[phenixbb] phenix.pdbtools question

[Simon Kolstoe]

Dear phenix list,

I am wanting to model a poly-proline structure. I created the file in  
PyMOL, saved it as a pdb, and then tried to regularize it with:

phenix.pdbtools polypro.pdb --geometry_regularization

However the program reported (snipped to the last few lines):

ATOM     63  CD  PRO     6      -3.290   3.487  -2.968  1.00   
0.00           C
       ATOM     69 2HD  PRO     6      -2.824   2.626  -3.453  1.00   
0.00           H
     Distance model: 1.09209 (ideal: 0.97)
       ATOM     63  CD  PRO     6      -3.290   3.487  -2.968  1.00   
0.00           C
       ATOM     70 3HD  PRO     6      -4.165   3.171  -2.396  1.00   
0.00           H
     Distance model: 1.44721 (ideal: 1.473)
       ATOM     57  N   PRO     6      -2.321   4.145  -2.118  1.00   
0.00           N
       ATOM     63  CD  PRO     6      -3.290   3.487  -2.968  1.00   
0.00           C
     Distance model: 1.53855 (ideal: 1.525)
       ATOM     58  CA  PRO     6      -1.810   5.407  -2.632  1.00   
0.00           C
       ATOM     59  C   PRO     6      -2.332   6.603  -1.817  1.00   
0.00           C
     Distance model: 1.23088 (ideal: 1.231)
       ATOM     59  C   PRO     6      -2.332   6.603  -1.817  1.00   
0.00           C
       ATOM     60  O   PRO     6      -3.080   6.424  -0.856  1.00   
0.00           O
Sorry: Number of bonds with excessive lengths: 74

I thought the whole purpose of geometry regularization was to get rid  
of excessive lengths, not just tell me they are there!! How do I get  
the program to really regularize my geometry?

Thanks,

Simon