[phenixbb] Refinement error with Se labeled DNA cif seting

[Lauren]

Dear all,

 
I have a protein complex with 10mer DNA with one adenine labeled with Se-CH3
at C2'. 
 
I gave the se labeled pdb structure to the Elbow or ReadySet, the program
gave me the cif as shown below. 
 
When I tried to refine the structure, phenix.refine ends with a Error
message:
 
   Chain: "A"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unexpected atoms: {'AMS,OP1': 1, 'AMS,OP2': 1}
          Classifications: {'DNA': 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
  Number of atoms with unknown nonbonded energy type symbols: 2
    "HETATM    2  OP1 AMS A   1 .*.A    O  "
    "HETATM    3  OP2 AMS A   1 .*.A    O  "

 

Any advice on how to modified the cif or pdb files?
 
Thanks so much in advance.

 

 

CIF files: 

AMS         P      P   P     .         10.3639   38.8090   53.6083

AMS         OP1    O   OH1   .          9.8621   39.4308   52.7650

AMS         OP2    O   O     .          9.6270   38.9790   55.3430

AMS         O5'    O   O2    .         11.5188   37.6926   53.7178

AMS         C5'    C   CH2   .         12.2621   37.6244   54.8065

AMS         C4'    C   CR15  .         13.5128   36.9044   54.7141

AMS         O4'    O   O     .         14.2653   37.1385   55.8584

AMS         C3'    C   CR15  .         13.2442   35.4155   54.6698

AMS         O3'    O   OH1   .         14.1003   34.8289   53.7923

AMS         C2'    C   CR15  .         13.5010   34.9324   55.9516

AMS        SE2'    SE  SE    .         11.8697   34.2402   56.7089

AMS         C1'    C   CR15  .         13.9654   36.1199   56.7679

AMS         CA'    C   CH3   .         11.5566   32.3937   56.0481

AMS         N9     N   NR5   .         15.1526   35.8937   57.6065

AMS         C8     C   CR15  .         16.4077   35.6661   57.1789

AMS         N7     N   N     .         17.1943   35.5119   58.2703

AMS         C5     C   CR56  .         16.4320   35.6429   59.3887

AMS         C4     C   CR56  .         15.1196   35.8884   58.9705

AMS         N1     N   N     .         15.6651   35.7647   61.7193

AMS         C2     C   CR16  .         14.4119   35.9994   61.2874

AMS         N3     N   N     .         14.1134   36.0657   59.9478

AMS         C6     C   CR6   .         16.7122   35.5796   60.8007

AMS         N6     N   NH2   .         18.1110   35.3174   61.2840

#

loop_

_chem_comp_bond.comp_id

_chem_comp_bond.atom_id_1

_chem_comp_bond.atom_id_2

_chem_comp_bond.type

_chem_comp_bond.value_dist

_chem_comp_bond.value_dist_esd

AMS   P       OP1   single        1.162 0.02

AMS   P       OP2   double        1.892 0.02

AMS   P       O5'   single        1.610 0.02

AMS   O5'     C5'   single        1.320 0.02

AMS   C5'     C4'   single        1.446 0.02

AMS   C4'     O4'   single        1.389 0.02

AMS   C4'     C3'   single        1.514 0.02

AMS   O4'     C1'   single        1.398 0.02

AMS   C3'     O3'   single        1.359 0.02

AMS   C3'     C2'   single        1.394 0.02

AMS   C2'    SE2'   single        1.927 0.02

AMS   C2'     C1'   single        1.514 0.02

AMS  SE2'     CA'   single        1.986 0.02

AMS   C1'     N9    single        1.471 0.02

AMS   N9      C8    aromatic      1.345 0.02

AMS   N9      C4    aromatic      1.364 0.02

AMS   C8      N7    aromatic      1.354 0.02

AMS   N7      C5    aromatic      1.360 0.02

AMS   C5      C4    aromatic      1.399 0.02

AMS   C5      C6    aromatic      1.441 0.02

AMS   C4      N3    aromatic      1.414 0.02

AMS   N1      C2    aromatic      1.346 0.02

AMS   N1      C6    aromatic      1.405 0.02

AMS   C2      N3    aromatic      1.374 0.02

AMS   C6      N6    single        1.503 0.02

 

Best Regards

 

Lauren 

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