INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7s9y_24941/01_2022/7s9y_24941_neut.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 7s9y_24941_neut.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    

  Build ligand and use monomer library to name atoms : PTY
  Using monomer library entry PTY as template

  Attempting to download Chemical Components file for HEB
  Running eLBOW on HEB.cif

   Residue has metal at the centre of a coordination sphere. Using input
   geometry to generate restraints. Hydrogens may not be added.
   

 Suspicious bonds
    Bond between
      Atom  CHA( 2) xyz:( 5.707,  5.554,  3.786) and
      Atom  HHA(44) xyz:(-10.527,  7.936,  3.906) should be unknown, not   16.41
    Bond between
      Atom  CHB( 3) xyz:( 1.941,  2.087,  5.191) and
      Atom  HHB(45) xyz:(-5.630,  4.139,  5.562) should be unknown, not    7.85
    Bond between
      Atom  CHC( 4) xyz:( 0.390,  5.884,  5.128) and
      Atom  HHC(46) xyz:(-2.486,  6.213,  0.361) should be unknown, not    5.58
    Bond between
      Atom  CHD( 5) xyz:( 5.404,  4.728,  3.512) and
      Atom  HHD(47) xyz:(-7.419,  9.802, -1.404) should be unknown, not   14.64
    Bond between
      Atom  C2A( 8) xyz:( 4.488,  3.343,  2.222) and
      Atom  CAA(12) xyz:(-10.322,  6.609,  6.244) should be unknown, not   15.69
    Bond between
      Atom  C3A( 9) xyz:( 3.683,  2.332,  2.679) and
      Atom  CMA(11) xyz:(-8.051,  4.405,  6.934) should be unknown, not   12.65
    Bond between
      Atom  C3B(20) xyz:(-0.415,  4.107,  6.695) and
      Atom  CAB(23) xyz:(-1.460,  4.635,  2.259) should be unknown, not    4.59
    Bond between
      Atom  C2C(27) xyz:( 1.661,  6.269,  2.380) and
      Atom  CMC(30) xyz:(-2.465,  7.744, -1.682) should be unknown, not    5.97
    Bond between
      Atom  C3C(28) xyz:( 2.843,  5.797,  1.889) and
      Atom  CAC(31) xyz:(-4.868,  9.678, -2.609) should be unknown, not    9.73
    Bond between
      Atom  C2D(35) xyz:( 7.034,  4.757,  4.842) and
      Atom  CMD(38) xyz:(-10.121, 10.366, -0.705) should be unknown, not   18.88
    Bond between
      Atom  C3D(36) xyz:( 7.014,  6.014,  5.101) and
      Atom  CAD(39) xyz:(-11.573,  9.487,  1.948) should be unknown, not   19.17


HEB  FE       NA    single        1.842 0.020     1.842
HEB  FE       NB    single        1.835 0.020     1.835
HEB  FE       NC    single        1.815 0.020     1.815
HEB  FE       ND    single        1.806 0.020     1.806
HEB   CHA     C1A   aromatic      1.839 0.020     1.839
HEB   CHA     C4D   aromatic      2.154 0.020     2.154
HEB   CHA     HHA   single        0.929 0.020     1.085
HEB   CHB     C4A   aromatic      1.832 0.020     1.832
HEB   CHB     C1B   aromatic      1.785 0.020     1.785
HEB   CHB     HHB   single        0.929 0.020     1.085
HEB   CHC     C4B   aromatic      1.775 0.020     1.775
HEB   CHC     C1C   aromatic      1.838 0.020     1.838
HEB   CHC     HHC   single        0.929 0.020     1.085
HEB   CHD     C4C   aromatic      1.884 0.020     1.884
HEB   CHD     C1D   aromatic      1.965 0.020     1.965
HEB   CHD     HHD   single        0.929 0.020     1.085
HEB   NA      C1A   aromatic      1.352 0.020     1.352
HEB   NA      C4A   aromatic      1.380 0.020     1.380
HEB   C1A     C2A   aromatic      1.488 0.020     1.488
HEB   C2A     C3A   aromatic      1.371 0.020     1.371
HEB   C2A     CAA   single       15.690 0.020    15.690
1.527126
Sorry: Bond length too long : 15.69