Ahh yes, I looked at the wrong line. My Rmsd bond angle is 2.55 degrees (not bond length). MolProbity states that my only abnormal angle is 124.23 degrees between O--C--N of an Arg. Real Space Refinement does not change anything and Regularizing the zone completely distorts the backbone. Any suggestions on how to fix this?
------------------------------------------------------------------------------- Greg Costakes PhD Candidate Department of Structural Biology Purdue University Hockmeyer Hall, Room 320 240 S. Martin Jischke Drive, West Lafayette, IN 47907 -------------------------------------------------------------------------------- ----- Original Message ----- From: "Bernard D. Santarsiero" <b...@uic.edu> To: "Greg Costakes" <gcost...@purdue.edu> Sent: Thursday, February 16, 2012 11:42:55 AM Subject: Re: [ccp4bb] Bond Length Outliers Greg, Your RMSD on bond lengths should be around 0.01A (your structure vs. idealized library), and the RMSD on bond angles should be around 1.5deg. You must be using an incorrect value of the weight factor between structure factors and geometric factors, and relying too heavily on structure factors. Bernie On Thu, February 16, 2012 10:31 am, Greg Costakes wrote: > I am currently in the final steps of refining a 1.3A structure and am > coming across a slight problem. According the the pdb file, I have an Rmsd > bond length of 2.55. MolProbity identifies three outliers which correspond > to the bond lengths of: > Asp: C--O , bond length = 1.2A > Arg: C--O , bond length = 1.15A > Ala: N--Ca , bond length = 1.43A > > > Real space refinement in Coot does not help and if I Regularize the zone > it completely distorts the backbone. So my question is, how do I fix these > bond length outliers? Do I need to be concerned with them? Any advice will > be much appreciated. Thank you! > > > > ------------------------------------------------------------------------------- > > Greg Costakes > PhD Candidate > Department of Structural Biology > Purdue University > Hockmeyer Hall, Room 320 > 240 S. Martin Jischke Drive, West Lafayette, IN 47907 > > -------------------------------------------------------------------------------- > > > >
