I wonder if your ZN atom name is in the correct position re PDB conventions
It needs to be moved one place to the Left relative to C N O etc..
And if you have the ATOMid in columns 79/80 that also must be correctly
positioned..
Some buglets are fixed immediately if you simply use
pdbset xyzin now.pdb xyzout now-fixed.pdb
end
But probably not a shift of atom name..
Eleanor
Vellieux Frederic wrote:
Dear all,
I have a structure (2.25 A resolution) that was refined with CNS and
I'm trying to see if I can improve it ever so slightly using Refmac5.
The structure has 31408 atoms in the asymmetric unit.
The run of Refmac ends with the following lines:
WARNING : link:SS is found dist = 2.063 ideal_dist= 2.031
ch:LL res:3872 CYS at:SG .->LL res:3873 CYS
at:SG .
INFO: link is found (not be used) dist= 2.142 ideal_dist= 1.990
ch:LL res:3813 ASP at:OD2 .->ch:Nv res:3995 ZN
at:ZN .
INFO: link is found (not be used) dist= 2.188 ideal_dist= 1.990
ch:LL res:3846 GLU at:OE2 .->ch:Nv res:3995 ZN
at:ZN .
INFO: link is found (not be used) dist= 2.317 ideal_dist= 2.070
ch:LL res:3947 HIS at:NE2 .->ch:Nv res:3995 ZN
at:ZN .
INFO: link is found (not be used) dist= 2.259 ideal_dist= 2.070
ch:LL res:3702 HIS at:NE2 .->ch:Nw res:3996 ZN
at:ZN .
INFO: link is found (not be used) dist= 2.180 ideal_dist= 1.990
ch:LL res:3813 ASP at:OD1 .->ch:Nw res:3996 ZN
at:ZN .
INFO: link is found (not be used) dist= 2.177 ideal_dist= 1.990
ch:LL res:3868 ASP at:OD1 .->ch:Nw res:3996 ZN
at:ZN .
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
Refmac_5.1.24: No match for full atom ID - subtract one character
Times: User: 47.5s System: 0.1s Elapsed: 0:48
</pre>
<!--SUMMARY_END--></FONT></B>
<B><FONT COLOR="#FF0000"><!--SUMMARY_BEGIN-->
</html>
<!--SUMMARY_END--></FONT></B>
It ends without creating an output PDB file. I can't see one in the
working directory. The last sentence is very cryptic to me (No match
for full atom ID - subtract one character).
Any idea?
Thank you in advance,
Fred.
