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*               Welcome to use the MCPB.py program               *
*                          Version 4.0                           *
*                       Author: Pengfei Li                       *
*                      Merz Research Group                       *
*                   Michigan State University                    *
*                              AND                               *
*                 Hammes-Schiffer Research Group                 *
*                         UIUC and Yale                          *
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The input file you are using is : 6OFV.in
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
The following is the input variable you have:
The variable ion_ids is :  [5436, 5437, 5438]
The variable ion_info is :  []
The variable ion_mol2files is :  ['MG.mol2']
The variable original_pdb is :  6ofv_fixed.pdb
The variable add_bonded_pairs is :  []
The variable add_redcrd is :  0
The variable additional_resids is :  []
The variable anglefc_avg is :  0
The variable bondfc_avg is :  0
The variable chgfix_resids is :  []
The variable cut_off is :  2.5
The variable force_field is :  ff14SB
The variable frcmod_files is :  ['POP.frcmod']
The variable gaff is :  1
The variable group_name is :  6OFV
The variable ion_paraset is :  CM (Only for nonbonded model)
The variable large_opt is :  1
The variable lgmodel_chg is :  -99
The variable lgmodel_spin is :  -99
             -99 means program will assign a charge automatically.
The variable naa_mol2files is :  ['POP.mol2', 'WAT.mol2']
The variable scale_factor is :  1.0
             ATTENTION: This is the scale factor of frequency. The
             force constants will be scaled by multiplying the square
             of scale_factor.
The variable smmodel_chg is :  -99
The variable smmodel_spin is :  -99
             -99 means program will assign a charge automatically.
The variable software_version is :  g09
The variable sqm_opt is :  0
The variable water_model is :  TIP3P
The variable xstru is :  0
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*                                                                *
*=======================Metal Site Information===================*
*                                                                *
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***Selected Metal ion MG is atom 5436 in residue 341-MG
***Selected Metal ion MG is atom 5437 in residue 342-MG
***Selected Metal ion MG is atom 5438 in residue 343-MG
84-ASP@OD1 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
344-POP@O2 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
345-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
347-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
349-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
350-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
84-ASP@OD2 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
344-POP@O6 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
346-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
351-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
225-ASN@OD1 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
229-SER@OG is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
233-GLU@OE2 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
344-POP@O1 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
344-POP@O4 is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
348-WAT@O is in 2.5 Angstrom of or set bonded (in the input file) to (one of) these metal ions
***The following residues are in the Metal Site:
Residue 84-ASP
Residue 225-ASN
Residue 229-SER
Residue 233-GLU
Residue 341-MG
Residue 342-MG
Residue 343-MG
Residue 344-POP
Residue 345-WAT
Residue 346-WAT
Residue 347-WAT
Residue 348-WAT
Residue 349-WAT
Residue 350-WAT
Residue 351-WAT
***The small model contains the following residues:
[84, 225, 229, 233, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351]
***The large model contains the following residues:
[83, 84, 85, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351]
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*                                                                *
*=======================Building models==========================*
*                                                                *
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***Creating the small model...
It contains the residue 84-ASP as sidechain coordinated.
It contains the residue 225-ASN as sidechain coordinated.
It contains the residue 229-SER as sidechain coordinated.
It contains the residue 233-GLU as sidechain coordinated.
It contains the residue 341-MG as normal.
It contains the residue 342-MG as normal.
It contains the residue 343-MG as normal.
It contains the residue 344-POP as normal.
It contains the residue 345-WAT as normal.
It contains the residue 346-WAT as normal.
It contains the residue 347-WAT as normal.
It contains the residue 348-WAT as normal.
It contains the residue 349-WAT as normal.
It contains the residue 350-WAT as normal.
It contains the residue 351-WAT as normal.
Totally there are 77 atoms in the small model.
Totally there are 344 electrons in the small model.
***Creating the standard model...
It contains the residue 84-ASP as normal.
It contains the residue 225-ASN as normal.
It contains the residue 229-SER as normal.
It contains the residue 233-GLU as normal.
It contains the residue 341-MG as normal.
It contains the residue 342-MG as normal.
It contains the residue 343-MG as normal.
It contains the residue 344-POP as normal.
It contains the residue 345-WAT as normal.
It contains the residue 346-WAT as normal.
It contains the residue 347-WAT as normal.
It contains the residue 348-WAT as normal.
It contains the residue 349-WAT as normal.
It contains the residue 350-WAT as normal.
It contains the residue 351-WAT as normal.
Totally there are 85 atoms in the standard model.
***Creating the large model...
Creating the residue 83-TRP into ACE...
It contains the residue 84-ASP as normal.
Creating the residue 85-ASP into NME...
Creating the residue 224-TYR into ACE...
It contains the residue 225-ASN as normal.
Creating the residue 226-ASP into GLY...
Creating the residue 227-LEU into GLY...
Creating the residue 228-CYS into GLY...
It contains the residue 229-SER as normal.
Creating the residue 230-LEU into GLY...
Creating the residue 231-PRO into GLY...
Creating the residue 232-LYS into GLY...
It contains the residue 233-GLU as normal.
Creating the residue 234-ILE into NME...
It contains the residue 341-MG as normal.
It contains the residue 342-MG as normal.
It contains the residue 343-MG as normal.
It contains the residue 344-POP as normal.
It contains the residue 345-WAT as normal.
It contains the residue 346-WAT as normal.
It contains the residue 347-WAT as normal.
It contains the residue 348-WAT as normal.
It contains the residue 349-WAT as normal.
It contains the residue 350-WAT as normal.
It contains the residue 351-WAT as normal.
Totally there are 151 atoms in the large model.
Totally there are 684 electrons in the large model.
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To cite MCPB.py please use the following reference:
Pengfei Li and Kenneth M. Merz, Jr., "MCPB.py: A Python Based
  Metal Center Parameter Builder." J. Chem. Inf. Model., 2016,
  56, 599-604.

