 2 except that I included the
> .cif file. This is when I got the peptide bond breaks for Ile
> residues. I figured it was a fluke, fixed the breaks in COOT and
> rebuilt a few more residues in the loops.
> I ran another round of refinement and the same breaks showed up in
> the pdb file. I double checked the .geo file to see if Real Space
> Refine had made the bond distances were too long, but all the
> input distances were within one or two hundredths of an angstrom
> from ideal.
> I considered it was maybe the ADP refinement as I was borderline
> pushing the number of parameters I was refining given the number
> of reflections I had. I turned off the individual_adp refinement
> and reran refine_003. No luck.
> I tried increasing the weight of the geometry restraints over the
> observed data. I did this by increasing target_weights.wxc_scale
> = 1.5. (I suspect that I got this wrong. As I understood the
> wxc_scale is the ratio of the geometry restraints to the observed
> data. Feel free to point and laugh as long as you also provide an
> explanation as to what this parameter really means and how I
> should have done it,please.) Still no luck.
> For future information none of the problem isoleucines were
> located near the ligand or near any of the loops I was
> I think that's everything. Any help would be appreciated,
> SIPPEL,KATHERINE H
> Ph. D. candidate
> McKenna Lab
> Department of Biochemistry and Molecular Biology
> College of Medicine
> University of Florida
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> phenixbb at phenix-online.org
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