INPUT
  
    Reading model from /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/4ce4_2490/04_2022/4ce4_2490_neut.pdb
    Reading option "hydrogens=False" from command line
    Writing effective parameters to 4ce4_2490_neut.eff

  Preparation for phenix.refine

    Ligand restraint generation using eLBOW, phenix.elbow
    
Problematic residue/ligand : N
================================================================================
Monomer lib overlaps
Known
> 
Unknown
> C1'  C2'  C3'  C4'  C5'  N1   O2'  O3'  O4'  O5'  OP1  OP2  P
Unused
> N
--------------------------------------------------------------------------------
Chemical components
Known
> C1'  C2'  C3'  C4'  C5'  O2'  O3'  O4'  O5'  OP1  OP2  P
Unknown
> N1
Unused
> OP3  HOP3 HOP2 H5'  H5'' H4'  H3'  HO3' H2'  HO2' H1'  H1'2
--------------------------------------------------------------------------------
Chemical components (alternate)
Known
> P
Unknown
> C1'  C2'  C3'  C4'  C5'  N1   O2'  O3'  O4'  O5'  OP1  OP2
Unused
> O3P  O1P  O2P  O5*  C5*  C4*  O4*  C3*  O3*  C2*  O2*  C1*  3HOP 2HOP 1H5* 
	2H5* H4*  H3*  H3T  H2*  2HO* H1*  2H1*
================================================================================

Residue name and atom names are grossly mismatched

  Build ligand from scratch : N

  There is a entry in the monomer library for N.  Because ReadySet!
  is building from scratch, the code may not be correct for the
  molecule in the input file.

  Duplicate entries can also cause problems in a refinement if there are
  other different molecules with the same code.


    Some suggestions for a new code
	Random code : UYO
	Code  "N??" : N1I
	Code  "NC?" : NC0
	You should not see this : NWX

  Forcing all chirals to be "both"

  Problems with matching atoms with library

    Perfectly matched atoms

	Atom  C2'( 2) xyz:(217.841, 175.680, 134.370)
	Atom  C3'( 3) xyz:(218.040, 175.136, 132.961)
	Atom  C4'( 4) xyz:(219.072, 174.038, 133.172)
	Atom  C5'( 5) xyz:(219.902, 173.671, 131.969)
	Atom  O2'( 7) xyz:(216.988, 174.828, 135.120)
	Atom  O3'( 8) xyz:(216.847, 174.665, 132.359)
	Atom  O4'( 9) xyz:(219.929, 174.556, 134.222)
	Atom  O5'(10) xyz:(220.541, 174.809, 131.410)
	Atom  OP1(11) xyz:(221.047, 173.802, 129.188)
	Atom  OP2(12) xyz:(222.143, 176.005, 129.921)

    Matched atoms with different names


    Unmatched atoms

	Atom  C1'( 1) xyz:(219.256, 175.570, 134.939)
	Atom  N1 ( 6) xyz:(220.013, 176.833, 134.792)
	Atom  P  (13) xyz:(221.630, 174.652, 130.257)

  Writing PDB file with better atom names to ready_set.N.atom_names.pdb
Sorry: 
  Possible reasons for current problems
    - Three letter code (%s) is not correct for molecule
    - Input geometry is not within bounds to accurately determine bonding