[phenixbb] unexpected automatic linking between ligands in phenix.refine

Tanner, John J. TannerJJ at missouri.edu
Sun Feb 5 09:00:20 PST 2017

Dear phenix users,

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.



  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
  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: tannerjj at missouri.edu<mailto:tannerjj at missouri.edu>

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