This is fixed in recent versions (nightly builds): http://phenix-online.org/download/nightly_builds.cgi Pavel On 2/22/19 06:11, Edwin Pozharski wrote:

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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