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.