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
