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<p class="MsoNormal"><span style="font-size:11.0pt">Pat,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">The Coot I�m using (Version 1.0.0) retains all the REMARK, LINK, CRYST1, and SCALE lines of the input .pdb file, as shown below. Is that what you mean by �refinement info�.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">BTW, for deposition I use PDB Extract (<a href="https://pdb-extract.wwpdb.org/">https://pdb-extract.wwpdb.org/</a>) to combine .pdb file from phenix.refine, .log file from phenix.refine, Fobs .mtz file, and
the aimless.log file into coordinate and structure factor cif files. PDB deposition with those two .cif files goes smoothly.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Jack <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 REFINEMENT.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???)
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 AUTHORS : Adams,Afonine,Bunkoczi,Burnley,Chen,Dar,Davis,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 : Draizen,Echols,Gildea,Gros,Grosse-Kunstleve,Headd,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 : Hintze,Hung,Ioerger,Liebschner,McCoy,McKee,Moriarty,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 : Oeffner,Poon,Read,Richardson,Richardson,Sacchettini,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 : Sauter,Sobolev,Storoni,Terwilliger,Williams,Zwart
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 X-RAY DATA.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 REFINEMENT TARGET : ML
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 DATA USED IN REFINEMENT.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.45
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.31
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 COMPLETENESS FOR RANGE (%) : 95.34
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 NUMBER OF REFLECTIONS : 532934
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 279452
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FIT TO DATA USED IN REFINEMENT.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 R VALUE (WORKING + TEST SET) : 0.1859
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 R VALUE (WORKING SET) : 0.1845
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FREE R VALUE : 0.2123
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.99
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FREE R VALUE TEST SET COUNT : 26580
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE CCWOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 1 97.45 - 5.22 0.96 17012 835 0.1455 0.1603 0.94
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 2 5.22 - 4.14 0.91 16171 830 0.1273 0.1507 0.95
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 3 4.14 - 3.62 0.93 16465 850 0.1374 0.1631 0.94
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 4 3.62 - 3.29 0.93 16487 906 0.1629 0.1857 0.92
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 5 3.29 - 3.05 0.93 16568 883 0.1837 0.2109 0.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 6 3.05 - 2.87 0.94 16518 860 0.1793 0.2086 0.91
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 7 2.87 - 2.73 0.94 16614 845 0.1880 0.2144 0.91
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 8 2.73 - 2.61 0.94 16719 839 0.1904 0.2314 0.91
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 9 2.61 - 2.51 0.92 16330 827 0.1983 0.2302 0.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 10 2.51 - 2.42 0.91 16213 834 0.1975 0.2285 0.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 11 2.42 - 2.35 0.95 16609 1002 0.1940 0.2298 0.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 12 2.35 - 2.28 0.95 16777 956 0.2002 0.2385 0.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 13 2.28 - 2.22 0.95 16840 860 0.2038 0.2425 0.89
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 14 2.22 - 2.17 0.96 17010 942 0.2020 0.2355 0.89
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 15 2.17 - 2.12 0.97 17059 880 0.2042 0.2325 0.89
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 16 2.12 - 2.07 0.97 17221 906 0.2109 0.2458 0.88
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 17 2.07 - 2.03 0.97 17215 906 0.2167 0.2377 0.86
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 18 2.03 - 1.99 0.97 17288 852 0.2269 0.2581 0.87
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 19 1.99 - 1.96 0.98 17264 909 0.2239 0.2558 0.86
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 20 1.96 - 1.92 0.97 17222 875 0.2256 0.2642 0.85
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 21 1.92 - 1.89 0.97 17217 857 0.2327 0.2573 0.83
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 22 1.89 - 1.86 0.98 17346 979 0.2347 0.2767 0.82
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 23 1.86 - 1.84 0.98 17292 941 0.2395 0.2591 0.82
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 24 1.84 - 1.81 0.98 17267 893 0.2418 0.2657 0.81
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 25 1.81 - 1.79 0.95 16887 859 0.2688 0.2934 0.77
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 26 1.79 - 1.76 0.93 16540 850 0.2846 0.3100 0.74
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 27 1.76 - 1.74 0.96 16937 908 0.2966 0.3255 0.72
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 28 1.74 - 1.72 0.97 17121 881 0.3095 0.3275 0.70
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 29 1.72 - 1.70 0.97 17057 934 0.3237 0.3415 0.68
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 30 1.70 - 1.68 0.96 17088 881 0.3408 0.3717 0.66
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 BULK SOLVENT MODELLING.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 SOLVENT RADIUS : 1.10
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 SHRINKAGE RADIUS : 0.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 GRID STEP FACTOR : 4.00
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ERROR ESTIMATES.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.24
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.74
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 STRUCTURE FACTORS CALCULATION ALGORITHM : FFT
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 B VALUES.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FROM WILSON PLOT (A**2) : 25.75
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 BOND : 0.006 0.063 18548 Z= 0.330
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ANGLE : 0.854 15.131 25270 Z= 0.436
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 CHIRALITY : 0.050 0.207 2961
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 PLANARITY : 0.008 0.082 3280
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 DIHEDRAL : 14.137 174.131 6734
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 MIN NONBONDED DISTANCE : 1.885
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 MOLPROBITY STATISTICS.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ALL-ATOM CLASHSCORE : 1.90
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 RAMACHANDRAN PLOT:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 OUTLIERS : 0.17 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ALLOWED : 1.91 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 FAVORED : 97.93 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ROTAMER OUTLIERS : 1.17 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 CBETA DEVIATIONS : 0.00 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 PEPTIDE PLANE:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 CIS-PROLINE : 3.23 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 CIS-GENERAL : 0.00 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 TWISTED PROLINE : 0.00 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 TWISTED GENERAL : 0.00 %
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 RAMA-Z (RAMACHANDRAN PLOT Z-SCORE):
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY;
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 WHOLE: -0.51 (0.16), RESIDUES: 2418
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 HELIX: -0.10 (0.13), RESIDUES: 1246
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 SHEET: -0.72 (0.26), RESIDUES: 379
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 LOOP : -0.18 (0.22), RESIDUES: 793
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 min max mean <Bi,j> iso aniso
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Overall: 14.31 89.25 29.87 2.50 20008 17938
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Protein: 14.31 89.25 29.51 2.50 17938 17938
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Water: 17.28 54.73 33.51 N/A 1781 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Other: 19.26 53.26 29.56 N/A 289 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain A: 16.68 89.25 29.50 N/A 9044 8987
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain B: 14.31 88.24 29.47 N/A 9012 8951
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain E: 25.39 33.97 29.46 N/A 44 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain F: 19.26 27.60 22.05 N/A 44 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain M: 34.40 39.36 36.19 N/A 3 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain P: 32.18 50.28 40.92 N/A 47 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain S: 17.28 54.73 33.51 N/A 1781 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain T: 21.64 53.26 37.38 N/A 30 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Chain X: 27.76 38.14 33.45 N/A 3 0
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Histogram:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 Values Number of atoms
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 14.31 - 21.81 3292
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 21.81 - 29.30 8566
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 29.30 - 36.80 4360
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 36.80 - 44.29 2144
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 44.29 - 51.78 972
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 51.78 - 59.28 379
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 59.28 - 66.77 157
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 66.77 - 74.27 99
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 74.27 - 81.76 26
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 81.76 - 89.25 13
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 TLS DETAILS.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 NUMBER OF TLS GROUPS: 2
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ORIGIN: CENTER OF MASS
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 TLS GROUP : 1
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 SELECTION: chain A and peptide
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ORIGIN FOR THE GROUP (A): -26.0410 66.5091 93.2207
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T TENSOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T11: 0.2116 T22: 0.1718
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T33: 0.1810 T12: 0.0121
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T13: 0.0145 T23: 0.0048
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L TENSOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L11: 0.5646 L22: 0.0929
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L33: 0.1416 L12: -0.0146
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L13: 0.1554 L23: -0.0132
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S TENSOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S11: -0.0191 S12: -0.0694 S13: 0.0144
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S21: 0.0239 S22: 0.0226 S23: 0.0103
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S31: -0.0166 S32: -0.0142 S33: -0.0028
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 TLS GROUP : 2
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 SELECTION: chain B and peptide
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 ORIGIN FOR THE GROUP (A): 5.5320 31.4735 91.7257
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T TENSOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T11: 0.1668 T22: 0.1762
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T33: 0.1657 T12: 0.0032
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 T13: 0.0030 T23: -0.0143
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L TENSOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L11: 0.1947 L22: 0.2023
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L33: 0.3985 L12: 0.0090
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 L13: 0.0872 L23: -0.0806
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S TENSOR
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S11: 0.0109 S12: -0.0350 S13: -0.0133
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S21: 0.0406 S22: 0.0104 S23: -0.0032
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3 S31: 0.0372 S32: -0.1005 S33: -0.0276
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">REMARK 3
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">LINK N5 FDA A1400 C3 CBG A1401
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">LINK N5 FDA B1400 C3 ACBG B1401
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">LINK N5 FDA B1400 C3 BCBG B1401
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">LINK N5 FDA A1400 C3 CBG A1401
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">LINK N5 FDA B1400 C3 ACBG B1401
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">LINK N5 FDA B1400 C3 BCBG B1401
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">CRYST1 101.669 102.628 126.672 90.00 106.57 90.00 P 1 21 1
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">SCALE1 0.009836 0.000000 0.002927 0.00000
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">SCALE2 0.000000 0.009744 0.000000 0.00000
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">SCALE3 0.000000 0.000000 0.008236 0.00000
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div id="mail-editor-reference-message-container">
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;color:black">From:
</span></b><span style="font-size:12.0pt;color:black">Patrick Loll <pjloll@gmail.com><br>
<b>Date: </b>Sunday, October 15, 2023 at 4:55 PM<br>
<b>To: </b>Tanner, John J. <TannerJJ@missouri.edu>, PHENIX user mailing list <phenixbb@phenix-online.org><br>
<b>Subject: </b>Re: [phenixbb] Renumbering while retaining refinement info<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks Jack! Although I�m finding that Coot isn�t writing the refinement info in the output file either� (this is for deposition, so I need the refinement data). Maybe I need to try a newer version.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">On 15 Oct 2023, at 3:36 PM, Tanner, John J. <<a href="mailto:TannerJJ@missouri.edu">TannerJJ@missouri.edu</a>> wrote:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;font-variant-caps: small-caps;font-stretch: normal">
<b><span style="font-size:10.5pt;font-family:"Arial",sans-serif;color:black">External.</span></b><b><span style="font-size:10.5pt;font-family:"Arial",sans-serif"><o:p></o:p></span></b></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Pat,</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Coot has a tool to shift the residue numbers by a positive or negative increment. See Edit�Renumber Residues.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Best Regards,</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Jack<span class="apple-converted-space"> </span></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt">From:<span class="apple-converted-space"> </span></span></b><span style="font-size:12.0pt"><a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a><span class="apple-converted-space"> </span><<a href="mailto:phenixbb-bounces@phenix-online.org">phenixbb-bounces@phenix-online.org</a>>
on behalf of Patrick Loll <<a href="mailto:pjloll@gmail.com">pjloll@gmail.com</a>><br>
<b>Date:<span class="apple-converted-space"> </span></b>Sunday, October 15, 2023 at 1:22 PM<br>
<b>To:<span class="apple-converted-space"> </span></b>PHENIX user mailing list <<a href="mailto:phenixbb@phenix-online.org">phenixbb@phenix-online.org</a>><br>
<b>Subject:<span class="apple-converted-space"> </span></b>[phenixbb] Renumbering while retaining refinement info</span></p>
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<p class="MsoNormal" style="line-height:12.0pt;background:#FFC7CE"><b><span style="color:#9C0006">WARNING:</span></b><span class="apple-converted-space"><span style="color:black"> </span></span><span style="color:black">This message has originated from an External
Source. This may be a phishing expedition that can result in unauthorized access to our IT System. Please use proper judgment and caution when opening attachments, clicking links, or responding to this email.</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hello all,<span class="apple-converted-space"> </span></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">I've finished refining a handful of related structures, but now I need to renumber the residues to reflect the fact that I�m working with a truncated construct (like a dope I didn�t do this at the outset).
However, when I run PDB Tools, it does not write the refinement information into the output CIF. </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Is there a way to get around this, other than re-running the final cycle of refinement with the renumbered coordinates (or entering the refinement info by hand? This would be easy in the PDB format, but not
so much in mmCIF). </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Cheers,</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Pat</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">__________________________________</span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">Patrick J. Loll, PhD (he, him, his)</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">Professor of Biochemistry & Molecular Biology</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">Drexel University College of Medicine</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">Room 10-102 New College Building</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">Philadelphia, PA 19102-1192 USA</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt"> </span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt">(267) 359-2653</span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt"><a href="mailto:pjl28@drexel.edu">pjl28@drexel.edu</a></span></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:Helvetica">_______________________________________________<br>
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</blockquote>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Patrick Loll<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><a href="mailto:pjloll@gmail.com">pjloll@gmail.com</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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