Fragment Picking with Chemical Shift Data

1. Preparation of Input Files:

Fragment picking requires only backbone chemical shifts and a fasta sequence. For published data chemical shifts can often be downloaded from the BMRB http://www.bmrb.wisc.edu/.
for example:

wget http://rest.bmrb.wisc.edu/bmrb/NMR-STAR2/15339 -O 2jrm.bmrb

For fragment picking we have to run TALOS+ or TALOS-N and thus the bmrb file has to be converted into NmrPipe/TALOS format.

bmrb2talos 2jrm.bmrb > 2jrm.tab

If you obtained chemical shifts in a different file format, you may have to convert to TALOS+ or TALOS-N format using a different command.
Check out our other File Format Converters.

2. Requirements to run this Tutorial:

  • Full installation of CS-Rostta (i.e., not installed with the option -nopicking)
  • backbone chemical shifts in TALOS format: 2jrm.tab

3. Pick Fragments from Backbone Chemical Shifts

3.1. Determine structurally well-defined (rigid) regions

Flexible regions of the protein backbone, often found in the tails and/or loops of the provided protein sequence, can disturb the structure calculation process due to unnecessary noise in the energy evaluation and by hampering the RMSD based diversity filter(see RASREC). Flexible residues in the tails are best trimmed off entirely before the structure calculation commences. Flexible loops should not be trimmed, but their position should be provided to the CS-Rosetta structure calculations explicitly which allows to neglect these regions from RMSD calculation and to restrict their contributions to the total energy to repulsive interactions.
Unless better data about flexibility is available we will characterize it from the chemical shifts using the random coil index (RCI) by applying TALOS+[PROVIDE REFERENCE] or TALOS-N. Accordingly, we run

talos+ -in 2jrm.tab

or

talosn -in 2jrm.tab

to analyse the backbone chemical shifts. This step should generate the file pred.tab, whose first lines should look like this:

VARS   RESID RESNAME PHI PSI DPHI DPSI DIST S2 COUNT CLASS 
FORMAT %4d %s %8.3f %8.3f %8.3f %8.3f %8.3f %5.3f %2d %s
   1 M 9999.000 9999.000    0.000    0.000    0.000 0.187  0 None
   2 K  -81.415  143.247   49.171   47.658   35.234 0.232 10 Dyn
   3 R -102.463  136.063   30.483   21.803   11.496 0.306  8 Dyn
   4 Q  -72.007  -33.294   17.747   12.857   10.222 0.415  5 Dyn
   5 K  -67.290  -36.356   13.430    9.240   10.105 0.535 10 Good

We focus on the last three columns. The predicted flexibility is given in the 3rd last column as an order parameter (1.0 means fully rigid, and less means the residue is more flexible). For CS-Rosetta calculations we consider residues with an order parameter of less than 0.7 as flexible.
Additionally, to the order parameter the file gives an overview of the coverage and quality of the chemical shift data. The last column has the words None, Dyn, Good and Warn, and informs us about the quality of the backbone chemical shift data. If too many residues have assignments different than 'Good' we usually cannot expect to obtain well-converged CS-Rosetta structures. Sometimes no chemical shift data has been obtained for dynamic loop-regions (status 'None') and in these cases the user might want to experiment with adding these to the list of dynamic residues, too.

3.2. Trim Protein Sequence

In this example, the coverage of the backbone chemical shift data is good at all residues, and we find that flexibility is high for residues 1-6, 31-32, 53-60. Hence, we trim the original protein sequence to exclude the flexible tails using renumber_talos:

renumber_talos -s 7 -e 52 2jrm.tab 2jrm_trim.tab 
talos2fasta 2jrm_trim.tab > 2jrm_trim.fasta 

as shown above we can easily obtain the corresponding FASTA sequence from the chemical shift file using talos2fasta. Alternatively, one could trim the fasta sequence using an editor and then run the command

renumber_talos -fasta 2jrm_trim.fasta 2jrm.tab 2jrm_trim.tab

3.3. Pick fragments for trimmed protein sequence

Using the prepared trimmed fasta and talos files, we are now able to pick fragments from the provided database of high resolution protein structures. Normally, we use 3-residue fragments and 9-residue fragments, but other fragment lengths can also be picked and used by CS-Rosetta.

$ pick_fragments -cs 2jrm_trim.tab >& picking.log

Use the flag "-nohom" if you are using CS-Rosetta for benchmarking with known structures to avoid that any information from the target structure or close homologues is used during the structure calculation process. This command should produce the files 2jrm_trim.frags3.dat.gz and 2jrm_trim.frags9.dat.gz, which containt 200 3mer and 9mer fragments, respectively, for every sequence position.

3.4. Pick fragments with auto-trimming

You can also add the flag -trim to the pick_fragment command which will determine a trimming using the command pred2rigid automatically. A file 2jrm.autotrim.tab will be generated and the fragment picker called

$ pick_fragments -cs 2jrm.tab -trim

3.5 Chemical shift re-referencing

The command pick_fragments detects if TALOS+ complains about errors in the chemical shift referencing and will correct them automatically. A file 2jrm.corrected.tab will be generated and the fragment picker is called with the re-referenced shifts. TALOS+ uses an algorithm similar to LACS that inspects correlation between CA-CB and CA/CB/C/HA shifts to identify the referencing offsets. However, only severe offsets with a detected offsets 3*expected error are reported.

4. Expected Results

After running through all steps of the tutorial the user should have obtained the following files:

2jrm_trim.tab backbone chemical shifts in TALOS file format
2jrm_trim.fasta corresponding FASTA sequence for structure calculation
2jrm_trim.frags3.dat.gz fragment library with 3mer fragments
2jrm_trim.frags9.dat.gz fragment library with 9mer fragments

5. Tutorial Script

The tutorial is provided as a script in csrosetta3/tutorials/pick_fragments/run_tutorial.sh. Just type

$ run_tutorial.sh

and all steps above will automatically proceed. Compare the result files with your own files. They should be the same.

sampling protocol:

C++ classes:

Comments

Good afternoon,

Executing the tutorial_pick_fragments.sh script gives me the following error, at the last line of the log:

protocols.frag_picker.scores.CSScore: caching CS score for 1ztx of size 101. The matrix is: 101 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 1zu0 of size 529
protocols.frag_picker.scores.CSScore: caching CS score for 1zu0 of size 529. Finished running command: /Users/tiago/software/rosetta3.4/rosetta_source/bin/fragment_picker.default.macosgccrelease @2jrm_trim.fasta.pick_flags
Error: expected creation of frags.fsc.score.200.9mers after running '/Users/tiago/software/rosetta3.4/rosetta_source/bin/fragment_picker.default.macosgccrelease @2jrm_trim.fasta.pick_flags'!
mv: rename frags.score.200.9mers to 2jrm_trim.frags9.dat: No such file or directory
---------------------------------------------------------------------------
--------- CS-Rosetta 3.0 (toolbox) -----------
----- -----
-- website: www.csrosetta.org --
-- copyright: Oliver Lange --
-- Reference: Lange et al. PNAS 2012, --
-- www.pnas.org/cgi/doi/10.1073/pnas.1203013109 --
-- --
-- program name: pick_fragments --
-- --
----- -----
-------- -------
---------------------------------------------------------------------------
Run TALOS+...
Checking for Chemical Shift Outliers ...
14 G C Secondary Shift: 2.918 Limit: 1.925
23 C HA Secondary Shift: -2.632 Limit: -1.080

Then it stopped. If i execute onlny the command "/Users/tiago/software/rosetta3.4/rosetta_source/bin/fragment_picker.default.macosgccrelease @2jrm_trim.fasta.pick_flags", it gives a segmentation fault after the "CS score for 1zu0 of size 529" line.

Also with my own data it happens the same.

Any ideas of what could be wrong? Any more info please ask and i´ll send it.

Thank you very much for the support,
cheers,
Tiago

Dear Tiago,

maybe some of the vall files are not downloaded completely ?
execute these commands

$ cd csrosetta3/frag_picker
$ rm -Rf csrosetta_vall
$ cd ..
$ install.py 

With a clean install this tutorial should run without problem. Let me know if problems persist.

I haven't tested fragment picking on MAC OS X. I will do that asap and let you know.

Best,
Oliver

P.S. the output should look like this

-------------------------start of fragment_picker.default.linuxgccrelease ----------------------------------------
Command: /home/sattler_software/rosetta/rosetta_source/bin/fragment_picker.default.linuxgccrelease @2jrm_trim.fasta.pick_flags
core.init: Mini-Rosetta version unknown from unknown
core.init: command: /home/sattler_software/rosetta/rosetta_source/bin/fragment_picker.default.linuxgccrelease @2jrm_trim.fasta.pick_flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=-388027255 seed_offset=0 real_seed=-388027255
core.init.random: RandomGenerator:init: Normal mode, seed=-388027255 RG_type=mt19937
protocols.frag_picker.FragmentPicker: reading a query profile from: 2jrm_trim.fasta.checkpoint
protocols.frag_picker.FragmentPicker: picking fragments for query profile: DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQ
protocols.frag_picker.FragmentPicker: reading a query sequence from: 2jrm_trim.fasta
protocols.frag_picker.FragmentPicker: picking fragments for query sequence: DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQ
protocols.frag_picker.VallProvider: vallChunksFromLibrary
protocols.frag_picker.VallProvider: Reading Vall library from /home/sattler_software/csrosetta3/frag_picker/csrosetta_vall/vall.dat.2008.apr24.vCS ... startline: 1  endline: 0
protocols.frag_picker.VallProvider: ... done.  Read 2330105 lines.  Time elapsed: 28 seconds.
protocols.frag_picker.VallProvider: Total chunks: 13717
protocols.frag_picker.VallProvider: Largest chunk: 1264 aa
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set.  Created 6225 residue types
protocols.frag_picker.FragmentPicker: Will pick fragments of size:3 9 
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme
protocols.frag_picker.TalosReader: read talos data from 2jrm_trim.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/rcprev.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/rcnext.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/rcadj.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/randcoil.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS sslimit data from external/SPARTA+/tab/sslimit.tab
protocols.frag_picker.scores.ProfileScoreL1: Profile scoring method is: L1
protocols.frag_picker.scores.ProfileScoreL1: Created cache for fraglen: 3 9
protocols.frag_picker.scores.PhiPsiSquareWell: Reference file for Phi,Psi scoring loaded from a TALOS file: 
protocols.frag_picker.PhiPsiTalosIO: read talos data from 2jrm_trim.fasta.talos/pred.tab
protocols.frag_picker.PhiPsiTalosIO: FIRST_RESID entry in TALOS file. Setting first-residue to 1
protocols.frag_picker.scores.PhiPsiSquareWell: Untrustworthy data at position 1 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: Untrustworthy data at position 24 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: Untrustworthy data at position 26 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: Untrustworthy data at position 46 due to prediction class None
protocols.frag_picker.FragmentPicker: Picking 200 fragments based on 200 candidates
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme for the selection step
protocols.frag_picker.FragmentPicker: Collector for fragment size: 3 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Collector for fragment size: 9 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Fragment scoring scheme used:
-----------------------------------------
id    fragment score method name   weight
  1                        CSScore    1
  2                 ProfileScoreL1  1.5
  3              TalosSSSimilarity 0.25
  4                      RamaScore    1
  5               PhiPsiSquareWell 0.15
-----------------------------------------

protocols.frag_picker.FragmentPicker: 
fragment_picker: After setup; size of a query is: 46
fragment_picker: Picking candidates
fragment_picker: Running bounded protocol
protocols.frag_picker.FragmentPicker: Picking candidates...
protocols.frag_picker.FragmentPicker: 100% done at 8tln
protocols.frag_picker.FragmentPicker: ... done.  Processed 13717 chunks.  Time elapsed: 436 seconds.
-------------------------------- Omitted the following table output ----------------------------------

Dear Oliver,

Thank you for your response.
I´ve tried the instructions you gave me and still gives the same errors with a segmentation fault. The log file is slightly different from yours, regarding the talos file.

core.init: Mini-Rosetta version unknown from unknown
core.init: command: /Users/tiago/software/rosetta3.4/rosetta_source/bin/fragment_picker.default.macosgccrelease @2jrm_trim.fasta.pick_flags
core.init: 'RNG device' seed mode, using '/dev/urandom', seed=1123850012 seed_offset=0 real_seed=1123850012
core.init.random: RandomGenerator:init: Normal mode, seed=1123850012 RG_type=mt19937
protocols.frag_picker.FragmentPicker: reading a query profile from: 2jrm_trim.fasta.checkpoint
protocols.frag_picker.FragmentPicker: picking fragments for query profile: DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQ
protocols.frag_picker.FragmentPicker: reading a query sequence from: 2jrm_trim.fasta
protocols.frag_picker.FragmentPicker: picking fragments for query sequence: DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQ
protocols.frag_picker.VallProvider: vallChunksFromLibrary
protocols.frag_picker.VallProvider: Reading Vall library from /Users/tiago/software/CS_rosetta_toolbox/csrosetta3/frag_picker/csrosetta_vall/vall.dat.2008.apr24.vCS ... startline: 1 endline: 0
protocols.frag_picker.VallProvider: ... done. Read 2330105 lines. Time elapsed: 27 seconds.
protocols.frag_picker.VallProvider: Total chunks: 13717
protocols.frag_picker.VallProvider: Largest chunk: 1264 aa
core.chemical.ResidueTypeSet: Finished initializing fa_standard residue type set. Created 6225 residue types
protocols.frag_picker.FragmentPicker: Will pick fragments of size:3 9
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme
protocols.frag_picker.TalosReader: read talos data from 2jrm_trim.tab
protocols.frag_picker.TalosReader: FIRST_RESID keyword didn't show up in a file header
Assuming the first residue id is 1
DATA FIRST_RESID 1
DATA SEQUENCE DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQARDEKQ
VARS RESID RESNAME ATOMNAME
FORMAT %4d %1s %4s %8.3f

1 D C 177.562
1 D CA 55.809
1 D CB 41.064
1 D HN 8.422
1 D HA 4.414
1 D HB2 2.629
1 D HB3 2.736
1 D N 120.954
2 R C 178.412
2 R CA 59.160
2 R CB 30.192
2 R CD 43.129
2 R CG 27.399
2 R HN 8.061
2 R HA 3.971
2 R HB2 1.830
2 R HB3 1.830
2 R HD2 3.171
2 R HD3 3.221
2 R HG2 1.412
2 R HG3 1.527
2 R N 119.853
3 L C 178.182
3 L CA 57.192
3 L CB 38.370
3 L CD1 24.599
3 L CD2 20.376
3 L CG 25.960
3 L HN 7.801
3 L HA 3.727
3 L HB2 -0.085
3 L HB3 1.261
3 L HD1 0.516
3 L HD2 0.263
3 L HG 1.361
3 L N 121.052
4 E C 180.022
4 E CA 59.504
4 E CB 29.451
4 E CG 36.677
4 E HN 8.172
4 E HA 4.014
4 E HB2 2.022
4 E HB3 2.022
4 E HG2 2.378
4 E HG3 2.230
4 E N 120.463
5 R C 178.321
5 R CA 59.328
5 R CB 29.798
5 R CD 43.509
5 R CG 27.678
5 R HN 8.202
5 R HA 4.117
5 R HB2 1.881
5 R HB3 1.881
5 R HD2 3.203
5 R HD3 3.243
5 R HG2 1.568
5 R HG3 1.754
5 R N 119.987
6 A C 179.757
6 A CA 55.536
6 A CB 18.423
6 A HN 7.661
6 A HA 4.603
6 A HB 1.453
6 A N 122.208
7 Q C 178.128
7 Q CA 59.565
7 Q CB 29.572
7 Q CG 33.403
7 Q HN 8.205
7 Q HA 4.332
7 Q HB2 2.329
7 Q HB3 2.414
7 Q HE21 7.739
7 Q HE22 6.707
7 Q HG2 2.340
7 Q HG3 2.406
7 Q N 118.449
7 Q NE2 110.948
8 S C 177.751
8 S CA 61.583
8 S CB 62.897
8 S HN 8.245
8 S HA 4.281
8 S HB2 4.083
8 S HB3 4.083
8 S N 115.275
9 Q C 179.621
9 Q CA 58.803
9 Q CB 28.201
9 Q CG 34.108
9 Q HN 8.686
9 Q HA 4.124
9 Q HB2 2.428
9 Q HB3 2.883
9 Q HE21 7.749
9 Q HE22 7.073
9 Q HG2 2.662
9 Q HG3 2.846
9 Q N 121.722
9 Q NE2 111.644
10 G C 175.080
10 G CA 45.784
10 G HN 8.439
10 G HA2 1.849
10 G HA3 3.742
10 G N 113.363
11 Y C 177.200
11 Y CA 60.567
11 Y CB 38.755
11 Y CD1 133.363
11 Y CD2 133.363
11 Y CE1 117.788
11 Y CE2 117.788
11 Y HN 8.167
11 Y HA 4.014
11 Y HB2 2.873
11 Y HB3 3.031
11 Y HD1 7.056
11 Y HD2 7.056
11 Y HE1 6.573
11 Y HE2 6.573
11 Y N 123.123
12 K C 178.838
12 K CA 59.677
12 K CB 32.393
12 K CD 29.409
12 K CE 42.149
12 K CG 25.416
12 K HN 8.003
12 K HA 3.681
12 K HB2 1.855
12 K HB3 1.906
12 K HD2 1.707
12 K HD3 1.707
12 K HE2 2.994
12 K HE3 2.994
12 K HG2 1.466
12 K HG3 1.614
12 K N 117.920
13 A C 180.263
13 A CA 55.349
13 A CB 19.039
13 A HN 8.067
13 A HA 4.194
13 A HB 1.612
13 A N 120.778
14 G C 177.818
14 G CA 47.102
14 G HN 8.527
14 G HA2 3.101
14 G HA3 3.303
14 G N 107.003
15 L C 178.603
15 L CA 57.417
15 L CB 41.798
15 L CD1 25.379
15 L CD2 22.745
15 L CG 25.781
15 L HN 8.310
15 L HA 3.696
15 L HB2 1.300
15 L HB3 1.554
15 L HD1 0.620
15 L HD2 0.577
15 L HG 1.221
15 L N 124.762
16 N C 175.456
16 N CA 53.292
16 N CB 39.188
16 N HN 7.628
16 N HA 4.701
16 N HB2 2.788
16 N HB3 2.976
16 N HD21 7.572
16 N HD22 7.014
16 N N 114.867
16 N ND2 112.816
17 G C 175.226
17 G CA 46.302
17 G HN 7.586
17 G HA2 3.810
17 G HA3 4.102
17 G N 106.650
18 R C 177.405
18 R CA 55.103
18 R CB 30.537
18 R CD 42.737
18 R CG 27.117
18 R HN 8.156
18 R HA 4.508
18 R HB2 1.810
18 R HB3 2.093
18 R HD2 3.276
18 R HD3 3.276
18 R HG2 1.801
18 R HG3 1.920
18 R N 118.161
19 S C 175.005
19 S CA 57.752
19 S CB 64.687
19 S HN 9.015
19 S HA 4.804
19 S HB2 4.010
19 S HB3 4.305
19 S N 119.720
20 Q C 177.736
20 Q CA 58.643
20 Q CB 27.352
20 Q CG 33.415
20 Q HN 8.662
20 Q HA 3.162
20 Q HB2 0.962
20 Q HB3 1.354
20 Q HE21 6.867
20 Q HE22 6.818
20 Q HG2 1.229
20 Q HG3 1.337
20 Q N 120.247
20 Q NE2 112.091
21 E C 176.177
21 E CA 57.807
21 E CB 28.583
21 E CG 36.628
21 E HN 8.244
21 E HA 3.886
21 E HB2 1.794
21 E HB3 1.976
21 E HG2 2.218
21 E HG3 2.169
21 E N 117.869
22 A C 176.063
22 A CA 51.945
22 A CB 18.113
22 A HN 7.451
22 A HA 4.070
22 A HB 1.546
22 A N 120.356
23 C CA 56.231
23 C CB 27.778
23 C HN 6.591
23 C HA 1.828
23 C HB2 2.250
23 C HB3 1.943
23 C N 121.588
24 P C 175.515
24 P CA 63.382
24 P CB 31.551
24 P CD 50.316
24 P CG 25.208
24 P HA 4.323
24 P HB2 1.555
24 P HB3 1.722
24 P HD2 2.123
24 P HD3 3.269
24 P HG2 0.637
24 P HG3 1.688
25 Y C 174.785
25 Y CA 58.348
25 Y CB 41.030
25 Y CD1 132.844
25 Y CD2 132.844
25 Y CE1 118.714
25 Y CE2 118.714
25 Y HN 6.804
25 Y HA 4.582
25 Y HB2 2.100
25 Y HB3 3.099
25 Y HD1 6.962
25 Y HD2 6.962
25 Y HE1 7.002
25 Y HE2 7.002
25 Y N 118.903
26 Q C 176.528
26 Q CA 55.996
26 Q CB 30.182
26 Q CG 33.828
26 Q HN 8.763
26 Q HA 4.344
26 Q HB2 1.898
26 Q HB3 2.133
26 Q HE21 7.424
26 Q HE22 6.726
26 Q HG2 2.309
26 Q HG3 2.309
26 Q N 120.327
26 Q NE2 112.951
27 Q C 177.216
27 Q CA 56.931
27 Q CB 28.699
27 Q CG 34.266
27 Q HN 8.230
27 Q HA 4.262
27 Q HB2 2.047
27 Q HB3 2.245
27 Q HE21 7.780
27 Q HE22 7.123
27 Q HG2 2.607
27 Q HG3 2.607
27 Q N 121.712
27 Q NE2 113.606
28 V C 177.685
28 V CA 66.570
28 V CB 31.946
28 V CG1 20.742
28 V CG2 21.379
28 V HN 8.484
28 V HA 3.551
28 V HB 2.091
28 V HG1 0.979
28 V HG2 1.043
28 V N 122.145
29 D C 177.892
29 D CA 56.826
29 D CB 38.807
29 D HN 8.324
29 D HA 4.434
29 D HB2 2.703
29 D HB3 2.836
29 D N 120.937
30 A C 178.949
30 A CA 55.327
30 A CB 17.371
30 A HN 8.431
30 A HA 3.598
30 A HB 0.696
30 A N 126.210
31 R C 177.746
31 R CA 60.636
31 R CB 29.931
31 R CD 43.387
31 R CG 28.346
31 R HN 8.458
31 R HA 3.857
31 R HB2 1.633
31 R HB3 1.799
31 R HD2 2.953
31 R HD3 3.106
31 R HE 7.276
31 R HG2 1.473
31 R HG3 1.743
31 R N 116.717
31 R NE 83.844
32 S C 178.293
32 S CA 62.627
32 S HN 8.173
32 S HA 4.130
32 S N 114.110
33 Y C 178.701
33 Y CA 62.466
33 Y CB 38.687
33 Y CD1 133.216
33 Y CD2 133.216
33 Y CE1 118.412
33 Y CE2 118.412
33 Y HN 8.343
33 Y HA 4.213
33 Y HB2 2.944
33 Y HB3 3.031
33 Y HD1 7.326
33 Y HD2 7.326
33 Y HE1 6.767
33 Y HE2 6.767
33 Y N 123.318
34 W C 179.359
34 W CA 61.953
34 W CB 31.349
34 W CD1 128.757
34 W CE3 121.109
34 W CH2 124.802
34 W CZ2 114.322
34 W CZ3 122.875
34 W HN 8.818
34 W HA 4.586
34 W HB2 3.364
34 W HB3 3.777
34 W HD1 7.653
34 W HE1 10.958
34 W HE3 7.343
34 W HH2 6.963
34 W HZ2 7.171
34 W HZ3 6.569
34 W N 123.286
34 W NE1 130.950
35 L C 179.498
35 L CA 58.206
35 L CB 41.754
35 L CD1 25.809
35 L CD2 23.315
35 L CG 27.678
35 L HN 9.368
35 L HA 4.405
35 L HB2 1.639
35 L HB3 2.113
35 L HD1 0.929
35 L HD2 0.980
35 L HG 2.177
35 L N 119.265
36 G C 176.508
36 G CA 47.412
36 G HN 8.283
36 G HA2 3.857
36 G HA3 3.929
36 G N 108.413
37 G C 174.891
37 G CA 47.341
37 G HN 8.181
37 G HA2 4.124
37 G HA3 4.258
37 G N 109.904
38 W C 178.547
38 W CA 62.646
38 W CB 29.467
38 W CD1 126.147
38 W CE3 120.891
38 W CH2 124.522
38 W CZ2 114.623
38 W CZ3 121.988
38 W HN 8.460
38 W HA 3.578
38 W HB2 2.200
38 W HB3 3.393
38 W HD1 6.383
38 W HE1 10.152
38 W HE3 7.436
38 W HH2 7.213
38 W HZ2 7.547
38 W HZ3 7.034
38 W N 124.152
38 W NE1 128.122
39 R C 178.784
39 R CA 59.785
39 R CB 30.295
39 R CD 43.592
39 R CG 28.252
39 R HN 8.759
39 R HA 3.669
39 R HB2 2.017
39 R HB3 2.142
39 R HD2 3.241
39 R HD3 3.354
39 R HE 7.454
39 R HG2 2.205
39 R HG3 1.742
39 R N 118.655
39 R NE 84.817
40 D C 178.818
40 D CA 57.518
40 D CB 39.752
40 D HN 8.084
40 D HA 4.362
40 D HB2 2.756
40 D HB3 3.138
40 D N 120.646
41 A C 179.397
41 A CA 54.962
41 A CB 18.940
41 A HN 7.873
41 A HA 3.627
41 A HB 0.818
41 A N 122.126
42 R C 178.647
42 R CA 57.880
42 R CB 28.753
42 R CD 42.205
42 R CG 25.305
42 R HN 7.587
42 R HA 3.538
42 R HB2 1.135
42 R HB3 1.135
42 R HD2 2.401
42 R HD3 2.603
42 R HE 7.000
42 R HG2 0.921
42 R HG3 1.614
42 R N 117.721
42 R NE 84.221
43 D C 178.360
43 D CA 56.330
43 D CB 40.401
43 D HN 8.249
43 D HA 4.383
43 D HB2 2.728
43 D HB3 2.728
43 D N 119.997
44 E C 178.675
44 E CA 58.740
44 E CB 29.585
44 E CG 36.270
44 E HN 8.060
44 E HA 4.007
44 E HB2 2.054
44 E HB3 2.054
44 E HG2 2.418
44 E HG3 2.191
44 E N 121.823
45 K C 178.241
45 K CA 57.727
45 K CB 32.090
45 K CD 28.920
45 K CE 41.985
45 K CG 24.798
45 K HN 8.089
45 K HA 4.057
45 K HB2 1.766
45 K HB3 1.766
45 K HD2 1.573
45 K HD3 1.573
45 K HE2 2.859
45 K HE3 2.897
45 K HG2 1.341
45 K HG3 1.408
45 K N 119.415
46 Q C 176.965
46 Q CA 56.977
46 Q CB 28.858
46 Q CG 33.839
46 Q HN 8.043
46 Q HA 4.189
46 Q HB2 2.120
46 Q HB3 2.091
46 Q HE21 7.472
46 Q HE22 6.818
46 Q HG2 2.330
46 Q HG3 2.330
46 Q N 118.262
46 Q NE2 112.140
protocols.frag_picker.scores.CSScore: READING SHIFTS!
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/rcprev.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/rcnext.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/rcadj.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS adjustment data from external/SPARTA+/tab/randcoil.tab
protocols.frag_picker.SecondaryShiftCalculator: read CS sslimit data from external/SPARTA+/tab/sslimit.tab
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA A -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C A -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA A -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB A -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N A -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN A -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA C -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C C -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA C -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB C -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N C -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN C -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA c -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C c -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA c -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB c -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N c -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN c -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA D -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C D -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA D -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB D -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N D -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN D -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA E -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C E -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA E -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB E -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N E -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN E -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA F -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C F -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA F -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB F -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N F -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN F -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA G -0.999 1.42
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C G -3.725 1.925
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA G -1.874 3.492
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N G -7.498 5.848
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN G -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA H -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C H -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA H -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB H -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N H -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN H -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA h -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C h -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA h -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB h -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N h -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN h -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA # -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C # -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA # -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB # -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N # -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN # -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA I -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C I -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA I -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB I -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N I -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN I -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA K -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C K -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA K -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB K -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N K -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN K -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA L -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C L -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA L -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB L -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N L -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN L -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA M -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C M -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA M -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB M -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N M -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN M -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA N -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C N -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA N -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB N -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N N -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN N -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA P -0.557 0.621
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C P -3.07 2.904
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA P -2.22 3.764
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB P -2.28 2.771
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N P -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA Q -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C Q -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA Q -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB Q -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N Q -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN Q -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA R -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C R -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA R -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB R -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N R -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN R -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA S -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C S -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA S -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB S -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N S -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN S -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA T -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C T -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA T -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB T -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N T -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN T -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA V -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C V -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA V -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB V -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N V -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN V -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA W -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C W -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA W -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB W -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N W -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN W -4 4
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HA Y -1.08 1.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST C Y -4.435 3.727
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CA Y -3.445 4.66
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST CB Y -3.765 6.317
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST N Y -11.301 10.047
protocols.frag_picker.SecondaryShiftCalculator: READ_SSLIST HN Y -4 4
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 1 D 120.954 120.4 N 0.554
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 1 D_aa N 0.554
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 1 D 4.414 4.64 HA -0.226
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 1 D_aa HA -0.226
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 1 D 177.562 176.3 C 1.262
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 1 D_aa C 1.262
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 1 D 55.809 54 CA 1.809
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 1 D_aa CA 1.809
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 1 D 41.064 40.8 CB 0.264
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 1 D_aa CB 0.264
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 1 D 8.422 8.37 HN 0.052
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 1 D_aa HN 0.052
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 2 R 119.853 121.675 N -1.822
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 2 R_aa N -1.822
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 2 R 3.971 4.34 HA -0.369
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 2 R_aa HA -0.369
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 2 R 178.412 176.3 C 2.112
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 2 R_aa C 2.112
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 2 R 59.16 56.1 CA 3.06
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 2 R_aa CA 3.06
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 2 R 30.192 30.3 CB -0.108
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 2 R_aa CB -0.108
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 2 R 8.061 8.27 HN -0.209
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 2 R_aa HN -0.209
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 3 L 121.052 122.669 N -1.617
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 3 L_aa N -1.617
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 3 L 3.727 4.34 HA -0.613
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 3 L_aa HA -0.613
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 3 L 178.182 176.87 C 1.312
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 3 L_aa C 1.312
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 3 L 57.192 54.84 CA 2.352
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 3 L_aa CA 2.352
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 3 L 38.37 42.059 CB -3.689
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 3 L_aa CB -3.689
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 3 L 7.801 8.23 HN -0.429
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 3 L_aa HN -0.429
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 4 E 120.463 121.7 N -1.237
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 4 E_aa N -1.237
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 4 E 4.014 4.35 HA -0.336
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 4 E_aa HA -0.336
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 4 E 180.022 176.6 C 3.422
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 4 E_aa C 3.422
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 4 E 59.504 56.4 CA 3.104
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 4 E_aa CA 3.104
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 4 E 29.451 29.7 CB -0.249
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 4 E_aa CB -0.249
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 4 E 8.172 8.36 HN -0.188
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 4 E_aa HN -0.188
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 5 R 119.987 122.3 N -2.313
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 5 R_aa N -2.313
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 5 R 4.117 4.34 HA -0.223
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 5 R_aa HA -0.223
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 5 R 178.321 176.3 C 2.021
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 5 R_aa C 2.021
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 5 R 59.328 56.1 CA 3.228
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 5 R_aa CA 3.228
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 5 R 29.798 30.3 CB -0.502
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 5 R_aa CB -0.502
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 5 R 8.202 8.27 HN -0.068
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 5 R_aa HN -0.068
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 6 A 122.208 124.266 N -2.058
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 6 A_aa N -2.058
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 6 A 4.603 4.32 HA 0.283
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 6 A_aa HA 0.283
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 6 A 179.757 177.584 C 2.173
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 6 A_aa C 2.173
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 6 A 55.536 52.037 CA 3.499
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 6 A_aa CA 3.499
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 6 A 18.423 19 CB -0.577
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 6 A_aa CB -0.577
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 6 A 7.661 8.15 HN -0.489
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 6 A_aa HN -0.489
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 7 Q 118.449 120.08 N -1.631
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 7 Q_aa N -1.631
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 7 Q 4.332 4.34 HA -0.008
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 7 Q_aa HA -0.008
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 7 Q 178.128 176 C 2.128
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 7 Q_aa C 2.128
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 7 Q 59.565 55.803 CA 3.762
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 7 Q_aa CA 3.762
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 7 Q 29.572 28.738 CB 0.834
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 7 Q_aa CB 0.834
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 7 Q 8.205 8.27 HN -0.065
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 7 Q_aa HN -0.065
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 8 S 115.275 117.274 N -1.999
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 8 S_aa N -1.999
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 8 S 4.281 4.47 HA -0.189
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 8 S_aa HA -0.189
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 8 S 177.751 174.6 C 3.151
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 8 S_aa C 3.151
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 8 S 61.583 58.2 CA 3.383
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 8 S_aa CA 3.383
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 8 S 62.897 63.2 CB -0.303
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 8 S_aa CB -0.303
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 8 S 8.245 8.31 HN -0.065
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 8 S_aa HN -0.065
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 9 Q 121.722 122.394 N -0.672
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 9 Q_aa N -0.672
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 9 Q 4.124 4.34 HA -0.216
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 9 Q_aa HA -0.216
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 9 Q 179.621 176.391 C 3.23
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 9 Q_aa C 3.23
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 9 Q 58.803 55.803 CA 3
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 9 Q_aa CA 3
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 9 Q 28.201 28.738 CB -0.537
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 9 Q_aa CB -0.537
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 9 Q 8.686 8.27 HN 0.416
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 9 Q_aa HN 0.416
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 10 G 113.363 110.374 N 2.989
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 10 G_aa N 2.989
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 10 G 5.591 3.96 HA -1.1645
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 10 G 0 -1.1645 Limit: -0.999
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 10 G 175.08 174.567 C 0.513
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 10 G_aa C 0.513
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 10 G 45.784 45.1 CA 0.684
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 10 G_aa CA 0.684
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 10 G 5.591 3.96 CB -1.1645
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 10 G 8.439 8.29 HN 0.149
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 10 G_aa HN 0.149
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 11 Y 123.123 121.367 N 1.756
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 11 Y_aa N 1.756
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 11 Y 4.014 4.55 HA -0.536
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 11 Y_aa HA -0.536
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 11 Y 177.2 175.9 C 1.3
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 11 Y_aa C 1.3
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 11 Y 60.567 58.1 CA 2.467
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 11 Y_aa CA 2.467
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 11 Y 38.755 38.46 CB 0.295
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 11 Y_aa CB 0.295
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 11 Y 8.167 8.28 HN -0.113
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 11 Y_aa HN -0.113
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 12 K 117.92 122.15 N -4.23
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 12 K_aa N -4.23
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 12 K 3.681 4.32 HA -0.639
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 12 K_aa HA -0.639
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 12 K 178.838 176.6 C 2.238
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 12 K_aa C 2.238
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 12 K 59.677 56.287 CA 3.39
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 12 K_aa CA 3.39
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 12 K 32.393 32.5 CB -0.107
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 12 K_aa CB -0.107
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 12 K 8.003 8.25 HN -0.247
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 12 K_aa HN -0.247
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 13 A 120.778 124.365 N -3.587
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 13 A_aa N -3.587
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 13 A 4.194 4.32 HA -0.126
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 13 A_aa HA -0.126
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 13 A 180.263 177.975 C 2.288
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 13 A_aa C 2.288
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 13 A 55.349 52.037 CA 3.312
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 13 A_aa CA 3.312
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 13 A 19.039 19 CB 0.039
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 13 A_aa CB 0.039
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 13 A 8.067 8.15 HN -0.083
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 13 A_aa HN -0.083
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 14 G 107.003 108.6 N -1.597
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 14 G_aa N -1.597
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 14 G 6.404 3.96 HA -0.758
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 14 G_aa HA -0.758
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 14 G 177.818 174.9 C 2.918
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 14 G 0 2.918 Limit: 1.925
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 14 G 47.102 45.1 CA 2.002
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 14 G_aa CA 2.002
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 14 G 6.404 3.96 CB -0.758
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 14 G 8.527 8.29 HN 0.237
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 14 G_aa HN 0.237
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 15 L 124.762 122.29 N 2.472
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 15 L_aa N 2.472
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 15 L 3.696 4.34 HA -0.644
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 15 L_aa HA -0.644
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 15 L 178.603 176.87 C 1.733
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 15 L_aa C 1.733
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 15 L 57.417 54.84 CA 2.577
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 15 L_aa CA 2.577
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 15 L 41.798 42.059 CB -0.261
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 15 L_aa CB -0.261
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 15 L 8.31 8.23 HN 0.08
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 15 L_aa HN 0.08
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 16 N 114.867 120.2 N -5.333
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 16 N_aa N -5.333
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 16 N 4.701 4.74 HA -0.039
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 16 N_aa HA -0.039
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 16 N 175.456 175.901 C -0.445
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 16 N_aa C -0.445
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 16 N 53.292 53.05 CA 0.242
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 16 N_aa CA 0.242
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 16 N 39.188 38.487 CB 0.701
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 16 N_aa CB 0.701
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 16 N 7.628 8.38 HN -0.752
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 16 N_aa HN -0.752
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 17 G 106.65 109.95 N -3.3
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 17 G_aa N -3.3
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 17 G 7.912 3.96 HA -0.004
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 17 G_aa HA -0.004
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 17 G 175.226 174.9 C 0.326
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 17 G_aa C 0.326
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 17 G 46.302 45.1 CA 1.202
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 17 G_aa CA 1.202
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 17 G 7.912 3.96 CB -0.004
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 17 G 7.586 8.29 HN -0.704
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 17 G_aa HN -0.704
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 18 R 118.161 122.047 N -3.886
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 18 R_aa N -3.886
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 18 R 4.508 4.34 HA 0.168
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 18 R_aa HA 0.168
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 18 R 177.405 176.3 C 1.105
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 18 R_aa C 1.105
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 18 R 55.103 56.1 CA -0.997
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 18 R_aa CA -0.997
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 18 R 30.537 30.3 CB 0.237
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 18 R_aa CB 0.237
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 18 R 8.156 8.27 HN -0.114
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 18 R_aa HN -0.114
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 19 S 119.72 117.146 N 2.574
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 19 S_aa N 2.574
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 19 S 4.804 4.47 HA 0.334
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 19 S_aa HA 0.334
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 19 S 175.005 174.6 C 0.405
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 19 S_aa C 0.405
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 19 S 57.752 58.2 CA -0.448
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 19 S_aa CA -0.448
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 19 S 64.687 63.2 CB 1.487
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 19 S_aa CB 1.487
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 19 S 9.015 8.31 HN 0.705
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 19 S_aa HN 0.705
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 20 Q 120.247 122.394 N -2.147
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 20 Q_aa N -2.147
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 20 Q 3.162 4.34 HA -1.178
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 20 Q 0 -1.178 Limit: -1.08
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 20 Q 177.736 176 C 1.736
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 20 Q_aa C 1.736
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 20 Q 58.643 55.803 CA 2.84
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 20 Q_aa CA 2.84
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 20 Q 27.352 28.738 CB -1.386
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 20 Q_aa CB -1.386
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 20 Q 8.662 8.27 HN 0.392
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 20 Q_aa HN 0.392
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 21 E 117.869 121.774 N -3.905
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 21 E_aa N -3.905
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 21 E 3.886 4.35 HA -0.464
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 21 E_aa HA -0.464
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 21 E 176.177 176.6 C -0.423
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 21 E_aa C -0.423
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 21 E 57.807 56.4 CA 1.407
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 21 E_aa CA 1.407
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 21 E 28.583 29.7 CB -1.117
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 21 E_aa CB -1.117
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 21 E 8.244 8.36 HN -0.116
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 21 E_aa HN -0.116
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 22 A 120.356 124.22 N -3.864
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 22 A_aa N -3.864
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 22 A 4.07 4.32 HA -0.25
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 22 A_aa HA -0.25
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 22 A 176.063 177.584 C -1.521
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 22 A_aa C -1.521
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 22 A 51.945 52.037 CA -0.092
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 22 A_aa CA -0.092
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 22 A 18.113 19 CB -0.887
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 22 A_aa CB -0.887
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 22 A 7.451 8.15 HN -0.699
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 22 A_aa HN -0.699
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 23 C 121.588 119.1 N 2.488
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 23 C_aa N 2.488
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 23 C 1.828 4.46 HA -2.632
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 23 C 0 -2.632 Limit: -1.08
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 23 C 56.231 59.018 CA -2.787
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 23 C_aa CA -2.787
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 23 C 27.778 27.74 CB 0.038
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 23 C_aa CB 0.038
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 23 C 6.591 8.23 HN -1.639
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 23 C_aa HN -1.639
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 24 P 4.323 4.42 HA -0.097
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 24 P_aa HA -0.097
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 24 P 175.515 176.967 C -1.452
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 24 P_aa C -1.452
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 24 P 63.382 63.1 CA 0.282
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 24 P_aa CA 0.282
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 24 P 31.551 31.7 CB -0.149
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 24 P_aa CB -0.149
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 25 Y 118.903 120.9 N -1.997
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 25 Y_aa N -1.997
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 25 Y 4.582 4.55 HA 0.032
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 25 Y_aa HA 0.032
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 25 Y 174.785 175.9 C -1.115
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 25 Y_aa C -1.115
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 25 Y 58.348 58.1 CA 0.248
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 25 Y_aa CA 0.248
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 25 Y 41.03 38.46 CB 2.57
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 25 Y_aa CB 2.57
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 25 Y 6.804 8.28 HN -1.476
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 25 Y_aa HN -1.476
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 26 Q 120.327 121.55 N -1.223
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 26 Q_aa N -1.223
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 26 Q 4.344 4.34 HA 0.004
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 26 Q_aa HA 0.004
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 26 Q 176.528 176 C 0.528
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 26 Q_aa C 0.528
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 26 Q 55.996 55.803 CA 0.193
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 26 Q_aa CA 0.193
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 26 Q 30.182 28.738 CB 1.444
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 26 Q_aa CB 1.444
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 26 Q 8.763 8.27 HN 0.493
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 26 Q_aa HN 0.493
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 27 Q 121.712 121.374 N 0.338
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 27 Q_aa N 0.338
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 27 Q 4.262 4.34 HA -0.078
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 27 Q_aa HA -0.078
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 27 Q 177.216 176 C 1.216
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 27 Q_aa C 1.216
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 27 Q 56.931 55.803 CA 1.128
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 27 Q_aa CA 1.128
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 27 Q 28.699 28.738 CB -0.039
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 27 Q_aa CB -0.039
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 27 Q 8.23 8.27 HN -0.04
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 27 Q_aa HN -0.04
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 28 V 122.145 121.488 N 0.657
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 28 V_aa N 0.657
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 28 V 3.551 4.12 HA -0.569
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 28 V_aa HA -0.569
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 28 V 177.685 175.771 C 1.914
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 28 V_aa C 1.914
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 28 V 66.57 62.3 CA 4.27
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 28 V_aa CA 4.27
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 28 V 31.946 31.823 CB 0.123
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 28 V_aa CB 0.123
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 28 V 8.484 8.19 HN 0.294
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 28 V_aa HN 0.294
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 29 D 120.937 124.225 N -3.288
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 29 D_aa N -3.288
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 29 D 4.434 4.64 HA -0.206
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 29 D_aa HA -0.206
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 29 D 177.892 176.3 C 1.592
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 29 D_aa C 1.592
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 29 D 56.826 54 CA 2.826
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 29 D_aa CA 2.826
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 29 D 38.807 40.8 CB -1.993
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 29 D_aa CB -1.993
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 29 D 8.324 8.37 HN -0.046
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 29 D_aa HN -0.046
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 30 A 126.21 123.995 N 2.215
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 30 A_aa N 2.215
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 30 A 3.598 4.32 HA -0.722
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 30 A_aa HA -0.722
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 30 A 178.949 177.584 C 1.365
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 30 A_aa C 1.365
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 30 A 55.327 52.037 CA 3.29
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 30 A_aa CA 3.29
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 30 A 17.371 19 CB -1.629
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 30 A_aa CB -1.629
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 30 A 8.431 8.15 HN 0.281
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 30 A_aa HN 0.281
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 31 R 116.717 120.78 N -4.063
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 31 R_aa N -4.063
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 31 R 3.857 4.34 HA -0.483
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 31 R_aa HA -0.483
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 31 R 177.746 176.3 C 1.446
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 31 R_aa C 1.446
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 31 R 60.636 56.1 CA 4.536
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 31 R_aa CA 4.536
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 31 R 29.931 30.3 CB -0.369
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 31 R_aa CB -0.369
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 31 R 8.458 8.27 HN 0.188
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 31 R_aa HN 0.188
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 32 S 114.11 117.146 N -3.036
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 32 S_aa N -3.036
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 32 S 4.13 4.47 HA -0.34
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 32 S_aa HA -0.34
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 32 S 178.293 174.267 C 4.026
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 32 S 0 4.026 Limit: 3.727
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 32 S 62.627 58.2 CA 4.427
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 32 S_aa CA 4.427
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 32 S 8.173 8.31 HN -0.137
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 32 S_aa HN -0.137
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 33 Y 123.318 122.394 N 0.924
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 33 Y_aa N 0.924
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 33 Y 4.213 4.55 HA -0.337
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 33 Y_aa HA -0.337
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 33 Y 178.701 175.9 C 2.801
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 33 Y_aa C 2.801
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 33 Y 62.466 58.1 CA 4.366
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 33 Y_aa CA 4.366
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 33 Y 38.687 38.46 CB 0.227
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 33 Y_aa CB 0.227
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 33 Y 8.343 8.28 HN 0.063
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 33 Y_aa HN 0.063
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 34 W 123.286 123.05 N 0.236
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 34 W_aa N 0.236
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 34 W 4.586 4.66 HA -0.074
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 34 W_aa HA -0.074
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 34 W 179.359 176.519 C 2.84
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 34 W_aa C 2.84
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 34 W 61.953 57.345 CA 4.608
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 34 W_aa CA 4.608
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 34 W 31.349 29.46 CB 1.889
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 34 W_aa CB 1.889
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 34 W 8.818 8.18 HN 0.638
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 34 W_aa HN 0.638
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 35 L 119.265 122.863 N -3.598
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 35 L_aa N -3.598
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 35 L 4.405 4.34 HA 0.065
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 35 L_aa HA 0.065
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 35 L 179.498 177.261 C 2.237
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 35 L_aa C 2.237
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 35 L 58.206 54.84 CA 3.366
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 35 L_aa CA 3.366
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 35 L 41.754 42.059 CB -0.305
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 35 L_aa CB -0.305
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 35 L 9.368 8.23 HN 1.138
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 35 L_aa HN 1.138
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 36 G 108.413 110.3 N -1.887
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 36 G_aa N -1.887
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 36 G 7.786 3.96 HA -0.067
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 36 G_aa HA -0.067
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 36 G 176.508 175.291 C 1.217
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 36 G_aa C 1.217
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 36 G 47.412 45.1 CA 2.312
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 36 G_aa CA 2.312
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 36 G 7.786 3.96 CB -0.067
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 36 G 8.283 8.29 HN -0.007
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 36 G_aa HN -0.007
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 37 G 109.904 109.367 N 0.537
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 37 G_aa N 0.537
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 37 G 8.382 3.96 HA 0.231
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 37 G_aa HA 0.231
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 37 G 174.891 174.9 C -0.009
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 37 G_aa C -0.009
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 37 G 47.341 45.1 CA 2.241
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 37 G_aa CA 2.241
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_G 37 G 8.382 3.96 CB 0.231
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 37 G 8.181 8.29 HN -0.109
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 37 G_aa HN -0.109
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 38 W 124.152 122.367 N 1.785
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 38 W_aa N 1.785
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 38 W 3.578 4.66 HA -1.082
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 38 W 0 -1.082 Limit: -1.08
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 38 W 178.547 176.519 C 2.028
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 38 W_aa C 2.028
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 38 W 62.646 57.345 CA 5.301
protocols.frag_picker.SecondaryShiftCalculator: SHIFT OUTLIER REMOVED: 38 W 0 5.301 Limit: 4.66
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 38 W 29.467 29.46 CB 0.007
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 38 W_aa CB 0.007
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 38 W 8.46 8.18 HN 0.28
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 38 W_aa HN 0.28
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 39 R 118.655 122.14 N -3.485
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 39 R_aa N -3.485
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 39 R 3.669 4.34 HA -0.671
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 39 R_aa HA -0.671
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 39 R 178.784 175.977 C 2.807
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 39 R_aa C 2.807
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 39 R 59.785 56.1 CA 3.685
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 39 R_aa CA 3.685
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 39 R 30.295 30.3 CB -0.005
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 39 R_aa CB -0.005
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 39 R 8.759 8.27 HN 0.489
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 39 R_aa HN 0.489
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 40 D 120.646 121.846 N -1.2
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 40 D_aa N -1.2
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 40 D 4.362 4.64 HA -0.278
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 40 D_aa HA -0.278
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 40 D 178.818 176.3 C 2.518
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 40 D_aa C 2.518
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 40 D 57.518 54 CA 3.518
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 40 D_aa CA 3.518
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 40 D 39.752 40.8 CB -1.048
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 40 D_aa CB -1.048
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 40 D 8.084 8.37 HN -0.286
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 40 D_aa HN -0.286
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 41 A 122.126 123.995 N -1.869
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 41 A_aa N -1.869
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 41 A 3.627 4.32 HA -0.693
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 41 A_aa HA -0.693
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 41 A 179.397 177.584 C 1.813
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 41 A_aa C 1.813
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 41 A 54.962 52.037 CA 2.925
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 41 A_aa CA 2.925
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 41 A 18.94 19 CB -0.06
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 41 A_aa CB -0.06
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 41 A 7.873 8.15 HN -0.277
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 41 A_aa HN -0.277
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 42 R 117.721 120.3 N -2.579
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 42 R_aa N -2.579
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 42 R 3.538 4.34 HA -0.802
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 42 R_aa HA -0.802
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 42 R 178.647 175.977 C 2.67
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 42 R_aa C 2.67
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 42 R 57.88 56.1 CA 1.78
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 42 R_aa CA 1.78
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 42 R 28.753 30.3 CB -1.547
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 42 R_aa CB -1.547
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 42 R 7.587 8.27 HN -0.683
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 42 R_aa HN -0.683
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 43 D 119.997 121.846 N -1.849
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 43 D_aa N -1.849
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 43 D 4.383 4.64 HA -0.257
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 43 D_aa HA -0.257
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 43 D 178.36 176.3 C 2.06
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 43 D_aa C 2.06
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 43 D 56.33 54 CA 2.33
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 43 D_aa CA 2.33
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 43 D 40.401 40.8 CB -0.399
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 43 D_aa CB -0.399
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 43 D 8.249 8.37 HN -0.121
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 43 D_aa HN -0.121
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 44 E 121.823 121.375 N 0.448
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 44 E_aa N 0.448
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 44 E 4.007 4.35 HA -0.343
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 44 E_aa HA -0.343
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 44 E 178.675 176.6 C 2.075
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 44 E_aa C 2.075
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 44 E 58.74 56.4 CA 2.34
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 44 E_aa CA 2.34
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 44 E 29.585 29.7 CB -0.115
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 44 E_aa CB -0.115
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 44 E 8.06 8.36 HN -0.3
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 44 E_aa HN -0.3
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 45 K 119.415 122.2 N -2.785
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 45 K_aa N -2.785
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 45 K 4.057 4.32 HA -0.263
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 45 K_aa HA -0.263
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 45 K 178.241 176.6 C 1.641
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 45 K_aa C 1.641
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 45 K 57.727 56.287 CA 1.44
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 45 K_aa CA 1.44
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 45 K 32.09 32.5 CB -0.41
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 45 K_aa CB -0.41
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 45 K 8.089 8.25 HN -0.161
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 45 K_aa HN -0.161
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 46 Q 118.262 121.345 N -3.083
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 46 Q_aa N -3.083
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 46 Q 4.189 4.34 HA -0.151
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 46 Q_aa HA -0.151
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 46 Q 176.965 176 C 0.965
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 46 Q_aa C 0.965
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 46 Q 56.977 55.803 CA 1.174
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 46 Q_aa CA 1.174
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 46 Q 28.858 28.738 CB 0.12
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 46 Q_aa CB 0.12
protocols.frag_picker.SecondaryShiftCalculator: CALC_SECONDARY_A 46 Q 8.043 8.27 HN -0.227
protocols.frag_picker.SecondaryShiftCalculator: USING_2ND_SHIFT: 46 Q_aa HN -0.227
protocols.frag_picker.scores.CSScore: SHOULD BE DONE WRITING 2nd SHIFTS
protocols.frag_picker.scores.ProfileScoreL1: Profile scoring method is: L1
protocols.frag_picker.scores.ProfileScoreL1: Created cache for fraglen: 3 9
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_N.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_CP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_CP.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_P.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Q.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_V.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_S.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_Y.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_L.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_G.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_W.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_W.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_A.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/E_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_R.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_D.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_E.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/H_K.counts
basic.io.database: Database file opened: sampling/fragpicker_rama_tables/L_K.counts
protocols.frag_picker.scores.PhiPsiSquareWell: Reference file for Phi,Psi scoring loaded from a TALOS file:
protocols.frag_picker.PhiPsiTalosIO: read talos data from 2jrm_trim.fasta.talos/pred.tab
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 1
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 2
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 3
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 4
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 5
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 6
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 7
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 8
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 9
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 10
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 11
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 12
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 13
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 14
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 15
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 16
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 17
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 18
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 19
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 20
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 21
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 22
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 23
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 24
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 25
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 26
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 27
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 28
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 29
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 30
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 31
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 32
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 33
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 34
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 35
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 36
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 37
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 38
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 39
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 40
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 41
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 42
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 43
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 44
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 45
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 46
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 47
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 48
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 49
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 50
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 51
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 52
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 53
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 54
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 55
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 56
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 57
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 58
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 59
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 60
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 61
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 62
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 63
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 64
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 65
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 66
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 67
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 68
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 69
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 70
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 71
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 72
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 73
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 74
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 75
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 76
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 77
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 78
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 79
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 80
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 81
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 82
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 83
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 84
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 85
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 86
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 87
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 88
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 89
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 90
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 91
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 92
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 93
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 94
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 95
protocols.frag_picker.scores.PhiPsiSquareWell: Lack of data for position 96
protocols.frag_picker.FragmentPicker: Picking 200 fragments based on 200 candidates
protocols.frag_picker.FragmentPicker: Creating fragment scoring scheme for the selection step
protocols.frag_picker.FragmentPicker: Collector for fragment size: 3 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Collector for fragment size: 9 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: Fragment scoring scheme used:
-----------------------------------------
id fragment score method name weight
1 CSScore 1
2 ProfileScoreL1 1.5
3 TalosSSSimilarity 0.25
4 RamaScore 1
5 PhiPsiSquareWell 0.15
-----------------------------------------

protocols.frag_picker.FragmentPicker:
fragment_picker: After setup; size of a query is: 46
fragment_picker: Picking candidates
fragment_picker: Running bounded protocol
protocols.frag_picker.FragmentPicker: Picking candidates...
protocols.frag_picker.scores.CSScore: caching CS score for 12as of size 327
protocols.frag_picker.scores.CSScore: caching CS score for 12as of size 327. The matrix is: 327 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 16pk of size 415
protocols.frag_picker.scores.CSScore: caching CS score for 16pk of size 415. The matrix is: 415 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 16vp of size 303
protocols.frag_picker.scores.CSScore: caching CS score for 16vp of size 303. The matrix is: 303 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 16vp of size 8
protocols.frag_picker.scores.CSScore: caching CS score for 16vp of size 8. The matrix is: 8 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 34
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 34. The matrix is: 34 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 51
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 51. The matrix is: 51 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 8
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 8. The matrix is: 8 x 52
protocols.frag_picker.scores.CSScore: caching CS score for 1914 of size 78

then it stopped with a segmentation fault on this line
protocols.frag_picker.scores.CSScore: caching CS score for 1zu0 of size 529

sorry for the long log file.

thank very much for the help,

cheers

tiago

Hi Tiago,

the output you show is surprisingly verbose to me. This looks like an older version of the fragment_picker code. When you patched the rosetta-release version with http://www.csr-dev.org/downloads/patch34, did that go smoothly without any error messages ? Look also at the instructions under http://www.csr-dev.org/node/1354 (Section 1.3).

Best,
Oliver

Hi Oliver,

Yes i did the patch, with version 1.1 of the patch file, and the output seemed ok. I did the patching again just to be sure and it gave the "patching file..." output.

Running the tutorial gave the same errors stopping at the line :
protocols.frag_picker.scores.CSScore: caching CS score for 1zud of size 65 , don´t now if it is some mac specific error.
What solved it was doing the fragment picking without the default extension (fragment_picker.macosgccrelease).
Tried it like that and i think it worked. Don´t know why...
The output:

Command: /Users/tiago/software/rosetta3.4//rosetta_source/bin/fragment_picker.macosgccrelease @2jrm_trim.fasta.pick_flags
core.init: (0) Mini-Rosetta version unknown from unknown
core.init: (0) command: /Users/tiago/software/rosetta3.4//rosetta_source/bin/fragment_picker.macosgccrelease @2jrm_trim.fasta.pick_flags
core.init: (0) 'RNG device' seed mode, using '/dev/urandom', seed=1255049581 seed_offset=0 real_seed=1255049581
core.init.random: (0) RandomGenerator:init: Normal mode, seed=1255049581 RG_type=mt19937
protocols.frag_picker.FragmentPicker: (0) reading a query profile from: 2jrm_trim.fasta.checkpoint
protocols.frag_picker.FragmentPicker: (0) picking fragments for query profile: DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQ
protocols.frag_picker.FragmentPicker: (0) reading a query sequence from: 2jrm_trim.fasta
protocols.frag_picker.FragmentPicker: (0) picking fragments for query sequence: DRLERAQSQGYKAGLNGRSQEACPYQQVDARSYWLGGWRDARDEKQ
protocols.frag_picker.VallProvider: (0) vallChunksFromLibrary
protocols.frag_picker.VallProvider: (0) Reading Vall library from /Users/tiago/software/CS_rosetta_toolbox/csrosetta3/frag_picker/csrosetta_vall/vall.dat.2008.apr24.vCS ... startline: 1 endline: 0
protocols.frag_picker.VallProvider: (0) ... done. Read 2330105 lines. Time elapsed: 25 seconds.
protocols.frag_picker.VallProvider: (0) Total chunks: 13717
protocols.frag_picker.VallProvider: (0) Largest chunk: 1264 aa
core.chemical.ResidueTypeSet: (0) Finished initializing fa_standard residue type set. Created 6225 residue types
protocols.frag_picker.FragmentPicker: (0) Will pick fragments of size:3 9
protocols.frag_picker.FragmentPicker: (0) Creating fragment scoring scheme
protocols.frag_picker.TalosReader: (0) read talos data from 2jrm_trim.tab
protocols.frag_picker.SecondaryShiftCalculator: (0) read CS adjustment data from external/SPARTA+/tab/rcprev.tab
protocols.frag_picker.SecondaryShiftCalculator: (0) read CS adjustment data from external/SPARTA+/tab/rcnext.tab
protocols.frag_picker.SecondaryShiftCalculator: (0) read CS adjustment data from external/SPARTA+/tab/rcadj.tab
protocols.frag_picker.SecondaryShiftCalculator: (0) read CS adjustment data from external/SPARTA+/tab/randcoil.tab
protocols.frag_picker.SecondaryShiftCalculator: (0) read CS sslimit data from external/SPARTA+/tab/sslimit.tab
protocols.frag_picker.scores.ProfileScoreL1: (0) Profile scoring method is: L1
protocols.frag_picker.scores.ProfileScoreL1: (0) Created cache for fraglen: 3 9
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Reference file for Phi,Psi scoring loaded from a TALOS file:
protocols.frag_picker.PhiPsiTalosIO: (0) read talos data from 2jrm_trim.fasta.talos/pred.tab
protocols.frag_picker.PhiPsiTalosIO: (0) FIRST_RESID entry in TALOS file. Setting first-residue to 1
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 1 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 24 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 26 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 46 due to prediction class None
protocols.frag_picker.FragmentPicker: (0) Picking 200 fragments based on 200 candidates
protocols.frag_picker.FragmentPicker: (0) Creating fragment scoring scheme for the selection step
protocols.frag_picker.FragmentPicker: (0) Collector for fragment size: 3 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: (0) Collector for fragment size: 9 set to: BoundedCollector
protocols.frag_picker.FragmentPicker: (0) Fragment scoring scheme used:
-----------------------------------------
id fragment score method name weight
1 CSScore 1
2 ProfileScoreL1 1.5
3 TalosSSSimilarity 0.25
4 RamaScore 1
5 PhiPsiSquareWell 0.15
-----------------------------------------
protocols.frag_picker.FragmentPicker: (0)
fragment_picker: (0) After setup; size of a query is: 46
fragment_picker: (0) Picking candidates
fragment_picker: (0) Running bounded protocol
protocols.frag_picker.FragmentPicker: (0) Picking candidates...
protocols.frag_picker.FragmentPicker: (0) 100% done at 8tln
protocols.frag_picker.FragmentPicker: (0) ... done. Processed 13717 chunks. Time elapsed: 340 seconds.
protocols.frag_picker.FragmentPicker: (0)
pos count best worst | pos count best worst | pos count best worst |
1 200 0.70 1.16 | 2 200 0.26 0.81 | 3 200 0.44 0.80 |
4 200 0.12 0.59 | 5 200 0.37 0.81 | 6 200 0.46 0.82 |
7 200 0.52 0.80 | 8 200 0.54 0.88 | 9 200 0.40 1.01 |
10 200 0.40 0.96 | 11 200 0.23 0.75 | 12 200 0.27 0.81 |
13 200 0.31 0.72 | 14 200 0.70 1.19 | 15 200 0.55 0.87 |
16 200 0.36 0.79 | 17 200 0.52 1.04 | 18 200 0.67 1.29 |
19 200 0.77 1.18 | 20 200 0.81 1.17 | 21 200 0.90 1.63 |
22 200 0.64 1.25 | 23 200 0.52 1.41 | 24 200 0.44 1.25 |
25 200 0.68 1.36 | 26 200 0.78 1.09 | 27 200 0.52 0.87 |
28 200 0.61 0.82 | 29 200 0.43 0.92 | 30 200 0.45 0.83 |
31 200 0.41 0.78 | 32 200 0.62 1.03 | 33 200 0.64 1.14 |
34 200 0.72 1.25 | 35 200 0.41 1.00 | 36 200 0.57 1.02 |
37 200 0.69 1.11 | 38 200 0.18 0.80 | 39 200 0.37 0.71 |
40 200 0.57 0.82 | 41 200 0.55 0.81 | 42 200 0.55 0.85 |
43 200 0.33 0.74 | 44 200 0.71 1.02 | 45 0 |
46 0 |
protocols.frag_picker.FragmentPicker: (0)
pos count best worst | pos count best worst | pos count best worst |
1 200 1.05 1.26 | 2 200 1.07 1.31 | 3 200 1.12 1.38 |
4 200 1.03 1.28 | 5 200 1.04 1.30 | 6 200 1.10 1.37 |
7 200 1.05 1.36 | 8 200 1.11 1.44 | 9 200 1.14 1.48 |
10 200 1.13 1.53 | 11 200 1.09 1.47 | 12 200 1.15 1.56 |
13 200 1.23 1.63 | 14 200 1.37 1.77 | 15 200 1.64 1.96 |
16 200 1.53 2.05 | 17 200 1.65 2.16 | 18 200 1.60 2.09 |
19 200 1.54 2.02 | 20 200 1.61 1.96 | 21 200 1.58 1.92 |
22 200 1.56 1.84 | 23 200 1.50 1.77 | 24 200 1.30 1.53 |
25 200 1.23 1.45 | 26 200 1.29 1.49 | 27 200 1.11 1.43 |
28 200 1.10 1.41 | 29 200 1.30 1.54 | 30 200 1.37 1.62 |
31 200 1.25 1.62 | 32 200 1.24 1.55 | 33 200 1.27 1.59 |
34 200 1.29 1.63 | 35 200 1.10 1.40 | 36 200 1.07 1.38 |
37 200 1.11 1.39 | 38 200 1.13 1.34 | 39 0 |
40 0 | 41 0 | 42 0 |
43 0 | 44 0 | 45 0 |
46 0 |
Finished running command: /Users/tiago/software/rosetta3.4//rosetta_source/bin/fragment_picker.macosgccrelease @2jrm_trim.fasta.pick_flags

Does it seem alright to you?
Thank you for the help,
cheers,

Tiago

Hi Tiago,

this looks perfect.

Glad it works,
Oliver

Hi Oliver,

I'm trying to do a fragment picking with incomplete chemical shift assignments (the missing assignments are continuous residues in a 104 residues protein, most of the protein has backbone assignments. The residues missing assignments are part of helices in the middle of protein)

When I did fragment picking as in the tutorial, I found these lines in the log:

... seems fine till here
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 1 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 24 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 26 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 27 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 28 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 29 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 30 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 53 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 54 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 55 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 56 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 57 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 58 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 59 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 79 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 80 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 81 due to prediction class Warn
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 88 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 89 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 90 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 91 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 92 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 93 due to prediction class None
protocols.frag_picker.scores.PhiPsiSquareWell: (0) Untrustworthy data at position 103 due to prediction class None
protocols.frag_picker.FragmentPicker: (0) Picking 200 fragments based on 200 candidates
...
protocols.frag_picker.FragmentPicker: (0) 98% done at 3bja
protocols.frag_picker.FragmentPicker: (0) 99% done at 5nul
protocols.frag_picker.FragmentPicker: (0) ... done. Processed 13717 chunks. Time elapsed: 474 seconds.
protocols.frag_picker.FragmentPicker: (0) Saving Fragments...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 28 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 28 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 53 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 53 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 54 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 54 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 55 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 55 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 56 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 56 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 57 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 57 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 88 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 88 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 89 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 89 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 90 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 90 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 91 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 91 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 22 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 23 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 23 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 24 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 24 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 25 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 25 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 26 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 26 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 27 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 27 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 28 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 28 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 47 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 47 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 57 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 57 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 82 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 82 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 91 is corrupted. skipping...
protocols.frag_picker.FragmentPicker: (0) final_frag candidate 22 at position 91 is corrupted. skipping...
protocols.frag_picker.FragmentScoreManager: (0) final_frag candidate 22 is corrupted. skipping...

When I checked the fragment files, the 3-mer fragments looked correct but the 9-mer fragments were missing for some of the regions missing assignments(residue 48-56 and 83-90 are missing 9-mer fragments, residue 28-30 still have 9-mer fragments although missing assignments). And these regions(residue 48-56 and 83-90) seemed to be unfolded in rosetta runs (due to missing fragments?). Is this a bug in the fragment picker? Should I just do a fragment picking using "quota-protocol" in rosetta and copy-paste the fragments for these regions into the "CS-Rosetta" fragments?

Best,

Yisong

Hi Ystao,

we just have been able to complete a bugfix for this type of problem.
I haven't had time to upload a new release, since there are also other changes that require testing.
The part important for you isn't actually that much code. You could also do it manually by adding in
into rosetta_source/src/protocols/frag_picker/RamaScore.cc

--> line 75 (ca. )
for( Size i = 2; i <= query_.size() -1; ++i ) {
std::string curr_aa, next_aa, aa_type, ss_type;
utility::vector1< core::Real > ss_weight( 3, 0 );
utility::vector1< std::string > ss_types( 3, "" );

ss_weight[1] = query_ss_->helix_fraction(i);
ss_weight[2] = query_ss_->strand_fraction(i);
ss_weight[3] = query_ss_->loop_fraction(i);
>>>> Add the following lines>>>>>>>>>>>>>>
if ( ( ss_weight[1] + ss_weight[2] + ss_weight[3]) == 0) {
ss_weight[1] = 1.0;
ss_weight[2] = 1.0;
ss_weight[3] = 1.0;
}
<<<<<<<<<<<<<<<<<<<<
ss_types[1] = "H";
ss_types[2] = "E";
ss_types[3] = "L";

Hi, I have installed all the software you mentioned in your install guide, but there are some errors when installing. So when I try the commend 'pick_fragments -cs 2jrm_trim.tab >& picking.log' The following error message shown. Do you know how can I solve my problems ? Thank you.

Rerun TALOS+ with 2jrm.autotrim.tab...
Can't locate /home/cxw/Software/CS-ROSETTA/csrosetta3/frag_picker/setup_paths.pl in @INC (@INC contains: /etc/perl /usr/local/lib/perl/5.14.2 /usr/local/share/perl/5.14.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.14 /usr/share/perl/5.14 /usr/local/lib/site_perl .) at /home/cxw/Software/CS-ROSETTA/csrosetta3/frag_picker/pick_fragments.pl line 58.

my distribution is missing bits, if you look in pick_fragments.pl :

# set these paths now in separate file: setup_paths.pl
# the goal is to keep the pick_fragments.pl clean from any user-specific changes...

$options{vall} = "/Applications/Darwin/csrosetta3/frag_picker/vall.dat.2008.apr24.vCS";
$options{mini_db} = "/Applications/Darwin/csrosetta3/minirosetta_database";
$options{blastpgp} = "/Applications/Darwin/csrosetta3/frag_picker/blast-2.2.26/bin/blastpgp";
$options{blast_db} = "/Applications/Darwin/csrosetta3/frag_picker/genomes/nr";
$options{vall_blast_db} = "/Applications/Darwin/csrosetta3/frag_picker/csrosetta_vall/vall.blast.2008.apr24";
$options{picker} = "/Applications/Darwin/csrosetta3/mini/bin/fragment_picker.default.linuxgccrelease";

my $prog_path = dirname(abs_path($0));

#require "$prog_path/setup_paths.pl";
#&add_paths(\%options);

my distro is still missing the "blast_db" and "picker" executable
logan

I downloaded blast 2.2.27 from the NCBI website for OS X.

I downloaded the nr database from ftp://zhanglab.ccmb.med.umich.edu/download/nr.tar.gz

"fragment_picker" is found in the rosetta3.4 distribution bin/ directory

Hi Logan,

great that you could solve the problem yourself.
However, it is weird that you had these problems in the first place, as the install script is supposed to get these files for you automatically.
Which command-line did you use to run install.py ?
what was the output ?

Best,
Oliver

I'm having difficulty executing the pick_fragments command. I get the following error. I've checked all of my .tab and .fasta files and they look OK. Any ideas how I can fix this? Please let me know if you need more info to help me. Thanks, Kim
Run TALOS+...
Traceback (most recent call last):
File "/home/kim/rosetta/csrosetta3/com_alias/pick_fragments", line 172, in
tab.read_file( cs_file )
File "/home/kim/rosetta/csrosetta3/python/cs.py", line 326, in read_file
NIH_table.read_file( self, file )
File "/home/kim/rosetta/csrosetta3/python/cs.py", line 71, in read_file
self.read( fd )
File "/home/kim/rosetta/csrosetta3/python/cs.py", line 79, in read
self.read_body( fd )
File "/home/kim/rosetta/csrosetta3/python/cs.py", line 136, in read_body
if floats[ct]: value[ct]=float(tags[ct])
ValueError: could not convert string to float: (Null)

This problem can arise when the input .tab file is in a different format than expected. Please see the File formats under CS Rosetta Manual

Hello, I have install the cs-rosetta. When I run the command pick_fragments -cs ntd_trim.tab >& pick.log, I got following errors in log file and no fragment files generated.

Expecting TALOS VERSION: post_2012
Command: bash talos.script
Finished running command: bash talos.script
Error: expected creation of ntd_trim.fasta.talos/predSS.tab after running 'bash talos.script'!
Command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: ELF: not found
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: @@˜*g@8: not found
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 2: Syntax error: ")" unexpected
Couldn't open ntd_trim.fasta.chk for reading.
Finished running command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
Error: expected creation of ntd_trim.fasta.chk after running '/data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4'!
---------------------------------------------------------------------------
--------- CS-Rosetta 3.0 (toolbox) -----------
----- -----
-- website: www.csrosetta.org --
-- copyright: Oliver Lange --
-- Reference: Lange et al. PNAS 2012, --
-- www.pnas.org/cgi/doi/10.1073/pnas.1203013109 --
-- --
-- program name: pick_fragments --
-- --
----- -----
-------- -------
---------------------------------------------------------------------------
Run TALOS+...

Anyone can help? Thanks,

Xiaogang