[phenixbb] Phenix.refine and Unusual residues

[Haytham Wahba]

Version: 1.7
  Release tag: 650
  Platform: intel-linux-2.6-x86_64 linux
  User: haytham

why phenix does not recognise ACT, PO4 Sn and Br (unusual residue) as you see in this part in the Log file.. (see below)

Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 4
          Unusual residues: {'ACT': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1,
 4
          Unusual residues: {'ACT': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' SN': 1}
          Classifications: {'undetermined': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
         
 Unusual residues: {' SN': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' SN': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4':
 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 5
          Unusual residues: {'PO4': 1}
          Classifications: {'undetermined': 1}
    Chain: "H"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' BR': 1}
         
 Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" SN   SN E   1 " occ=0.70
    residue:
      pdb=" SN   SN E   2 " occ=0.20
---------------------------------------------------------
when i try to refine specially the Tin atom (not other, ACT,...) in coot after phenix.refine. coot display ((no restraints Found,...lablabla))

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this is the PDB (what is the wrong with that)
HETATM 3552  O   HOH S 361      11.670  -4.327   9.559  1.00 34.14           O  
TER    3553      HOH S
 361                                                      
HETATM 3554  OXT ACT C   1      10.133  -3.417   7.937  1.00 20.00           O  
HETATM 3555  C   ACT C   1       9.911  -2.331   7.357  1.00 20.00           C  
HETATM 3556  O   ACT C   1      10.897  -1.607   7.183  1.00 20.00           O  
HETATM 3557 
 CH3 ACT C   1       8.550  -1.912   6.905  1.00 20.00           C
TER    3558      ACT C   1
HETATM 3559  OXT ACT C   2      10.700  -2.628   9.985  1.00 20.00           O  
HETATM 3560  C   ACT C   2      10.962  -1.952  11.000  1.00 20.00           C  
HETATM 3561  O   ACT C   2      11.756  -2.461  11.809  1.00 20.00           O  
HETATM 3562  CH3 ACT C   2      10.364  -0.601 
 11.240  1.00 20.00           C
TER    3563      ACT C   2
HETATM 3564  SN   SN E   1       6.346  -4.396 -16.894  0.70 20.00          SN
TER    3565       SN E   1
HETATM 3566  SN   SN E   2       6.492  -2.146 -14.779  0.20 20.00          SN
TER    3567       SN E   2
HETATM 3568  SN   SN F   1      10.186   0.632   6.366  1.00 30.00          SN
TER   
 3569       SN F   1
HETATM 3570  P   PO4 G   1       5.763  10.047  -3.974  1.00 30.00           P  
HETATM 3571  O1  PO4 G   1       6.960  10.924  -4.190  1.00 30.00           O  
HETATM 3572  O2  PO4 G   1       4.531  10.872  -4.101  1.00 30.00           O  
HETATM 3573  O3  PO4 G   1       5.758   8.978  -5.017  1.00 30.00           O  
HETATM 3574  O4  PO4 G  
 1       5.835   9.456  -2.607  1.00 30.00           O
TER    3575      PO4 G   1
HETATM 3576  P   PO4 G   2       9.060  -4.976 -17.812  1.00 30.00           P  
HETATM 3577  O1  PO4 G   2      10.418  -5.179 -18.415  1.00 30.00           O  
HETATM 3578  O2  PO4 G   2       8.223  -4.116 -18.710  1.00 30.00           O  
HETATM 3579  O3  PO4 G   2       8.412  -6.316 -17.597  1.00
 30.00           O  
HETATM 3580  O4  PO4 G   2       9.172  -4.280 -16.485  1.00 30.00           O
TER    3581      PO4 G   2
HETATM 3582  BR   BR H   1       9.484  11.317 -29.959  1.00 20.00          BR
TER    3583       BR H   1
END
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