Conflicting definitions in the `_ihm_cross_link_restraint.model_granularity`

[aozalevsky]

Entry PDBDEV_00000068 has crosslinking restraints defined at the atomic and residue levels at the same time.

loop_
_ihm_cross_link_restraint.id
_ihm_cross_link_restraint.group_id
_ihm_cross_link_restraint.entity_id_1
_ihm_cross_link_restraint.asym_id_1
_ihm_cross_link_restraint.atom_id_1
_ihm_cross_link_restraint.seq_id_1
_ihm_cross_link_restraint.comp_id_1
_ihm_cross_link_restraint.entity_id_2
_ihm_cross_link_restraint.asym_id_2
_ihm_cross_link_restraint.atom_id_2
_ihm_cross_link_restraint.seq_id_2
_ihm_cross_link_restraint.comp_id_2
_ihm_cross_link_restraint.conditional_crosslink_flag
_ihm_cross_link_restraint.model_granularity
_ihm_cross_link_restraint.distance_threshold
_ihm_cross_link_restraint.restraint_type
_ihm_cross_link_restraint.psi
_ihm_cross_link_restraint.sigma_1
_ihm_cross_link_restraint.sigma_2
  1    1  1  A OD1  67  ASN  2  B C5   3  DT  ANY  by-residue  6.0  'upper bound'  0.05  0.01  0.01  
  2    2  1  A NZ   68  LYS  2  B C5   3  DT  ANY  by-residue  6.0  'upper bound'  0.05  0.01  0.01  
  3    3  1  A NZ   69  LYS  2  B C5   3  DT  ANY  by-residue  6.0  'upper bound'  0.05  0.01  0.01  
  4    4  1  A CD1  70  ILE  2  B C5   3  DT  ANY  by-residue  6.0  'upper bound'  0.05  0.01  0.01  
  5    5  1  A CD   71  PRO  2  B C5   3  DT  ANY  by-residue  6.0  'upper bound'  0.05  0.01  0.01  
  6    6  1  A NH2  72  ARG  2  B C5   3  DT  ANY  by-residue  6.0  'upper bound'  0.05  0.01  0.01 

According to dictionary, by-residue means a Ca atom; however, additional atom names are provided here. At the same time, by-residue doesn't define any default particles for non-aminoacids (for instance, nucleic acids like here). I assume the entry can be updated to by-atom.

[aozalevsky]

@brindakv we might want to update this entry to by-atom

[brindakv]

Thanks @aozalevsky This will be addressed during remediation.