randomi_498_> Atoms,selected atoms,random_seed,amplitude:     2031       11        1        4.0000
randomi_496_> Amplitude is > 0; randomization is done.
check_inf__E> Atom 206 has out-of-range coordinates (usually infinity).
              The objective function can thus not be calculated.

Traceback (most recent call last):
  File "/Users/arjun/script/mutate_model.py", line 157, in <module>
    optimize(s, sched)
  File "/Users/arjun/script/mutate_model.py", line 28, in optimize
    step.optimize(atmsel, max_iterations=200, min_atom_shift=0.001)
  File "/Library/modeller-9.11/modlib/modeller/schedule.py", line 71, in optimize
    return o.optimize(atmsel, schedule_scale=self.scale, **vars)
  File "/Library/modeller-9.11/modlib/modeller/optimizers/conjugate_gradients.py", line 38, in optimize
    ret = func(self._modpt, mdl.modpt, edat.modpt, libs.modpt, inds, **vars)
OverflowError: check_inf__E> Atom 206 has out-of-range coordinates (usually infinity).
              The objective function can thus not be calculated.


It generates the following 2a01.pdbARG26.tmp file. I notice 7 atoms of the ARG have"0" value on the last column. What does that mean?

ORIGINAL PDB:

ATOM    203  N   GLY A  26      84.766 -21.780 101.354  1.00 23.56           N 
ATOM    204  CA  GLY A  26      85.026 -21.762  99.961  1.00 25.16           C 
ATOM    205  C   GLY A  26      86.327 -21.144  99.510  1.00 25.70           C 
ATOM    206  O   GLY A  26      86.994 -21.670  98.600  1.00 26.35           O 

MUTATED MODEL:

ATOM    203  N   ARG A  26      84.766 -21.780 101.354  1.00 23.56           N
ATOM    204  CA  ARG A  26      85.026 -21.762  99.961  1.00 25.16           C
ATOM    205  CB  ARG A  26      83.792 -21.092  99.292  1.00  0.00           C
ATOM    206  CG  ARG A  26      83.847 -20.959  97.751  1.00  0.00           C
ATOM    207  CD  ARG A  26      82.605 -20.290  97.136  1.00  0.00           C
ATOM    208  NE  ARG A  26      82.821 -20.241  95.649  1.00  0.00           N
ATOM    209  CZ  ARG A  26      81.927 -19.718  94.798  1.00  0.00           C
ATOM    210  NH1 ARG A  26      82.220 -19.725  93.500  1.00  0.00           N
ATOM    211  NH2 ARG A  26      80.764 -19.224  95.210  1.00  0.00           N
ATOM    212  C   ARG A  26      86.327 -21.144  99.510  1.00 25.70           C
ATOM    213  O   ARG A  26      86.994 -21.670  98.600  1.00 26.35           O

The script also gave this error when I am trying to mutate to ARG60. Rest of the ARG  and other mutations worked on the model.

Would be helpful if someone could explain the error and how may I fix it.

Regards

Arjun

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