Brief Diff:
Files /home/benchmark/working_dir/main:62109/cyclization/log_cyclize and /home/benchmark/working_dir/commits:20410/cyclization/log_cyclize differ
Full Diff:
diff -r '--exclude=command.sh' '--exclude=command.mpi.sh' '--exclude=observers' '--exclude=*.ignore' /home/benchmark/working_dir/main:62109/cyclization/log_cyclize /home/benchmark/working_dir/commits:20410/cyclization/log_cyclize
7148d7147
< core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/branching/C-linked_conjugation.txt
7172d7170
< core.chemical.Patch: Reading patch file: ROSETTA/database/chemical/residue_type_sets/fa_standard/patches/Nterm2_Oxobutrylation.txt
10206,10209d10203
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinFull
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:N_formylated
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue MET:NtermProteinMethylated
10302,10305d10295
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinFull
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:N_formylated
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue MET:NtermProteinMethylated
10979d10968
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
11003d10991
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
11127d11114
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
11151d11137
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
11275d11260
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU
11299d11283
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU
11423d11406
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PHE
11447d11429
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PHE
11571d11552
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
11595d11575
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
11715d11694
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE
11739d11717
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE
11863d11840
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue PRO
11887d11863
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue PRO
12010d11985
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
12034d12008
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
12157d12130
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
12181d12153
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
12305d12276
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
12329d12299
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
12452d12421
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
12476d12444
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
12599d12566
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
12623d12589
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
12743d12708
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR
12767d12731
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR
12890d12853
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
12914d12876
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
13038d12999
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU
13062d13022
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU
13186d13145
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ASN
13210d13168
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ASN
13333d13290
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
13357d13313
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
13480d13435
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
13504d13458
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
13627d13580
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU
13651d13603
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU
13774d13725
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
13798d13748
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
13921d13870
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
13945d13893
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
14064d14011
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
14088d14034
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
14208d14153
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP
14232d14176
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP
14355d14298
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
14379d14321
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
14502d14443
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR
14526d14466
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR
14649d14588
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR
14673d14611
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR
14796d14733
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE
14820d14756
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE
14943d14878
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
14967d14901
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
15091d15024
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER
15115d15047
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER
15238d15169
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE
15262d15192
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE
15385d15314
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU
15409d15337
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU
15532d15459
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue THR
15556d15482
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue THR
15679d15604
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
15703d15627
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
15826d15749
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
15850d15772
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
15973d15894
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
15997d15917
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
16116d16035
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER
16140d16058
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER
16263d16180
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
16287d16203
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
16406d16321
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
16430d16344
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
16549d16462
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU
16573d16485
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU
16696d16607
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER
16720d16630
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER
16843d16752
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU
16867d16775
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU
16990d16897
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU
17014d16920
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU
17137d17042
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
17161d17065
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
17284d17187
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
17308d17210
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
17431d17332
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
17455d17355
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
17578d17477
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
17602d17500
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
17722d17619
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG
17746d17642
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG
17869d17764
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU
17893d17787
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU
18016d17909
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue SER
18040d17932
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue SER
18163d18054
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE
18187d18077
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE
18310d18199
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
18334d18222
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
18457d18344
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
18481d18367
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
18605d18490
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TYR
18629d18513
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TYR
18752d18635
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LEU
18776d18658
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LEU
18899d18780
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
18923d18803
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
19046d18925
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
19070d18948
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
19193d19070
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLU
19217d19093
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLU
19340d19215
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE
19364d19238
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE
19487d19360
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
19511d19383
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
19634d19505
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
19658d19528
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
19781d19650
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
19805d19673
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
19928d19795
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue GLY
19952d19818
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue GLY
20071d19936
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue LYS
20095d19959
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue LYS
20218d20081
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ARG
20242d20104
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ARG
20365d20226
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
20389d20249
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
20512d20371
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue VAL
20536d20394
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue VAL
20659d20516
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ILE
20683d20539
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ILE
20806d20661
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue ALA
20830d20684
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue ALA
21025,21026d20878
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP
< core.chemical.ResidueTypeFinder: Checking if patch C-conjugated applies to residue TRP:CtermProteinFull
21073,21074d20924
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP
< core.chemical.ResidueTypeFinder: Checking if patch Nterm2_Oxobutrylation applies to residue TRP:CtermProteinFull