[phenixbb] Zinc-cysteine bond refinement in phenix_refine
Nigel Moriarty
nwmoriarty at lbl.gov
Wed Aug 31 10:30:56 PDT 2011
The bond angles are taken from the input file, so its a good idea to
remove them in the initial rounds of refinement.
Nigel
On Wed, Aug 31, 2011 at 10:05 AM, Zhang yu <phenixzyfish at gmail.com> wrote:
> Dear all,
> I have been stuck in the problem for a while. I appreciate any suggestions.
> I have two zinc binding domain in my 3A structure which are Cys4 type. The
> geometry is OK for one domain, but it is not refined properly in the other
> one.
> The problems during phenix refinement are
> 1. Zinc is always refined to position ~0.5A off from its correct position
> 2. The refined bond lengths of four Cys-Zn are all below 2.3
> 3. Sometimes, distances between SG atoms of nearby cysteines are too close,
> and coot just connect them as disulfate bond.
> 4. Sometimes, I get the following message showing that all bond angles are
> outliers with >8 sigmas, I listed part of the outliers.
>
> Top angle outliers (sorted by deviation):
> atoms ideal model difference
> deviation (sigma)
> ----------------------------------------------------------------------------
> SG CYS D1204 57.894 104.470 46.576 9.32
> ZN ZN D2001
> SG CYS D1112
> SG CYS D1201 50.842 92.496 41.654
> 8.33
> ZN ZN D2001
> SG CYS D1204
> SG CYS D1204 126.952 92.496 -34.455 -6.89
> ZN ZN D2001
> SG CYS D1201
> SG CYS D1201 52.183 86.105 33.922 6.78
> ZN ZN D2001
> SG CYS D1112
> SG CYS D1194 152.275 119.729 -32.546 -6.51
> ZN ZN D2001
> SG CYS D1112
> SG CYS D1112 89.273 119.729 30.456 6.09
> ZN ZN D2001
> SG CYS D1194
> I also post my metal.edit file for refinement
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq 1201
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq 1194
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq 1112
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
> refinement.geometry_restraints.edits {
> bond {
> action = *add
> atom_selection_1 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_2 = name SG and chain D and resname CYS and resseq 1204
> distance_ideal = 2.310000
> sigma = 0.100
> }
> }
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1194
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1201
> angle_ideal = 112.172178
> sigma = 5
> }
> }
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1112
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1201
> angle_ideal = 87.092184
> sigma = 5
> }
> }
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1112
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1194
> angle_ideal = 118.116518
> sigma = 5
> }
> }
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1201
> angle_ideal = 91.677138
> sigma = 5
> }
> }
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1194
> angle_ideal = 130.829256
> sigma = 5
> }
> }
> refinement.geometry_restraints.edits {
> angle {
> action = *add
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1112
> angle_ideal = 104.886672
> sigma = 5
> }
> }
>
> Questions,
> 1. Why the ideal bond angle are different in the metal.edit file and final
> model ? How does phenix determine the ideal bond_angle?
> For example, in the metal.edit file
> atom_selection_1 = name SG and chain D and resname CYS and resseq 1204
> atom_selection_2 = name ZN and chain D and resname ZN and resseq 2001
> atom_selection_3 = name SG and chain D and resname CYS and resseq 1112
> The angle_ideal = 104.886672
> But in the final model
>
> atoms ideal model difference
> deviation (sigma)
> ----------------------------------------------------------------------------
> SG CYS D1204 57.894 104.470 46.576 9.32
> ZN ZN D2001
> SG CYS D1112
> 2. Do I need to put the following LINK in the pdb header to run refinement?
> LINK ZN ZN D2001 SG CYS D1201 1555 1555
> 2.34
> LINK ZN ZN D2001 SG CYS D1112 1555 1555
> 2.33
> LINK ZN ZN D2001 SG CYS D1194 1555 1555
> 2.38
> LINK ZN ZN D2001 SG CYS D1204 1555 1555
> 2.37
> 3. After phenix refinement, the output pdb doesn't contain these LINK lines
> no matter what the inpout pdb is. Does phenix_refine use these restrains of
> LINK lines?
> Thanks.
> Yu Zhang
> Postdoc fellow
> Rutgers University
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>
>
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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