I’m refining a model that has FAD and SO4 ligands. Phenix makes a covalent bond between the N3 of the FAD and an O atom of SO4 during the automatic linking stage, even though the distance between the atoms is larger than the automatic link distance. The covalent bond yanks the ligands out of their density. I suppose I could disable automatic linking, but I’ve never seen this happen. I note that we recently upgraded to phenix-1.11.1-2575, and this may be my first refinement calculation with the new version. Output is shown below.

I welcome any suggestions.

Thanks,

Jack

              -------------------------------------------------------------------------------

                PHENIX: Python-based Hierarchical ENvironment
                for Integrated Xtallography

                Version: 1.11.1

                Release tag: 2575

                Platform: intel-linux-2.6-x86_64

                User: tannerjj

              -------------------------------------------------------------------------------

---------------------------------------------------------------

From the phenix.refine log file:

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : False - 3.50
        Amimo acid           : False - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Amino acid - RNA/DNA : False


                
  Number of custom bonds: simple=2,
                    symmetry=0
  Number of additional bonds: simple=2,
                    symmetry=0
  Coordination:
  Other bonds:

                     
                    Simple bond:   pdb=" N3  FAD C 601 " - pdb=" O2  SO4 F 605 "

                     
                    Simple bond:   pdb=" N3  FAD D 601 " - pdb=" O4  SO4 F 606 "
  Time building additional restraints: 2.29
  Conformation dependent library (CDL)
                    restraints added in 636.6 milliseconds
.
.
.


                
  Bond restraints:
                        15971
  Sorted by
                        residual:

                       
                        bond pdb=" N3  FAD D 601 "

                        
                            pdb=" O4  SO4 F 606 "
    ideal  model 
                        delta    sigma   weight residual
    1.297  3.084
                        -1.787 1.00e-02 1.00e+04 3.19e+04

                       
                        bond pdb=" N3  FAD C 601 "

                        
                            pdb=" O2  SO4 F 605 "
    ideal  model 
                        delta    sigma   weight residual
    1.297  2.975
                        -1.678 1.00e-02 1.00e+04 2.81e+04


                      
---------------------------------------------------------------


                    
The output refined PDB file shows the
                      links were made. The LINK lines were not in the
                      input PDB file. 


                    

                  LINK         N3  FAD C
                  601                 O2  SO4 F
                  605

                  LINK         N3  FAD D
                  601                 O4  SO4 F
                  606

---------------------------------------------------------------

John J. Tanner, PhD
Professor of Biochemistry and Chemistry

Director, Biochemistry Graduate Admissions Committee

Department of Biochemistry

University of Missouri-Columbia
117 Schweitzer Hall
503 S. College Avenue
Columbia, MO 65211
Phone: 573-884-1280
Fax: 573-882-2754
Email: [email protected]
http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html