Dear CCP4 users,
I am a beginner in this field. It would be kind of all of you if can help
me how to move ahead with my problem.
I have an output file from CNS of a binary complex (DNA-protein) and I am
trying to refine it with refmac5 (restrain refinement) and job is failing
with error messages (written below)
Before restrain refinement, I converted the CNS output file (pdb) from
Codconv of CCP4 to pdb format.
Thanks in advance
Vidisha
INFO: link is found (not be used) dist= 3.003 ideal_dist= 2.400
ch:CC res: 1 GUA at:C2' .->ch:Ca res: 2 GUA
at:O2P
.
INFO: link is found (not be used) dist= 2.625 ideal_dist= 2.400
ch:CC res: 1 GUA at:C3' .->ch:Ca res: 2 GUA
at:P .
INFO: link is found (not be used) dist= 2.797 ideal_dist= 2.400
ch:CC res: 1 GUA at:C3' .->ch:Ca res: 2 GUA
at:O2P
.
INFO: link is found (not be used) dist= 1.606 ideal_dist= 2.400
ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA
at:P .
INFO: link is found (not be used) dist= 2.499 ideal_dist= 2.400
ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA
at:O1P
.
INFO: link is found (not be used) dist= 2.504 ideal_dist= 2.400
ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA
at:O2P
.
INFO: link is found (not be used) dist= 2.507 ideal_dist= 2.400
ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA
at:O5'
.
INFO: link is found (not be used) dist= 2.843 ideal_dist= 2.400
ch:CC res: 1 GUA at:O3' .->ch:Ca res: 2 GUA
at:C5'
.
INFO: link is found (not be used) dist= 2.637 ideal_dist= 2.400
ch:Ca res: 2 GUA at:C3' .->ch:Cb res: 3 ADE
at:P .
INFO: link is found (not be used) dist= 3.116 ideal_dist= 2.400
ch:Ca res: 2 GUA at:C3' .->ch:Cb res: 3 ADE
at:O1P
.
INFO: link is found (not be used) dist= 1.604 ideal_dist= 2.400
ch:Ca res: 2 GUA at:O3' .->ch:Cb res: 3 ADE
at:P .
INFO: link is found (not be used) dist= 2.504 ideal_dist= 2.400
ch:Ca res: 2 GUA at:O3' .->ch:Cb res: 3 ADE
at:O1P
.
INFO: link is found (not be used) dist= 2.514 ideal_dist= 2.400
ch:Ca res: 2 GUA at:O3' .->ch:Cb res: 3 ADE
at:O2P
.
ATTENTION: atom:O4 GUA 1 CC is missing in the structure
ATTENTION: atom:O3 GUA 1 CC is missing in the structure
ATTENTION: atom:C3 GUA 1 CC is missing in the structure
ATTENTION: atom:C1 GUA 1 CC is missing in the structure
ATTENTION: atom:O1 GUA 1 CC is missing in the structure
ATTENTION: atom:O2 GUA 1 CC is missing in the structure
===> Error: Fatal error. Cannot continue
