[phenixbb] Phenix Autobuild error

Xiao Lei xiaoleiusc at gmail.com
Fri Jul 24 14:31:40 PDT 2015

Hi All,

I am using Phenix autobuild (version 1.10pre on CentOS) and I failed with
an error message (I put it below). My input experimental data (in MTZ
format) is 2.5A, with space group C2, and 1 molecule per ASU (No NCS
copies), the molecule contains two protein chains and one double-strand DNA
(heterodimer protein bound to dsDNA). It seems to me the error is because
in my model PDB there are different atoms in DNA with the same name.

How can I fix this problem?

Error message from phenix.refine:  number of groups of duplicate atom
labels: 4
  total number of affected atoms:          8
  group "HETATM 4930  O3'  DT C 716 .*.     O  "
        "HETATM 5471  O3'  DT C 716 .*.     O  "
  group "HETATM 4937  C7   DT C 716 .*.     C  "
        "HETATM 5472  C7   DT C 716 .*.     C  "
  group "HETATM 4950  O3'  DG C 717 .*.     O  "
        "HETATM 5473  O3'  DG C 717 .*.     O  "
  group "HETATM 4964  O6   DG C 717 .*.     O  "
        "HETATM 5474  O6   DG C 717 .*.     O  "
Refinement failed...

Thanks ahead.

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