Pat,

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”.

BTW, for deposition I use PDB Extract (https://pdb-extract.wwpdb.org/) 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.

Jack

REMARK 3

REMARK 3 REFINEMENT.

REMARK 3 PROGRAM : PHENIX (1.20.1_4487: ???)

REMARK 3 AUTHORS : Adams,Afonine,Bunkoczi,Burnley,Chen,Dar,Davis,

REMARK 3 : Draizen,Echols,Gildea,Gros,Grosse-Kunstleve,Headd,

REMARK 3 : Hintze,Hung,Ioerger,Liebschner,McCoy,McKee,Moriarty,

REMARK 3 : Oeffner,Poon,Read,Richardson,Richardson,Sacchettini,

REMARK 3 : Sauter,Sobolev,Storoni,Terwilliger,Williams,Zwart

REMARK 3

REMARK 3 X-RAY DATA.

REMARK 3

REMARK 3 REFINEMENT TARGET : ML

REMARK 3

REMARK 3 DATA USED IN REFINEMENT.

REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68

REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 97.45

REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.31

REMARK 3 COMPLETENESS FOR RANGE (%) : 95.34

REMARK 3 NUMBER OF REFLECTIONS : 532934

REMARK 3 NUMBER OF REFLECTIONS (NON-ANOMALOUS) : 279452

REMARK 3

REMARK 3 FIT TO DATA USED IN REFINEMENT.

REMARK 3 R VALUE (WORKING + TEST SET) : 0.1859

REMARK 3 R VALUE (WORKING SET) : 0.1845

REMARK 3 FREE R VALUE : 0.2123

REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.99

REMARK 3 FREE R VALUE TEST SET COUNT : 26580

REMARK 3

REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).

REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE CCWOR

REMARK 3 1 97.45 - 5.22 0.96 17012 835 0.1455 0.1603 0.94

REMARK 3 2 5.22 - 4.14 0.91 16171 830 0.1273 0.1507 0.95

REMARK 3 3 4.14 - 3.62 0.93 16465 850 0.1374 0.1631 0.94

REMARK 3 4 3.62 - 3.29 0.93 16487 906 0.1629 0.1857 0.92

REMARK 3 5 3.29 - 3.05 0.93 16568 883 0.1837 0.2109 0.90

REMARK 3 6 3.05 - 2.87 0.94 16518 860 0.1793 0.2086 0.91

REMARK 3 7 2.87 - 2.73 0.94 16614 845 0.1880 0.2144 0.91

REMARK 3 8 2.73 - 2.61 0.94 16719 839 0.1904 0.2314 0.91

REMARK 3 9 2.61 - 2.51 0.92 16330 827 0.1983 0.2302 0.90

REMARK 3 10 2.51 - 2.42 0.91 16213 834 0.1975 0.2285 0.90

REMARK 3 11 2.42 - 2.35 0.95 16609 1002 0.1940 0.2298 0.90

REMARK 3 12 2.35 - 2.28 0.95 16777 956 0.2002 0.2385 0.90

REMARK 3 13 2.28 - 2.22 0.95 16840 860 0.2038 0.2425 0.89

REMARK 3 14 2.22 - 2.17 0.96 17010 942 0.2020 0.2355 0.89

REMARK 3 15 2.17 - 2.12 0.97 17059 880 0.2042 0.2325 0.89

REMARK 3 16 2.12 - 2.07 0.97 17221 906 0.2109 0.2458 0.88

REMARK 3 17 2.07 - 2.03 0.97 17215 906 0.2167 0.2377 0.86

REMARK 3 18 2.03 - 1.99 0.97 17288 852 0.2269 0.2581 0.87

REMARK 3 19 1.99 - 1.96 0.98 17264 909 0.2239 0.2558 0.86

REMARK 3 20 1.96 - 1.92 0.97 17222 875 0.2256 0.2642 0.85

REMARK 3 21 1.92 - 1.89 0.97 17217 857 0.2327 0.2573 0.83

REMARK 3 22 1.89 - 1.86 0.98 17346 979 0.2347 0.2767 0.82

REMARK 3 23 1.86 - 1.84 0.98 17292 941 0.2395 0.2591 0.82

REMARK 3 24 1.84 - 1.81 0.98 17267 893 0.2418 0.2657 0.81

REMARK 3 25 1.81 - 1.79 0.95 16887 859 0.2688 0.2934 0.77

REMARK 3 26 1.79 - 1.76 0.93 16540 850 0.2846 0.3100 0.74

REMARK 3 27 1.76 - 1.74 0.96 16937 908 0.2966 0.3255 0.72

REMARK 3 28 1.74 - 1.72 0.97 17121 881 0.3095 0.3275 0.70

REMARK 3 29 1.72 - 1.70 0.97 17057 934 0.3237 0.3415 0.68

REMARK 3 30 1.70 - 1.68 0.96 17088 881 0.3408 0.3717 0.66

REMARK 3

REMARK 3 BULK SOLVENT MODELLING.

REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL

REMARK 3 SOLVENT RADIUS : 1.10

REMARK 3 SHRINKAGE RADIUS : 0.90

REMARK 3 GRID STEP FACTOR : 4.00

REMARK 3

REMARK 3 ERROR ESTIMATES.

REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.24

REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.74

REMARK 3

REMARK 3 STRUCTURE FACTORS CALCULATION ALGORITHM : FFT

REMARK 3 B VALUES.

REMARK 3 FROM WILSON PLOT (A**2) : 25.75

REMARK 3

REMARK 3 GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2

REMARK 3 DEVIATIONS FROM IDEAL VALUES - RMSD. RMSZ FOR BONDS AND ANGLES.

REMARK 3 BOND : 0.006 0.063 18548 Z= 0.330

REMARK 3 ANGLE : 0.854 15.131 25270 Z= 0.436

REMARK 3 CHIRALITY : 0.050 0.207 2961

REMARK 3 PLANARITY : 0.008 0.082 3280

REMARK 3 DIHEDRAL : 14.137 174.131 6734

REMARK 3 MIN NONBONDED DISTANCE : 1.885

REMARK 3

REMARK 3 MOLPROBITY STATISTICS.

REMARK 3 ALL-ATOM CLASHSCORE : 1.90

REMARK 3 RAMACHANDRAN PLOT:

REMARK 3 OUTLIERS : 0.17 %

REMARK 3 ALLOWED : 1.91 %

REMARK 3 FAVORED : 97.93 %

REMARK 3 ROTAMER OUTLIERS : 1.17 %

REMARK 3 CBETA DEVIATIONS : 0.00 %

REMARK 3 PEPTIDE PLANE:

REMARK 3 CIS-PROLINE : 3.23 %

REMARK 3 CIS-GENERAL : 0.00 %

REMARK 3 TWISTED PROLINE : 0.00 %

REMARK 3 TWISTED GENERAL : 0.00 %

REMARK 3

REMARK 3 RAMA-Z (RAMACHANDRAN PLOT Z-SCORE):

REMARK 3 INTERPRETATION: BAD |RAMA-Z| > 3; SUSPICIOUS 2 < |RAMA-Z| < 3; GOOD

REMARK 3 SCORES FOR WHOLE/HELIX/SHEET/LOOP ARE SCALED INDEPENDENTLY;

REMARK 3 THEREFORE, THE VALUES ARE NOT RELATED IN A SIMPLE MANNER.

REMARK 3 WHOLE: -0.51 (0.16), RESIDUES: 2418

REMARK 3 HELIX: -0.10 (0.13), RESIDUES: 1246

REMARK 3 SHEET: -0.72 (0.26), RESIDUES: 379

REMARK 3 LOOP : -0.18 (0.22), RESIDUES: 793

REMARK 3

REMARK 3 min max mean <Bi,j> iso aniso

REMARK 3 Overall: 14.31 89.25 29.87 2.50 20008 17938

REMARK 3 Protein: 14.31 89.25 29.51 2.50 17938 17938

REMARK 3 Water: 17.28 54.73 33.51 N/A 1781 0

REMARK 3 Other: 19.26 53.26 29.56 N/A 289 0

REMARK 3 Chain A: 16.68 89.25 29.50 N/A 9044 8987

REMARK 3 Chain B: 14.31 88.24 29.47 N/A 9012 8951

REMARK 3 Chain E: 25.39 33.97 29.46 N/A 44 0

REMARK 3 Chain F: 19.26 27.60 22.05 N/A 44 0

REMARK 3 Chain M: 34.40 39.36 36.19 N/A 3 0

REMARK 3 Chain P: 32.18 50.28 40.92 N/A 47 0

REMARK 3 Chain S: 17.28 54.73 33.51 N/A 1781 0

REMARK 3 Chain T: 21.64 53.26 37.38 N/A 30 0

REMARK 3 Chain X: 27.76 38.14 33.45 N/A 3 0

REMARK 3 Histogram:

REMARK 3 Values Number of atoms

REMARK 3 14.31 - 21.81 3292

REMARK 3 21.81 - 29.30 8566

REMARK 3 29.30 - 36.80 4360

REMARK 3 36.80 - 44.29 2144

REMARK 3 44.29 - 51.78 972

REMARK 3 51.78 - 59.28 379

REMARK 3 59.28 - 66.77 157

REMARK 3 66.77 - 74.27 99

REMARK 3 74.27 - 81.76 26

REMARK 3 81.76 - 89.25 13

REMARK 3

REMARK 3 TLS DETAILS.

REMARK 3 NUMBER OF TLS GROUPS: 2

REMARK 3 ORIGIN: CENTER OF MASS

REMARK 3 TLS GROUP : 1

REMARK 3 SELECTION: chain A and peptide

REMARK 3 ORIGIN FOR THE GROUP (A): -26.0410 66.5091 93.2207

REMARK 3 T TENSOR

REMARK 3 T11: 0.2116 T22: 0.1718

REMARK 3 T33: 0.1810 T12: 0.0121

REMARK 3 T13: 0.0145 T23: 0.0048

REMARK 3 L TENSOR

REMARK 3 L11: 0.5646 L22: 0.0929

REMARK 3 L33: 0.1416 L12: -0.0146

REMARK 3 L13: 0.1554 L23: -0.0132

REMARK 3 S TENSOR

REMARK 3 S11: -0.0191 S12: -0.0694 S13: 0.0144

REMARK 3 S21: 0.0239 S22: 0.0226 S23: 0.0103

REMARK 3 S31: -0.0166 S32: -0.0142 S33: -0.0028

REMARK 3 TLS GROUP : 2

REMARK 3 SELECTION: chain B and peptide

REMARK 3 ORIGIN FOR THE GROUP (A): 5.5320 31.4735 91.7257

REMARK 3 T TENSOR

REMARK 3 T11: 0.1668 T22: 0.1762

REMARK 3 T33: 0.1657 T12: 0.0032

REMARK 3 T13: 0.0030 T23: -0.0143

REMARK 3 L TENSOR

REMARK 3 L11: 0.1947 L22: 0.2023

REMARK 3 L33: 0.3985 L12: 0.0090

REMARK 3 L13: 0.0872 L23: -0.0806

REMARK 3 S TENSOR

REMARK 3 S11: 0.0109 S12: -0.0350 S13: -0.0133

REMARK 3 S21: 0.0406 S22: 0.0104 S23: -0.0032

REMARK 3 S31: 0.0372 S32: -0.1005 S33: -0.0276

REMARK 3

LINK N5 FDA A1400 C3 CBG A1401

LINK N5 FDA B1400 C3 ACBG B1401

LINK N5 FDA B1400 C3 BCBG B1401

LINK N5 FDA A1400 C3 CBG A1401

LINK N5 FDA B1400 C3 ACBG B1401

LINK N5 FDA B1400 C3 BCBG B1401

CRYST1 101.669 102.628 126.672 90.00 106.57 90.00 P 1 21 1

SCALE1 0.009836 0.000000 0.002927 0.00000

SCALE2 0.000000 0.009744 0.000000 0.00000

SCALE3 0.000000 0.000000 0.008236 0.00000

From: Patrick Loll <[email protected]>
Date: Sunday, October 15, 2023 at 4:55 PM
To: Tanner, John J. <[email protected]>, PHENIX user mailing list <[email protected]>
Subject: Re: [phenixbb] Renumbering while retaining refinement info

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.

On 15 Oct 2023, at 3:36 PM, Tanner, John J. <[email protected]> wrote:

External.

Hi Pat,

Coot has a tool to shift the residue numbers by a positive or negative increment. See Edit…Renumber Residues.

Best Regards,

Jack

From: [email protected] <[email protected]> on behalf of Patrick Loll <[email protected]>
Date: Sunday, October 15, 2023 at 1:22 PM
To: PHENIX user mailing list <[email protected]>
Subject: [phenixbb] Renumbering while retaining refinement info

WARNING: 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.

Hello all,

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.

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).

Cheers,

Pat

__________________________________

Patrick J. Loll, PhD (he, him, his)

Professor of Biochemistry & Molecular Biology

Drexel University College of Medicine

Room 10-102 New College Building

245 N. 15th St.

Philadelphia, PA 19102-1192 USA

(267) 359-2653

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