grade web server http://grade.globalphasing.org

• Grade Web Server version Pre-Release Test v0.004 Mar 06 2012
• grade web server conditions of use
• Run by: Oliver Smart (grade dopamin tutorial 1) osmart@globalphasing.com 81.179.12.212
• Command run by server:
  

  grade 'c1cc(c(cc1CCN)O)O' -resname LIG

• Job completed successfully
• grade version 1.1.1 <2011-06-10>

• grade-LIG.cif - cif restraint dictionary
• grade-LIG.pdb - ideal coordinates in PDB format
• grade_log.txt - grade log file
• obprop.txt - Open Babel obprop results for output pdb file.
LIG.gradeserver_all.tgz - gzipped tar ball containing all results
• recognise-compound (new BUSTER utility) thinks:
  

  Input is known PDB chemical component "l-dopamine" with three-letter code LDP
  To get the correct PDB atom names re-run grade web server for pdb three-letter code LDP

• Useful information from comments at top of grade-LIG.cif:
  

   Number of restraints found:
   Bond lengths
       lengths/sigmas set by mogul                10
       bonds to hydrogen set to neutron values    11
       bonds lengths set by partial QM             1
   Bond Angles
       angles/sigmas set by mogul                 12
       non-H angles set by partial QM              2
       H bond angles set by partial QM            21
   Trigonal planes (atoms bonded to 3 others that are held flat)
       trigonal atoms from 3 mogul bond angles     3
       atoms NOT trigonal from 3 mogul angles      0
       trigonal atoms from partial QM              3
       atoms not trigonal from partial QM          1
   Torsions and 1-4 planes                                      
       bonds where mogul states cis/trans          0
       bonds mogul indicates flat                  0
       bonds mogul indicates 3-fold staggered      0
       bonds mogul indicates not flat              0
       in flat 5/6 membered rings after PQM        6
       other flat bonds after partial QM           0
       sp3-sp3 set 3-fold staggered by QM          1
       All other torsions (unrestrained)           4
   Mogul version used: /home/software/xtal/CSD/2012/20120127/csd/as533be
   GEN: Generated by GRADE 1.1.1 from SMILES string
   GEN: c1cc(c(cc1CCN)O)O
   GEN: using mogul+qm
  

• Job queued for 1 secs and grade ran for 14 wallclock secs ( 0.00 usr 0.00 sys + 13.79 cusr 3.69 csys = 17.48 CPU)
• Run completed Fri Mar 9 17:56:20 2012

For help and further details see grade section on the BUSTER wiki.

Please email buster-develop@globalphasing.com with any problems, queries or suggestions.