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. 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]mailto:[email protected] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html

Hi Jack, this is a automatic linking bug in 1.11.1_2575 Official Release. I checked this with the latest code and this does not happen anymore. Anyone else experiencing this problem please update to most recent nightly build: http://phenix-online.org/download/nightly_builds.cgi Pavel On 2/5/17 09:00, Tanner, John J. wrote:

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.

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] mailto:[email protected] http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html http://faculty.missouri.edu/%7Etannerjj/tannergroup/tanner.html

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