INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7md2_23763/04_2022/7md2_23763_trim.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7md2_23763_trim.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Attempting to download Chemical Components file for ZHD
  Running eLBOW on ZHD.cif
 Processing a loop

ZHD   O51     C50   single        1.587 0.020     1.587
ZHD   O49     C48   single        1.603 0.020     1.603
ZHD   C50     C48   single        1.389 0.020     1.389
ZHD   C50     C52   single        1.496 0.020     1.496
ZHD   C48     C46   single        1.452 0.020     1.452
ZHD   C53     C52   single        1.427 0.020     1.427
ZHD   C52     O54   single        1.580 0.020     1.580
ZHD   C46     O47   single        1.595 0.020     1.595
ZHD   C46     C45   single        1.471 0.020     1.471
ZHD   O54     C45   single        1.332 0.020     1.332
ZHD   C45     O44   single        1.564 0.020     1.564
ZHD   O44     C43   single        1.066 0.020     1.066
ZHD   C56     C55   single        1.452 0.020     1.452
ZHD   C55     C43   single        2.361 0.020     2.361
ZHD   C55     C57   single        0.054 0.020     0.054
ZHD   C43     C41   single        1.893 0.020     1.893
ZHD   C59     C58   single        1.965 0.020     1.965
ZHD   C57     C58   double        0.925 0.020     0.925
ZHD   C41     C42   single        2.146 0.020     2.146
ZHD   C41     C40   double        1.135 0.020     1.135
ZHD   C58     C60   single        2.998 0.020     2.998
ZHD   C63     O62   single        1.753 0.020     1.753
ZHD   C40     C38   single        1.134 0.020     1.134
ZHD   O62     C61   single        1.216 0.020     1.216
ZHD   C60     C61   double        3.034 0.020     3.034
1.527126
Sorry: Bond length too long : 3.03