covalent bond between symmetry related halves of a spermine molecule

[Gerard 'CD' Kleywegt]

>In this regime, the enery between your ligand and itself won't
>be calculated, so there will be no self repulsion.

nor will the ligand obey the crystallographic symmetry
(unless you introduce strong "ncs" restraints internally)

a much simpler solution is to use a strong harmonic
restraint on the offending carbon (you have to put
it into the density such that it is at a normal
distance from its symmetry mate; use the symm_sphere
and dist_def or neigh_at commands in O)
alternative: fix the carbon entirely (but it think
a harmonic restraint is better)

you can use the same tricks if you have for example a
disulfide bridge between two xtallographically related
cysteines

--gerard