Hi All,

I am refining a protein nucleic acid complex in Refmac5 and came across a
couple of issues. Some of the nucleic acid residues are modified [eg: 2'-Fluoro cytidine monophosphate (CFZ) and 2'Fluoro adenosine monophosphate (AF2); both the monomer dictionaries are defined in CCP4 database (ccp4-6.3.0, linux version). While refining,
the program gives the message "link is found (not be used)". Why this happens and
how to fix this?

-------------(from log file)
  I am reading library. Please wait.
                mon_lib.cif
  INFO:     link is found (not be used) dist=   1.411 ideal_dist=   1.510
            ch:CC   res:   5  CFZ              at:P   .->ch:CC   res: 104  AF2              at:OP2 .
  INFO:     link is found (not be used) dist=   1.539 ideal_dist=   1.510
            ch:CC   res:   5  CFZ              at:P   .->ch:CC   res: 104  AF2              at:OP1 .
  INFO:     link is found (not be used) dist=   1.698 ideal_dist=   1.610
            ch:CC   res:   5  CFZ              at:P   .->ch:CC   res: 104  AF2              at:O5' .
  INFO:     link is found (not be used) dist=   1.412 ideal_dist=   1.510
            ch:CC   res:   5  CFZ              at:O1P .->ch:CC   res: 104  AF2              at:P   .
  INFO:     link is found (not be used) dist=   0.112 ideal_dist=   1.150
            ch:CC   res:   5  CFZ              at:O1P .->ch:CC   res: 104  AF2              at:OP1 .
  INFO:     link is found (not be used) dist=   1.650 ideal_dist=   1.510
            ch:CC   res:   5  CFZ              at:O2P .->ch:CC   res: 104  AF2              at:P   .
  INFO:     link is found (not be used) dist=   0.715 ideal_dist=   1.150
            ch:CC   res:   5  CFZ              at:O2P .->ch:CC   res: 104  AF2              at:OP2 .
  INFO:     link is found (not be used) dist=   1.725 ideal_dist=   1.610
            ch:CC   res:   5  CFZ              at:O5' .->ch:CC   res: 104  AF2              at:P   .

  ..........................and so on

-------------(also for CFZ)
  INFO:     link is found (not be used) dist=   0.140 ideal_dist=   2.214
            ch:CC   res:   6  CFZ              at:P   .->ch:CC   res: 105  CFZ              at:P   .
  INFO:     link is found (not be used) dist=   1.490 ideal_dist=   1.510
            ch:CC   res:   6  CFZ              at:P   .->ch:CC   res: 105  CFZ              at:O1P .
  INFO:     link is found (not be used) dist=   1.397 ideal_dist=   1.510
            ch:CC   res:   6  CFZ              at:P   .->ch:CC   res: 105  CFZ              at:O2P .
  INFO:     link is found (not be used) dist=   1.596 ideal_dist=   1.610
            ch:CC   res:   6  CFZ              at:P   .->ch:CC   res: 105  CFZ              at:O5' .
  INFO:     link is found (not be used) dist=   1.427 ideal_dist=   1.510
            ch:CC   res:   6  CFZ              at:O1P .->ch:CC   res: 105  CFZ              at:P   .
  INFO:     link is found (not be used) dist=   0.146 ideal_dist=   1.150
            ch:CC   res:   6  CFZ              at:O1P .->ch:CC   res: 105  CFZ  


............................ and so on


In addition, in the output PDB, I find a few angles that are not ideal 97 degrees
(ideal 109 deg) and 129 degrees (ideal 109 deg). For the links, is it necessary to
put the link records in the pdb and then define it in the dictionary as well? Is there
a column format that one should follow in order to get the dictionary to be read?
In this particular case, the dictionary contains only description of links as the
monomers are available in the ccp4 database.


# --- DESCRIPTION OF LINKS ---
.
.
.

data_link_AF2-CFZ
#
loop_
_chem_link_bond.link_id
.
.
.
 AF2-CFZ    1 "O3'"   2 P      single        1.580    0.020
loop_
_chem_link_angle.link_id
.
.
.
 AF2-CFZ     1 "C3'"   1 "O3'"        2   P            118.7     3.00
 AF2-CFZ     1 "O3'"   2   P          2   O1P          108.7     3.00
 AF2-CFZ     1 "O3'"   2   P          2   O2P          108.7     3.00
 AF2-CFZ     1 "O3'"   2   P          2 "O5'"          108.7     3.00


What's the best way to correct the above errors, any suggestions?

Thank you,
Pradeep Pallan