[ccp4bb]: Mannose branching error in refmac

[David W Borhani]

Hi, I'm getting this error from Refmac (5.2.0005) with a N-linked carbohydrate chain:

  Number of atoms    :    3558
  Number of residues :     434
  Number of chains   :      22
  I am reading library. Please wait.
                mon_lib.cif
  WARNING : CIS peptide bond is found, angle =      6.41
            ch:AA res: 373  TYR      --> 374  PRO
  WARNING : CIS peptide bond is found, angle =      4.93
            ch:BB res: 373  TYR      --> 374  PRO
  WARNING : link:SS       is found dist =     2.034 ideal_dist=     2.031
            ch:AA res: 261  CYS      at:SG  .->AA res: 321  CYS      at:SG  .
  WARNING : link:SS       is found dist =     1.992 ideal_dist=     2.031
            ch:AA res: 367  CYS      at:SG  .->AA res: 425  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.001 ideal_dist=     2.031
            ch:BB res: 261  CYS      at:SG  .->BB res: 321  CYS      at:SG  .
  WARNING : link:SS       is found dist =     2.043 ideal_dist=     2.031
            ch:BB res: 367  CYS      at:SG  .->BB res: 425  CYS      at:SG  .
  WARNING : link:NAG-ASN  is found dist =     1.392 ideal_dist=     1.439
            ch:BB res: 297  ASN      at:ND2 .->DD res:   1  NAG      at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.390 ideal_dist=     1.439
            ch:DD res:   1  NAG      at:O4  .->Da res:   2  NAG      at:C1  .
  WARNING : link:BETA1-4  is found dist =     1.399 ideal_dist=     1.439
            ch:Da res:   2  NAG      at:O4  .->Db res:   3  MAN      at:C1  .
  WARNING : link:ALPHA1-6 is found dist =     1.405 ideal_dist=     1.439
            ch:Db res:   3  MAN      at:O6  .->Dc res:   4  MAN      at:C1  .
  WARNING : link:ALPHA1-3 is found dist =     1.339 ideal_dist=     1.439
            ch:Db res:   3  MAN      at:O3  .->De res:   6  MAN      at:C1  .
  WARNING : link:BETA1-2  is found dist =     1.465 ideal_dist=     1.439
            ch:Dc res:   4  MAN      at:O2  .->Dd res:   5  NAG      at:C1  .
  ERROR: wrong tree structure .....
 IERR =  1
 
There is error. See above
===> Error: Fatal error. Cannot continue

(The links reported above are correct.)

I see Prem got same error last year (http://www.dl.ac.uk/list-archive-public/ccp4bb/2005-01/msg00211.html), but I could not find a reply/fix.

What is wrong (what does "wrong tree structure" mean?), and do I fix it so that Refmac will run?

Thanks,

Dave
~~~~~~~~~~~~~~~~~~~~~~~~
David W. Borhani, Ph.D.
Structural Biology Group Leader
Chemistry Department
Abbott Bioresearch Center
Vox: 508-688-3944
Fax: 508-754-7784
Email: [EMAIL PROTECTED]
Smail:  Abbott Bioresearch Center, Inc.
100 Research Drive
Worcester, MA 01605 U.S.A.
http://abbott.com
~~~~~~~~~~~~~~~~~~~~~~~~