[phenixbb] real space refine generates non-compliant PDB files

[Edwin Pozharski]

Not sure whether anyone would care now that we got our marching orders to
abandon PDB format and move to mmCIF, but the output of
phenix.real_space_refine includes a number of lines that are not legit PDB
records, i.e. this section

...
REMARK   3

GEOMETRY RESTRAINTS LIBRARY: CDL v1.2
DEVIATIONS FROM IDEAL VALUES.
  BOND      :  0.004   0.049  74053
  ANGLE     :  0.747  12.299 100513
  CHIRALITY :  0.052   0.232  11312
  PLANARITY :  0.006   0.069  13125
  DIHEDRAL  : 11.589 179.958  44947
  MIN NONBONDED DISTANCE : 2.276

MOLPROBITY STATISTICS.
  ALL-ATOM CLASHSCORE : 5.04
  RAMACHANDRAN PLOT:
    OUTLIERS : 0.30  %
    ALLOWED  : 8.63  %
    FAVORED  : 91.06 %
  ROTAMER OUTLIERS : 8.76 %
  CBETA DEVIATIONS : 0
  PEPTIDE PLANE:
    CIS-PROLINE     : 3.7037037037
    CIS-GENERAL     : 0.0
    TWISTED PROLINE : 1.85185185185
    TWISTED GENERAL : 0.316455696203
REMARK   3
...

This does result in errors when this output PDB file is used as input to
other software that is more stringent with format compliance.

Cheers,

Ed.
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