Histidine mapping with "martini3001" force-field

[Oishika-1]

Hello everyone,

I am not able to understand how to define charged and neutral histidine using martini3001 force-field. I have gone through a previous issue raised here "Histidine mapping with "elnedyn22p" force-field #389". As suggested by @pckroon, I did the following things:

1. In the folder-- vermouth/data/mappings/martini30/martini3001-- to create mappings for HSE | HSD | HSP, I copied the HIS mapping and made three files hse.charmm36.map, hsd.charmm36.map, hsp.charmm36.map with changing the name under the [molecule] block as HSE, HSD, and HSP respectively.
2. in the forlder-- vermouth/data/force_fields/universal/aminoacids.rtp -- universal defines HSE | HSD | HSP already
3. in the folder-- vermouth/data/force_fields/martini3001/aminoacids.ff-- i changed HIH to HSP and copied HIS as HSE, HSD changeing the names under [moleculetype] and [atoms] respectively
4. the input atomistic PDB (containing hydrogens) for martinize contains Histidines as HIS
5. the command i am using is like- martinize2 -f input.pdb -ff martini3001 -o out.top -x out.pdb -dssp /usr/local/bin/dssp -p backbone -cys auto -mutate A-HIS1:HSP -mutate A-HIS2:HSE -mutate A-HIS3:HSD
6. I have the directory-- vermouth-martinize-master in my working directory

the warning i am getting is WARNING - unmapped-atom - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. (residues include HSE | HSD | HSP | CYS)

Can someone please help me out. Thank you

[pckroon]

Your overall plan looks good... Let's focus on HSE as example problem. Could you post your HSE mapping file and martini3 definition? And could you also run with -v and post the full output?

Nice use of -mutate by the way!

[Oishika-1]

thanks Peter

following is the HSE mapping file---

; Copyright 2018 University of Groningen
;
; Licensed under the Apache License, Version 2.0 (the "License");
; you may not use this file except in compliance with the License.
; You may obtain a copy of the License at
;
;    http://www.apache.org/licenses/LICENSE-2.0
;
; Unless required by applicable law or agreed to in writing, software
; distributed under the License is distributed on an "AS IS" BASIS,
; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
; See the License for the specific language governing permissions and
; limitations under the License.

[ molecule ]
HSE  ;;;; is in fact HSP but if one of hydrogen on a nitrogen is missing in the input topology file, will become HSE or HSD automatically

[from]
universal

[to]
martini3001

[ martini ]
BB SC1 SC2 SC3

[ mapping ]
charmm27 charmm36

[ atoms ]
    1     N    BB
    2    HN    BB
    3    CA    BB
    4    HA    !BB
    5    CB   SC1
    6   HB1   !SC1
    7   HB2   !SC1
    8   CD2   SC2
    9   HD2   SC2
   10    CG   SC1
   11   NE2   SC2
   12   HE2   SC2
   13   ND1   SC3
   14   HD1   SC3
   15   CE1   SC3
   16   HE1   SC3
   17     C    BB
   18     O    BB

[ chiral ]
  CB     CA    N    C
  HB1    CA    N    C
  HB2    CA    N    C

[ chiral ]
  HA     CA    N    CB    C ; L-His
; HA     CA    N    C    CB ; D-His

[out]
HD1 ND1 CG NE2
HD2 CD2 CE1 CG
HE2 NE2 CE1 CD2

With -v, the full output is the following ---

    INFO - general - vermouth.pdb.pdb - Read 1 molecules from PDB file all_and_notwater_his.pdb
    INFO - step - vermouth - Guessing the bonds.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1X-ALA1:N and 2X-ALA1:H1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1X-ALA1:N and 3X-ALA1:H2 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1X-ALA1:N and 4X-ALA1:H3 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 11X-ALA1:C and 13X-ALA2:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 21X-ALA2:C and 23X-GLY3:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 28X-GLY3:C and 30X-GLY4:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 35X-GLY4:C and 37X-TYR5:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 56X-TYR5:C and 58X-VAL6:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 72X-VAL6:C and 74X-ALA7:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 82X-ALA7:C and 84X-LEU8:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 101X-LEU8:C and 103X-GLY9:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 108X-GLY9:C and 110X-ASP10:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 120X-ASP10:C and 122X-SER11:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 131X-SER11:C and 133X-TYR12:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 152X-TYR12:C and 154X-SER13:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 163X-SER13:C and 165X-SER14:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 174X-SER14:C and 176X-GLY15:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 181X-GLY15:C and 183X-VAL16:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 197X-VAL16:C and 199X-GLY17:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 204X-GLY17:C and 206X-ALA18:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 214X-ALA18:C and 216X-GLY19:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 221X-GLY19:C and 223X-SER20:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 232X-SER20:C and 234X-TYR21:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 253X-TYR21:C and 255X-ASP22:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 265X-ASP22:C and 267X-SER23:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 276X-SER23:C and 278X-GLY24:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 283X-GLY24:C and 285X-SER25:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 294X-SER25:C and 296X-GLY26:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 301X-GLY26:C and 303X-ASP27:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 313X-ASP27:C and 315X-CYS228:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 323X-CYS228:C and 325X-ARG29:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 347X-ARG29:C and 349X-ARG30:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 371X-ARG30:C and 373X-THR31:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 385X-THR31:C and 387X-PRO32:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 399X-PRO32:C and 401X-LYS33:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 421X-LYS33:C and 423X-ALA34:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 431X-ALA34:C and 433X-TYR35:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 452X-TYR35:C and 454X-PRO36:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 466X-PRO36:C and 468X-ALA37:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 476X-ALA37:C and 478X-LEU38:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 495X-LEU38:C and 497X-TRP39:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 519X-TRP39:C and 521X-ALA40:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 529X-ALA40:C and 531X-ALA41:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 539X-ALA41:C and 541X-ALA42:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 549X-ALA42:C and 551X-ASN43:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 563X-ASN43:C and 565X-SER44:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 574X-SER44:C and 576X-PRO45:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 588X-PRO45:C and 590X-ALA46:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 598X-ALA46:C and 600X-SER47:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 609X-SER47:C and 611X-PHE48:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 629X-PHE48:C and 631X-ASP49:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 641X-ASP49:C and 643X-PHE50:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 661X-PHE50:C and 663X-VAL51:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 677X-VAL51:C and 679X-ALA52:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 687X-ALA52:C and 689X-CYS253:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 322X-CYS228:SG and 696X-CYS253:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 697X-CYS253:C and 699X-SER54:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 708X-SER54:C and 710X-GLY55:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 715X-GLY55:C and 717X-ALA56:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 725X-ALA56:C and 727X-VAL57:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 741X-VAL57:C and 743X-THR58:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 755X-THR58:C and 757X-SER59:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 766X-SER59:C and 768X-ASP60:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 778X-ASP60:C and 780X-VAL61:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 794X-VAL61:C and 796X-LEU62:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 813X-LEU62:C and 815X-ASN63:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 827X-ASN63:C and 829X-LYS64:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 849X-LYS64:C and 851X-GLN65:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 866X-GLN65:C and 868X-MET66:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 883X-MET66:C and 885X-GLY67:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 890X-GLY67:C and 892X-PRO68:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 904X-PRO68:C and 906X-LEU69:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 923X-LEU69:C and 925X-ASN70:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 937X-ASN70:C and 939X-SER71:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 948X-SER71:C and 950X-SER72:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 959X-SER72:C and 961X-THR73:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 973X-THR73:C and 975X-SER74:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 984X-SER74:C and 986X-LEU75:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1003X-LEU75:C and 1005X-VAL76:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1019X-VAL76:C and 1021X-SER77:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1030X-SER77:C and 1032X-LEU78:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1049X-LEU78:C and 1051X-THR79:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1063X-THR79:C and 1065X-ILE80:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1082X-ILE80:C and 1084X-GLY81:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1089X-GLY81:C and 1091X-GLY82:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1096X-GLY82:C and 1098X-ASN83:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1110X-ASN83:C and 1112X-ASP84:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1122X-ASP84:C and 1124X-ALA85:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1132X-ALA85:C and 1134X-GLY86:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1139X-GLY86:C and 1141X-PHE87:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1159X-PHE87:C and 1161X-ALA88:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1169X-ALA88:C and 1171X-ASP89:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1181X-ASP89:C and 1183X-VAL90:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1197X-VAL90:C and 1199X-MET91:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1214X-MET91:C and 1216X-THR92:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1228X-THR92:C and 1230X-THR93:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1242X-THR93:C and 1244X-CYS294:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1252X-CYS294:C and 1254X-VAL95:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1268X-VAL95:C and 1270X-LEU96:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1287X-LEU96:C and 1289X-GLN97:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1304X-GLN97:C and 1306X-SER98:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1315X-SER98:C and 1317X-GLU99:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1330X-GLU99:C and 1332X-ALA100:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1340X-ALA100:C and 1342X-ASN101:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1354X-ASN101:C and 1356X-CYS2102:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1251X-CYS294:SG and 1363X-CYS2102:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1364X-CYS2102:C and 1366X-ILE103:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1383X-ILE103:C and 1385X-ALA104:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1393X-ALA104:C and 1395X-ARG105:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1417X-ARG105:C and 1419X-VAL106:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1433X-VAL106:C and 1435X-ASN107:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1447X-ASN107:C and 1449X-THR108:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1461X-THR108:C and 1463X-ALA109:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1471X-ALA109:C and 1473X-LYS110:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1493X-LYS110:C and 1495X-ALA111:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1503X-ALA111:C and 1505X-PHE112:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1523X-PHE112:C and 1525X-VAL113:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1539X-VAL113:C and 1541X-GLU114:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1554X-GLU114:C and 1556X-SER115:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1565X-SER115:C and 1567X-THR116:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1579X-THR116:C and 1581X-LEU117:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1598X-LEU117:C and 1600X-PRO118:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1612X-PRO118:C and 1614X-GLY119:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1619X-GLY119:C and 1621X-ARG120:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1643X-ARG120:C and 1645X-LEU121:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1662X-LEU121:C and 1664X-ASP122:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1674X-ASP122:C and 1676X-SER123:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1685X-SER123:C and 1687X-VAL124:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1701X-VAL124:C and 1703X-TYR125:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1722X-TYR125:C and 1724X-SER126:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1733X-SER126:C and 1735X-GLN127:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1750X-GLN127:C and 1752X-VAL128:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1766X-VAL128:C and 1768X-ARG129:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1790X-ARG129:C and 1792X-ALA130:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1800X-ALA130:C and 1802X-LYS131:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1822X-LYS131:C and 1824X-ALA132:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1832X-ALA132:C and 1834X-PRO133:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1846X-PRO133:C and 1848X-SER134:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1857X-SER134:C and 1859X-ALA135:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1867X-ALA135:C and 1869X-ASN136:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1881X-ASN136:C and 1883X-VAL137:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1897X-VAL137:C and 1899X-VAL138:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1913X-VAL138:C and 1915X-VAL139:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1929X-VAL139:C and 1931X-LEU140:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1948X-LEU140:C and 1950X-GLY141:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1955X-GLY141:C and 1957X-TYR142:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1976X-TYR142:C and 1978X-PRO143:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1990X-PRO143:C and 1992X-ARG144:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2014X-ARG144:C and 2016X-PHE145:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2034X-PHE145:C and 2036X-TYR146:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2055X-TYR146:C and 2057X-LYS147:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2077X-LYS147:C and 2079X-LEU148:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2096X-LEU148:C and 2098X-ASN149:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2110X-ASN149:C and 2112X-GLY150:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2117X-GLY150:C and 2119X-THR151:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2131X-THR151:C and 2133X-CYS2152:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2141X-CYS2152:C and 2143X-VAL153:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2157X-VAL153:C and 2159X-ALA154:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2167X-ALA154:C and 2169X-GLY155:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2174X-GLY155:C and 2176X-LEU156:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2193X-LEU156:C and 2195X-THR157:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2207X-THR157:C and 2209X-GLU158:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2222X-GLU158:C and 2224X-GLY159:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2229X-GLY159:C and 2231X-GLU160:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2244X-GLU160:C and 2246X-ARG161:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2268X-ARG161:C and 2270X-THR162:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2282X-THR162:C and 2284X-ALA163:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2292X-ALA163:C and 2294X-ILE164:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2311X-ILE164:C and 2313X-ASN165:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2325X-ASN165:C and 2327X-GLY166:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2332X-GLY166:C and 2334X-ALA167:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2342X-ALA167:C and 2344X-ALA168:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2352X-ALA168:C and 2354X-ASP169:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2364X-ASP169:C and 2366X-LEU170:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2383X-LEU170:C and 2385X-LEU171:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2402X-LEU171:C and 2404X-ASN172:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2416X-ASN172:C and 2418X-SER173:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2427X-SER173:C and 2429X-VAL174:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2443X-VAL174:C and 2445X-ILE175:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2462X-ILE175:C and 2464X-SER176:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2473X-SER176:C and 2475X-LYS177:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2495X-LYS177:C and 2497X-ARG178:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2519X-ARG178:C and 2521X-ALA179:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2529X-ALA179:C and 2531X-ALA180:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2539X-ALA180:C and 2541X-ASP181:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2551X-ASP181:C and 2553X-HIS182:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2568X-HIS182:C and 2570X-GLY183:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2575X-GLY183:C and 2577X-TYR184:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2596X-TYR184:C and 2598X-ALA185:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2606X-ALA185:C and 2608X-TYR186:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2627X-TYR186:C and 2629X-GLY187:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2634X-GLY187:C and 2636X-ASP188:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2646X-ASP188:C and 2648X-ILE189:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2665X-ILE189:C and 2667X-ALA190:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2675X-ALA190:C and 2677X-ALA191:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2685X-ALA191:C and 2687X-ALA192:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2695X-ALA192:C and 2697X-PHE193:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2715X-PHE193:C and 2717X-THR194:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2729X-THR194:C and 2731X-GLY195:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2736X-GLY195:C and 2738X-HIS196:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2745X-HIS196:ND1 and 2746X-HIS196:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2753X-HIS196:C and 2755X-GLU197:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2768X-GLU197:C and 2770X-ILE198:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2787X-ILE198:C and 2789X-CYS2199:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2140X-CYS2152:SG and 2796X-CYS2199:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2797X-CYS2199:C and 2799X-SER200:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2808X-SER200:C and 2810X-GLY201:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2815X-GLY201:C and 2817X-ASP202:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2827X-ASP202:C and 2829X-SER203:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2838X-SER203:C and 2840X-TRP204:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2862X-TRP204:C and 2864X-LEU205:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2881X-LEU205:C and 2883X-HIS206:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2898X-HIS206:C and 2900X-SER207:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2909X-SER207:C and 2911X-VAL208:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2925X-VAL208:C and 2927X-LYS209:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2947X-LYS209:C and 2949X-TRP210:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2971X-TRP210:C and 2973X-THR211:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2985X-THR211:C and 2987X-GLY212:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2992X-GLY212:C and 2994X-ILE213:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3011X-ILE213:C and 3013X-ASN214:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3025X-ASN214:C and 3027X-ASP215:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3037X-ASP215:C and 3039X-SER216:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3048X-SER216:C and 3050X-TYR217:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3069X-TYR217:C and 3071X-HIS218:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3083X-HIS218:ND1 and 3084X-HIS218:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3087X-HIS218:C and 3089X-PRO219:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3101X-PRO219:C and 3103X-THR220:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3115X-THR220:C and 3117X-ALA221:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3125X-ALA221:C and 3127X-ALA222:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3135X-ALA222:C and 3137X-GLY223:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3142X-GLY223:C and 3144X-GLN224:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3159X-GLN224:C and 3161X-SER225:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3170X-SER225:C and 3172X-GLY226:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3177X-GLY226:C and 3179X-GLY227:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3184X-GLY227:C and 3186X-TYR228:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3205X-TYR228:C and 3207X-LEU229:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3224X-LEU229:C and 3226X-PRO230:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3238X-PRO230:C and 3240X-VAL231:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3254X-VAL231:C and 3256X-LEU232:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3273X-LEU232:C and 3275X-ASN233:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3287X-ASN233:C and 3289X-SER234:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3298X-SER234:C and 3300X-LYS235:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3320X-LYS235:C and 3322X-ALA236:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3330X-ALA236:C and 3331X-ALA236:OT1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3330X-ALA236:C and 3332X-ALA236:OT2 based on distance.
    INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
   DEBUG - step - vermouth - Annotating required mutations and modifications.
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-ALA1 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-ALA236 with modification C-ter
    INFO - step - vermouth - Repairing the graph.
   DEBUG - step - vermouth.processors.repair_graph - Making reference graph
    INFO - general - vermouth.processors.repair_graph - Applying modification N-ter to residue X-ALA1
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA1 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA2 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY3 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY4 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR5 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL6 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA7 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU8 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY9 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP10 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER11 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR12 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER13 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER14 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY15 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL16 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY17 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA18 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY19 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER20 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR21 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP22 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER23 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY24 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER25 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY26 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP27 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS228 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG29 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG30 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR31 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO32 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS33 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA34 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR35 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO36 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA37 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU38 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TRP39 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA40 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA41 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA42 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN43 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER44 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO45 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA46 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER47 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE48 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP49 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE50 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL51 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA52 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS253 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER54 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY55 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA56 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL57 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR58 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER59 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP60 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL61 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU62 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN63 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS64 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN65 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-MET66 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY67 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO68 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU69 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN70 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER71 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER72 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR73 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER74 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU75 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL76 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER77 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU78 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR79 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE80 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY81 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY82 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN83 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP84 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA85 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY86 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE87 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA88 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP89 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL90 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-MET91 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR92 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR93 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS294 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL95 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU96 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN97 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER98 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU99 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA100 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN101 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS2102 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE103 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA104 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG105 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL106 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN107 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR108 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA109 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS110 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA111 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE112 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL113 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU114 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER115 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR116 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU117 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO118 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY119 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG120 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU121 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP122 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER123 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL124 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR125 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER126 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN127 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL128 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG129 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA130 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS131 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA132 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO133 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER134 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA135 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN136 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL137 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL138 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL139 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU140 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY141 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR142 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO143 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG144 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE145 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR146 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS147 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU148 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN149 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY150 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR151 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS2152 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL153 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA154 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY155 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU156 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR157 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU158 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY159 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU160 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG161 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR162 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA163 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE164 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN165 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY166 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA167 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA168 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP169 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU170 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU171 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN172 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER173 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL174 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE175 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER176 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS177 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG178 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA179 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA180 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP181 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HIS182 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY183 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR184 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA185 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR186 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY187 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP188 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE189 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA190 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA191 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA192 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE193 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR194 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY195 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HIS196 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU197 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE198 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS2199 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER200 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY201 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP202 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER203 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TRP204 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU205 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HIS206 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER207 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL208 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS209 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TRP210 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR211 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY212 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE213 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN214 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP215 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER216 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR217 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HIS218 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO219 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR220 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA221 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA222 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY223 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN224 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER225 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY226 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY227 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR228 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU229 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO230 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL231 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU232 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN233 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER234 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS235 to its reference
    INFO - general - vermouth.processors.repair_graph - Applying modification C-ter to residue X-ALA236
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA236 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA1
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA2
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY3
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY4
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR5
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL6
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA7
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU8
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY9
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP10
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER11
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR12
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER13
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER14
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY15
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL16
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY17
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA18
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY19
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER20
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR21
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP22
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER23
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY24
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER25
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY26
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP27
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS228
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG29
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG30
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR31
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO32
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS33
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA34
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR35
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO36
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA37
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU38
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TRP39
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA40
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA41
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA42
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN43
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER44
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO45
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA46
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER47
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE48
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP49
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE50
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL51
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA52
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS253
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER54
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY55
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA56
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL57
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR58
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER59
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP60
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL61
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU62
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN63
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS64
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN65
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue MET66
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY67
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO68
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU69
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN70
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER71
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER72
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR73
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER74
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU75
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL76
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER77
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU78
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR79
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE80
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY81
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY82
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN83
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP84
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA85
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY86
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE87
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA88
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP89
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL90
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue MET91
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR92
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR93
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS294
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL95
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU96
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN97
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER98
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU99
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA100
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN101
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS2102
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE103
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA104
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG105
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL106
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN107
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR108
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA109
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS110
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA111
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE112
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL113
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU114
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER115
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR116
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU117
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO118
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY119
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG120
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU121
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP122
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER123
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL124
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR125
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER126
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN127
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL128
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG129
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA130
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS131
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA132
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO133
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER134
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA135
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN136
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL137
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL138
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL139
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU140
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY141
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR142
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO143
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG144
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE145
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR146
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS147
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU148
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN149
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY150
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR151
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS2152
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL153
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA154
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY155
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU156
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR157
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU158
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY159
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU160
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG161
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR162
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA163
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE164
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN165
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY166
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA167
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA168
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP169
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU170
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU171
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN172
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER173
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL174
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE175
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER176
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS177
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG178
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA179
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA180
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP181
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HIS182
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY183
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR184
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA185
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR186
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY187
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP188
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE189
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA190
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA191
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA192
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE193
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR194
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY195
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HIS196
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU197
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE198
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS2199
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER200
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY201
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP202
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER203
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TRP204
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU205
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HIS206
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER207
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL208
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS209
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TRP210
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR211
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY212
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE213
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN214
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP215
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER216
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR217
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HIS218
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO219
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR220
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA221
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA222
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY223
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN224
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER225
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY226
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY227
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR228
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU229
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO230
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL231
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU232
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN233
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER234
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS235
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA236
    INFO - step - vermouth - Dealing with modifications.
    INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['N-ter'] on residues ['ALA1', 'ALA1', 'ALA1', 'ALA1']
    INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['HSD'] on residues ['HIS196']
    INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['HSD'] on residues ['HIS218']
    INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['C-ter'] on residues ['ALA236', 'ALA236', 'ALA236']
    INFO - step - vermouth - Read input.
   DEBUG - step - vermouth - Read molecule molecule with 3333 atoms, and 3371 edges.
   DEBUG - general - vermouth.dssp.dssp - No DSSP assignation to convert to Martini secondary structure intermediates.
    INFO - step - vermouth - Creating the graph at the target resolution.
 WARNING - unmapped-atom - vermouth.processors.do_mapping - Can't find modification mappings for the modifications ['HSD']. The following modification mappings are known: {('C-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469390>, ('N-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469290>, ('COOH-ter',): <vermouth.map_parser.Mapping object at 0x2b7a8247d150>, ('NH2-ter',): <vermouth.map_parser.Mapping object at 0x2b7a824694d0>}
 WARNING - unmapped-atom - vermouth.processors.do_mapping - Can't find modification mappings for the modifications ['HSD']. The following modification mappings are known: {('C-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469390>, ('N-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469290>, ('COOH-ter',): <vermouth.map_parser.Mapping object at 0x2b7a8247d150>, ('NH2-ter',): <vermouth.map_parser.Mapping object at 0x2b7a824694d0>}
    INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('N-ter',)
    INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('C-ter',)
   DEBUG - unmapped-atom - vermouth.processors.do_mapping - These hydrogen atoms are not covered by a mapping. This is not the best idea. ['3084X-HIS218:HD1', '690X-CYS253:HN', '692X-CYS253:HA', '694X-CYS253:HB1', '695X-CYS253:HB2', '2746X-HIS196:HD1', '316X-CYS228:HN', '318X-CYS228:HA', '320X-CYS228:HB1', '321X-CYS228:HB2', '1357X-CYS2102:HN', '1359X-CYS2102:HA', '1361X-CYS2102:HB1', '1362X-CYS2102:HB2', '2134X-CYS2152:HN', '2136X-CYS2152:HA', '2138X-CYS2152:HB1', '2139X-CYS2152:HB2', '1245X-CYS294:HN', '1247X-CYS294:HA', '1249X-CYS294:HB1', '1250X-CYS294:HB2', '2790X-CYS2199:HN', '2792X-CYS2199:HA', '2794X-CYS2199:HB1', '2795X-CYS2199:HB2']
 WARNING - unmapped-atom - vermouth.processors.do_mapping - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. ['689X-CYS253:N', '691X-CYS253:CA', '693X-CYS253:CB', '696X-CYS253:SG', '697X-CYS253:C', '698X-CYS253:O', '315X-CYS228:N', '317X-CYS228:CA', '319X-CYS228:CB', '322X-CYS228:SG', '323X-CYS228:C', '324X-CYS228:O', '1356X-CYS2102:N', '1358X-CYS2102:CA', '1360X-CYS2102:CB', '1363X-CYS2102:SG', '1364X-CYS2102:C', '1365X-CYS2102:O', '2133X-CYS2152:N', '2135X-CYS2152:CA', '2137X-CYS2152:CB', '2140X-CYS2152:SG', '1244X-CYS294:N', '1246X-CYS294:CA', '2141X-CYS2152:C', '1248X-CYS294:CB', '2142X-CYS2152:O', '1251X-CYS294:SG', '1252X-CYS294:C', '1253X-CYS294:O', '2789X-CYS2199:N', '2791X-CYS2199:CA', '2793X-CYS2199:CB', '2796X-CYS2199:SG', '2797X-CYS2199:C', '2798X-CYS2199:O']
    INFO - step - vermouth - Averaging the coordinates.
    INFO - step - vermouth - Applying the links.
    INFO - step - vermouth - Placing the charge dummies.
    INFO - step - vermouth - Applying position restraints.
    INFO - step - vermouth - Writing output.
   DEBUG - step - vermouth - Writing molecule molecule_0 with 514 atoms, 230 position_restraints, 542 bonds, 174 constraints, 483 angles, 14 impropers, 89 exclusions, and 3 virtual_sitesn.
    INFO - general - vermouth - Please cite: Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J;  Nature Methods 2021; 10.1038/s41592-021-01098-3
   ERROR - general - vermouth - 3 warnings were encountered after accounting for the -maxwarn flag. No output files will be written. Consider fixing the warnings, or if you are sure they are harmless, use the -maxwarn flag.

[pckroon]

Cherry picking some of the more interesting lines in your output:

   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 322X-CYS228:SG and 696X-CYS253:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1251X-CYS294:SG and 1363X-CYS2102:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2745X-HIS196:ND1 and 2746X-HIS196:HD1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 2140X-CYS2152:SG and 2796X-CYS2199:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 3083X-HIS218:ND1 and 3084X-HIS218:HD1 based on distance.
    INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['HSD'] on residues ['HIS196']
    INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['HSD'] on residues ['HIS218']
 WARNING - unmapped-atom - vermouth.processors.do_mapping - Can't find modification mappings for the modifications ['HSD']. The following modification mappings are known: {('C-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469390>, ('N-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469290>, ('COOH-ter',): <vermouth.map_parser.Mapping object at 0x2b7a8247d150>, ('NH2-ter',): <vermouth.map_parser.Mapping object at 0x2b7a824694d0>}
 WARNING - unmapped-atom - vermouth.processors.do_mapping - Can't find modification mappings for the modifications ['HSD']. The following modification mappings are known: {('C-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469390>, ('N-ter',): <vermouth.map_parser.Mapping object at 0x2b7a82469290>, ('COOH-ter',): <vermouth.map_parser.Mapping object at 0x2b7a8247d150>, ('NH2-ter',): <vermouth.map_parser.Mapping object at 0x2b7a824694d0>}
    INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('N-ter',)
    INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('C-ter',)
   DEBUG - unmapped-atom - vermouth.processors.do_mapping - These hydrogen atoms are not covered by a mapping. This is not the best idea. ['3084X-HIS218:HD1', '690X-CYS253:HN', '692X-CYS253:HA', '694X-CYS253:HB1', '695X-CYS253:HB2', '2746X-HIS196:HD1', '316X-CYS228:HN', '318X-CYS228:HA', '320X-CYS228:HB1', '321X-CYS228:HB2', '1357X-CYS2102:HN', '1359X-CYS2102:HA', '1361X-CYS2102:HB1', '1362X-CYS2102:HB2', '2134X-CYS2152:HN', '2136X-CYS2152:HA', '2138X-CYS2152:HB1', '2139X-CYS2152:HB2', '1245X-CYS294:HN', '1247X-CYS294:HA', '1249X-CYS294:HB1', '1250X-CYS294:HB2', '2790X-CYS2199:HN', '2792X-CYS2199:HA', '2794X-CYS2199:HB1', '2795X-CYS2199:HB2']
 WARNING - unmapped-atom - vermouth.processors.do_mapping - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. ['689X-CYS253:N', '691X-CYS253:CA', '693X-CYS253:CB', '696X-CYS253:SG', '697X-CYS253:C', '698X-CYS253:O', '315X-CYS228:N', '317X-CYS228:CA', '319X-CYS228:CB', '322X-CYS228:SG', '323X-CYS228:C', '324X-CYS228:O', '1356X-CYS2102:N', '1358X-CYS2102:CA', '1360X-CYS2102:CB', '1363X-CYS2102:SG', '1364X-CYS2102:C', '1365X-CYS2102:O', '2133X-CYS2152:N', '2135X-CYS2152:CA', '2137X-CYS2152:CB', '2140X-CYS2152:SG', '1244X-CYS294:N', '1246X-CYS294:CA', '2141X-CYS2152:C', '1248X-CYS294:CB', '2142X-CYS2152:O', '1251X-CYS294:SG', '1252X-CYS294:C', '1253X-CYS294:O', '2789X-CYS2199:N', '2791X-CYS2199:CA', '2793X-CYS2199:CB', '2796X-CYS2199:SG', '2797X-CYS2199:C', '2798X-CYS2199:O']

I notice the following:

• Your molecule doesn't contain HSD/HSE residues. The residues are called HIS. Your -mutate flag tries to mutate, e.g. A-HIS2 (chain A, residuename HIS, residue ID 2) to residuename HSE. But, you don't have a residue A-HIS2 in your input. You do have a X-HIS196 and X-HIS218. *
• Your HIS have a HD1 hydrogen bonded to ND1. This identifies them as having a HSD /modification/. You can map modifications, but it could be a bit more tricky, have a look at how we deal with termini. (https://github.com/marrink-lab/vermouth-martinize/blob/master/vermouth/data/mappings/martini30/martini3001/modifications.mapping)
• You have disulphide bonds between CYS228 and CYS253; and CYS2152 and CYS2199. I'm a little bit puzzled why this breaks the mapping of the CYS residues. Did you change anything about CYS? If so, could you post your changes?

For HSE/HSD the easiest way forward I think is to either rename the HIS residues in your PDB to HSE/HSD; or use the -mutate flag to do that automagically. Alternatively you could try making the modification mappings.

*) You can omit part of the specification. E.g. -mutate HIS:HSD to mutate /all/ HIS to HSD. Or HIS196:HSE to mutate HIS196 in all chains.

[Oishika-1]

1. For CYS, the input pdb has entry as CYS2 because it was an output file from a previous all-atom simulation run. Now if i change CYS2 to CYS then I am not getting any modification problem from CYS.

2. If the input pdb

   • does not any hydrogen
   • all HISTIDINES named as HIS
   • CYS2 changed to CYS
   • command is : martinize2 -f gentop_notwater_noh_his_cys.pdb -ff martini3001 -o out.top -x out.pdb -p backbone -cys auto -mutate X-HIS218:HSP -mutate X-HIS182:HSE -mutate X-HIS196:HSD -mutate X-HIS206:HSE -v

3. the output is

   martinize2 -f gentop_notwater_noh_his_cys.pdb -ff martini3001 -o out.top -x out.pdb -p backbone -cys auto -mutate X-HIS218:HSP -mutate X-HIS182:HSE -mutate X-HIS196:HSD -mutate X-HIS206:HSE -v
   INFO - general - vermouth.pdb.pdb - Read 1 molecules from PDB file gentop_notwater_noh_his_cys.pdb
   INFO - step - vermouth - Guessing the bonds.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 4X-ALA1:C and 6X-ALA2:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 9X-ALA2:C and 11X-GLY3:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 13X-GLY3:C and 15X-GLY4:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 17X-GLY4:C and 19X-TYR5:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 29X-TYR5:C and 31X-VAL6:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 36X-VAL6:C and 38X-ALA7:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 41X-ALA7:C and 43X-LEU8:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 49X-LEU8:C and 51X-GLY9:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 53X-GLY9:C and 55X-ASP10:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 61X-ASP10:C and 63X-SER11:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 67X-SER11:C and 69X-TYR12:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 79X-TYR12:C and 81X-SER13:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 85X-SER13:C and 87X-SER14:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 91X-SER14:C and 93X-GLY15:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 95X-GLY15:C and 97X-VAL16:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 102X-VAL16:C and 104X-GLY17:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 106X-GLY17:C and 108X-ALA18:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 111X-ALA18:C and 113X-GLY19:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 115X-GLY19:C and 117X-SER20:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 121X-SER20:C and 123X-TYR21:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 133X-TYR21:C and 135X-ASP22:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 141X-ASP22:C and 143X-SER23:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 147X-SER23:C and 149X-GLY24:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 151X-GLY24:C and 153X-SER25:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 157X-SER25:C and 159X-GLY26:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 161X-GLY26:C and 163X-ASP27:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 169X-ASP27:C and 171X-CYS28:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 175X-CYS28:C and 177X-ARG29:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 186X-ARG29:C and 188X-ARG30:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 197X-ARG30:C and 199X-THR31:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 204X-THR31:C and 206X-PRO32:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 211X-PRO32:C and 213X-LYS33:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 220X-LYS33:C and 222X-ALA34:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 225X-ALA34:C and 227X-TYR35:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 237X-TYR35:C and 239X-PRO36:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 244X-PRO36:C and 246X-ALA37:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 249X-ALA37:C and 251X-LEU38:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 257X-LEU38:C and 259X-TRP39:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 271X-TRP39:C and 273X-ALA40:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 276X-ALA40:C and 278X-ALA41:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 281X-ALA41:C and 283X-ALA42:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 286X-ALA42:C and 288X-ASN43:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 294X-ASN43:C and 296X-SER44:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 300X-SER44:C and 302X-PRO45:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 307X-PRO45:C and 309X-ALA46:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 312X-ALA46:C and 314X-SER47:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 318X-SER47:C and 320X-PHE48:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 329X-PHE48:C and 331X-ASP49:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 337X-ASP49:C and 339X-PHE50:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 348X-PHE50:C and 350X-VAL51:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 355X-VAL51:C and 357X-ALA52:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 360X-ALA52:C and 362X-CYS53:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 174X-CYS28:SG and 365X-CYS53:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 366X-CYS53:C and 368X-SER54:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 372X-SER54:C and 374X-GLY55:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 376X-GLY55:C and 378X-ALA56:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 381X-ALA56:C and 383X-VAL57:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 388X-VAL57:C and 390X-THR58:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 395X-THR58:C and 397X-SER59:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 401X-SER59:C and 403X-ASP60:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 409X-ASP60:C and 411X-VAL61:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 416X-VAL61:C and 418X-LEU62:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 424X-LEU62:C and 426X-ASN63:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 432X-ASN63:C and 434X-LYS64:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 441X-LYS64:C and 443X-GLN65:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 450X-GLN65:C and 452X-MET66:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 458X-MET66:C and 460X-GLY67:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 462X-GLY67:C and 464X-PRO68:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 469X-PRO68:C and 471X-LEU69:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 477X-LEU69:C and 479X-ASN70:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 485X-ASN70:C and 487X-SER71:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 491X-SER71:C and 493X-SER72:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 497X-SER72:C and 499X-THR73:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 504X-THR73:C and 506X-SER74:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 510X-SER74:C and 512X-LEU75:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 518X-LEU75:C and 520X-VAL76:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 525X-VAL76:C and 527X-SER77:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 531X-SER77:C and 533X-LEU78:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 539X-LEU78:C and 541X-THR79:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 546X-THR79:C and 548X-ILE80:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 554X-ILE80:C and 556X-GLY81:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 558X-GLY81:C and 560X-GLY82:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 562X-GLY82:C and 564X-ASN83:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 570X-ASN83:C and 572X-ASP84:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 578X-ASP84:C and 580X-ALA85:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 583X-ALA85:C and 585X-GLY86:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 587X-GLY86:C and 589X-PHE87:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 598X-PHE87:C and 600X-ALA88:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 603X-ALA88:C and 605X-ASP89:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 611X-ASP89:C and 613X-VAL90:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 618X-VAL90:C and 620X-MET91:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 626X-MET91:C and 628X-THR92:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 633X-THR92:C and 635X-THR93:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 640X-THR93:C and 642X-CYS94:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 646X-CYS94:C and 648X-VAL95:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 653X-VAL95:C and 655X-LEU96:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 661X-LEU96:C and 663X-GLN97:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 670X-GLN97:C and 672X-SER98:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 676X-SER98:C and 678X-GLU99:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 685X-GLU99:C and 687X-ALA100:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 690X-ALA100:C and 692X-ASN101:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 698X-ASN101:C and 700X-CYS102:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 645X-CYS94:SG and 703X-CYS102:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 704X-CYS102:C and 706X-ILE103:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 712X-ILE103:C and 714X-ALA104:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 717X-ALA104:C and 719X-ARG105:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 728X-ARG105:C and 730X-VAL106:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 735X-VAL106:C and 737X-ASN107:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 743X-ASN107:C and 745X-THR108:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 750X-THR108:C and 752X-ALA109:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 755X-ALA109:C and 757X-LYS110:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 764X-LYS110:C and 766X-ALA111:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 769X-ALA111:C and 771X-PHE112:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 780X-PHE112:C and 782X-VAL113:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 787X-VAL113:C and 789X-GLU114:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 796X-GLU114:C and 798X-SER115:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 802X-SER115:C and 804X-THR116:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 809X-THR116:C and 811X-LEU117:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 817X-LEU117:C and 819X-PRO118:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 824X-PRO118:C and 826X-GLY119:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 828X-GLY119:C and 830X-ARG120:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 839X-ARG120:C and 841X-LEU121:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 847X-LEU121:C and 849X-ASP122:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 855X-ASP122:C and 857X-SER123:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 861X-SER123:C and 863X-VAL124:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 868X-VAL124:C and 870X-TYR125:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 880X-TYR125:C and 882X-SER126:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 886X-SER126:C and 888X-GLN127:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 895X-GLN127:C and 897X-VAL128:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 902X-VAL128:C and 904X-ARG129:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 913X-ARG129:C and 915X-ALA130:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 918X-ALA130:C and 920X-LYS131:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 927X-LYS131:C and 929X-ALA132:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 932X-ALA132:C and 934X-PRO133:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 939X-PRO133:C and 941X-SER134:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 945X-SER134:C and 947X-ALA135:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 950X-ALA135:C and 952X-ASN136:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 958X-ASN136:C and 960X-VAL137:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 965X-VAL137:C and 967X-VAL138:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 972X-VAL138:C and 974X-VAL139:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 979X-VAL139:C and 981X-LEU140:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 987X-LEU140:C and 989X-GLY141:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 991X-GLY141:C and 993X-TYR142:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1003X-TYR142:C and 1005X-PRO143:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1010X-PRO143:C and 1012X-ARG144:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1021X-ARG144:C and 1023X-PHE145:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1032X-PHE145:C and 1034X-TYR146:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1044X-TYR146:C and 1046X-LYS147:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1053X-LYS147:C and 1055X-LEU148:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1061X-LEU148:C and 1063X-ASN149:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1069X-ASN149:C and 1071X-GLY150:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1073X-GLY150:C and 1075X-THR151:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1080X-THR151:C and 1082X-CYS152:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1086X-CYS152:C and 1088X-VAL153:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1093X-VAL153:C and 1095X-ALA154:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1098X-ALA154:C and 1100X-GLY155:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1102X-GLY155:C and 1104X-LEU156:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1110X-LEU156:C and 1112X-THR157:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1117X-THR157:C and 1119X-GLU158:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1126X-GLU158:C and 1128X-GLY159:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1130X-GLY159:C and 1132X-GLU160:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1139X-GLU160:C and 1141X-ARG161:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1150X-ARG161:C and 1152X-THR162:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1157X-THR162:C and 1159X-ALA163:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1162X-ALA163:C and 1164X-ILE164:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1170X-ILE164:C and 1172X-ASN165:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1178X-ASN165:C and 1180X-GLY166:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1182X-GLY166:C and 1184X-ALA167:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1187X-ALA167:C and 1189X-ALA168:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1192X-ALA168:C and 1194X-ASP169:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1200X-ASP169:C and 1202X-LEU170:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1208X-LEU170:C and 1210X-LEU171:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1216X-LEU171:C and 1218X-ASN172:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1224X-ASN172:C and 1226X-SER173:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1230X-SER173:C and 1232X-VAL174:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1237X-VAL174:C and 1239X-ILE175:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1245X-ILE175:C and 1247X-SER176:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1251X-SER176:C and 1253X-LYS177:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1260X-LYS177:C and 1262X-ARG178:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1271X-ARG178:C and 1273X-ALA179:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1276X-ALA179:C and 1278X-ALA180:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1281X-ALA180:C and 1283X-ASP181:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1289X-ASP181:C and 1291X-HIS182:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1299X-HIS182:C and 1301X-GLY183:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1303X-GLY183:C and 1305X-TYR184:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1315X-TYR184:C and 1317X-ALA185:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1320X-ALA185:C and 1322X-TYR186:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1332X-TYR186:C and 1334X-GLY187:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1336X-GLY187:C and 1338X-ASP188:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1344X-ASP188:C and 1346X-ILE189:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1352X-ILE189:C and 1354X-ALA190:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1357X-ALA190:C and 1359X-ALA191:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1362X-ALA191:C and 1364X-ALA192:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1367X-ALA192:C and 1369X-PHE193:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1378X-PHE193:C and 1380X-THR194:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1385X-THR194:C and 1387X-GLY195:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1389X-GLY195:C and 1391X-HIS196:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1399X-HIS196:C and 1401X-GLU197:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1408X-GLU197:C and 1410X-ILE198:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1416X-ILE198:C and 1418X-CYS199:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1085X-CYS152:SG and 1421X-CYS199:SG based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1422X-CYS199:C and 1424X-SER200:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1428X-SER200:C and 1430X-GLY201:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1432X-GLY201:C and 1434X-ASP202:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1440X-ASP202:C and 1442X-SER203:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1446X-SER203:C and 1448X-TRP204:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1460X-TRP204:C and 1462X-LEU205:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1468X-LEU205:C and 1470X-HIS206:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1478X-HIS206:C and 1480X-SER207:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1484X-SER207:C and 1486X-VAL208:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1491X-VAL208:C and 1493X-LYS209:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1500X-LYS209:C and 1502X-TRP210:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1514X-TRP210:C and 1516X-THR211:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1521X-THR211:C and 1523X-GLY212:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1525X-GLY212:C and 1527X-ILE213:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1533X-ILE213:C and 1535X-ASN214:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1541X-ASN214:C and 1543X-ASP215:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1549X-ASP215:C and 1551X-SER216:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1555X-SER216:C and 1557X-TYR217:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1567X-TYR217:C and 1569X-HIS218:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1577X-HIS218:C and 1579X-PRO219:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1584X-PRO219:C and 1586X-THR220:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1591X-THR220:C and 1593X-ALA221:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1596X-ALA221:C and 1598X-ALA222:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1601X-ALA222:C and 1603X-GLY223:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1605X-GLY223:C and 1607X-GLN224:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1614X-GLN224:C and 1616X-SER225:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1620X-SER225:C and 1622X-GLY226:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1624X-GLY226:C and 1626X-GLY227:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1628X-GLY227:C and 1630X-TYR228:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1640X-TYR228:C and 1642X-LEU229:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1648X-LEU229:C and 1650X-PRO230:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1655X-PRO230:C and 1657X-VAL231:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1662X-VAL231:C and 1664X-LEU232:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1670X-LEU232:C and 1672X-ASN233:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1678X-ASN233:C and 1680X-SER234:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1684X-SER234:C and 1686X-LYS235:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1693X-LYS235:C and 1695X-ALA236:N based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1698X-ALA236:C and 1699X-ALA236:OT1 based on distance.
   DEBUG - general - vermouth.processors.make_bonds - Guessed bond between 1698X-ALA236:C and 1700X-ALA236:OT2 based on distance.
   INFO - general - vermouth.processors.make_bonds - 1 molecules after guessing bonds
   DEBUG - step - vermouth - Annotating required mutations and modifications.
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-ALA1 with modification N-ter
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-HIS182 with mutation HSE
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-HIS196 with mutation HSD
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-HIS206 with mutation HSE
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-HIS218 with mutation HSP
   DEBUG - general - vermouth.processors.annotate_mut_mod - Annotating X-ALA236 with modification C-ter
   INFO - step - vermouth - Repairing the graph.
   DEBUG - step - vermouth.processors.repair_graph - Making reference graph
   INFO - general - vermouth.processors.repair_graph - Applying modification N-ter to residue X-ALA1
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA1 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA2 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY3 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY4 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR5 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL6 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA7 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU8 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY9 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP10 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER11 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR12 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER13 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER14 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY15 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL16 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY17 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA18 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY19 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER20 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR21 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP22 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER23 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY24 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER25 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY26 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP27 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS28 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG29 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG30 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR31 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO32 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS33 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA34 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR35 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO36 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA37 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU38 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TRP39 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA40 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA41 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA42 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN43 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER44 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO45 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA46 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER47 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE48 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP49 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE50 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL51 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA52 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS53 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER54 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY55 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA56 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL57 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR58 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER59 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP60 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL61 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU62 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN63 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS64 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN65 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-MET66 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY67 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO68 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU69 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN70 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER71 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER72 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR73 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER74 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU75 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL76 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER77 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU78 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR79 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE80 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY81 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY82 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN83 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP84 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA85 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY86 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE87 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA88 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP89 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL90 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-MET91 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR92 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR93 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS94 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL95 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU96 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN97 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER98 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU99 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA100 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN101 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS102 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE103 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA104 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG105 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL106 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN107 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR108 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA109 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS110 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA111 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE112 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL113 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU114 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER115 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR116 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU117 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO118 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY119 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG120 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU121 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP122 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER123 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL124 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR125 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER126 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN127 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL128 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG129 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA130 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS131 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA132 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO133 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER134 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA135 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN136 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL137 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL138 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL139 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU140 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY141 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR142 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO143 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG144 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE145 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR146 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS147 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU148 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN149 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY150 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR151 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS152 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL153 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA154 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY155 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU156 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR157 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU158 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY159 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU160 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG161 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR162 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA163 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE164 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN165 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY166 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA167 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA168 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP169 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU170 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU171 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN172 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER173 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL174 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE175 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER176 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS177 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ARG178 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA179 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA180 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP181 to its reference
   INFO - general - vermouth.processors.repair_graph - Mutating residue X-HIS182 to HSE
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HSE182 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY183 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR184 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA185 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR186 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY187 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP188 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE189 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA190 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA191 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA192 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PHE193 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR194 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY195 to its reference
   INFO - general - vermouth.processors.repair_graph - Mutating residue X-HIS196 to HSD
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HSD196 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLU197 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE198 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-CYS199 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER200 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY201 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP202 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER203 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TRP204 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU205 to its reference
   INFO - general - vermouth.processors.repair_graph - Mutating residue X-HIS206 to HSE
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HSE206 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER207 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL208 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS209 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TRP210 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR211 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY212 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ILE213 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN214 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASP215 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER216 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR217 to its reference
   INFO - general - vermouth.processors.repair_graph - Mutating residue X-HIS218 to HSP
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-HSP218 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO219 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-THR220 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA221 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA222 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY223 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLN224 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER225 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY226 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-GLY227 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-TYR228 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU229 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-PRO230 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-VAL231 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LEU232 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ASN233 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-SER234 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-LYS235 to its reference
   INFO - general - vermouth.processors.repair_graph - Applying modification C-ter to residue X-ALA236
   DEBUG - step - vermouth.processors.repair_graph - Matching residue X-ALA236 to its reference
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA1
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA2
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY3
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY4
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR5
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL6
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA7
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU8
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY9
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP10
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER11
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR12
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER13
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER14
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY15
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL16
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY17
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA18
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY19
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER20
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR21
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP22
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER23
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY24
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER25
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY26
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP27
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS28
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG29
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG30
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR31
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO32
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS33
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA34
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR35
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO36
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA37
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU38
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TRP39
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA40
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA41
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA42
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN43
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER44
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO45
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA46
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER47
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE48
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP49
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE50
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL51
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA52
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS53
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER54
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY55
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA56
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL57
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR58
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER59
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP60
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL61
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU62
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN63
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS64
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN65
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue MET66
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY67
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO68
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU69
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN70
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER71
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER72
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR73
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER74
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU75
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL76
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER77
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU78
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR79
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE80
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY81
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY82
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN83
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP84
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA85
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY86
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE87
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA88
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP89
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL90
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue MET91
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR92
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR93
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS94
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL95
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU96
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN97
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER98
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU99
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA100
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN101
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS102
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE103
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA104
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG105
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL106
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN107
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR108
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA109
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS110
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA111
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE112
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL113
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU114
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER115
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR116
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU117
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO118
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY119
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG120
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU121
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP122
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER123
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL124
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR125
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER126
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN127
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL128
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG129
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA130
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS131
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA132
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO133
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER134
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA135
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN136
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL137
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL138
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL139
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU140
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY141
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR142
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO143
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG144
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE145
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR146
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS147
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU148
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN149
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY150
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR151
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS152
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL153
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA154
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY155
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU156
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR157
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU158
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY159
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU160
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG161
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR162
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA163
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE164
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN165
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY166
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA167
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA168
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP169
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU170
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU171
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN172
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER173
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL174
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE175
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER176
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS177
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ARG178
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA179
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA180
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP181
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HSE182
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY183
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR184
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA185
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR186
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY187
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP188
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE189
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA190
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA191
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA192
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PHE193
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR194
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY195
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HSD196
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLU197
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE198
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue CYS199
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER200
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY201
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP202
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER203
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TRP204
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU205
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HSE206
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER207
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL208
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS209
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TRP210
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR211
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY212
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ILE213
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN214
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASP215
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER216
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR217
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue HSP218
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO219
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue THR220
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA221
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA222
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY223
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLN224
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER225
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY226
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue GLY227
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue TYR228
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU229
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue PRO230
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue VAL231
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LEU232
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ASN233
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue SER234
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue LYS235
   DEBUG - step - vermouth.processors.repair_graph - Repairing residue ALA236
   INFO - step - vermouth - Dealing with modifications.
   INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['N-ter'] on residues ['ALA1', 'ALA1', 'ALA1', 'ALA1']
   INFO - general - vermouth.processors.canonicalize_modifications - Identified the modifications ['C-ter'] on residues ['ALA236', 'ALA236', 'ALA236']
   INFO - step - vermouth - Read input.
   DEBUG - step - vermouth - Read molecule molecule with 3338 atoms, and 3376 edges.
   INFO - step - vermouth - Creating the graph at the target resolution.
   INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('C-ter',)
   INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('N-ter',)
   DEBUG - unmapped-atom - vermouth.processors.do_mapping - These hydrogen atoms are not covered by a mapping. This is not the best idea. ['3209X-HSP218:HN', '3210X-HSP218:HB1', '3211X-HSP218:HD2', '3212X-HSP218:HD1', '3213X-HSP218:HA', '3214X-HSP218:HE2', '3215X-HSP218:HB2', '3216X-HSP218:HE1', '2968X-HSE182:HN', '2969X-HSE182:HB1', '2970X-HSE182:HE1', '2971X-HSE182:HD2', '2972X-HSE182:HA', '2973X-HSE182:HE2', '2974X-HSE182:HB2', '3120X-HSE206:HN', '3121X-HSE206:HB1', '3122X-HSE206:HE1', '3123X-HSE206:HD2', '3124X-HSE206:HA', '3125X-HSE206:HE2', '3126X-HSE206:HB2', '3053X-HSD196:HN', '3054X-HSD196:HB1', '3055X-HSD196:HD1', '3056X-HSD196:HD2', '3057X-HSD196:HA', '3058X-HSD196:HE1', '3059X-HSD196:HB2']
   WARNING - unmapped-atom - vermouth.processors.do_mapping - These atoms are not covered by a mapping. Either your mappings don't describe all atoms (bad idea), or, there's no mapping available for all residues. ['1291X-HSE182:N', '1292X-HSE182:CA', '1293X-HSE182:CB', '1294X-HSE182:ND1', '1295X-HSE182:CG', '1296X-HSE182:CE1', '1297X-HSE182:NE2', '1298X-HSE182:CD2', '1299X-HSE182:C', '1300X-HSE182:O', '1569X-HSP218:N', '1570X-HSP218:CA', '1571X-HSP218:CB', '1572X-HSP218:CD2', '1573X-HSP218:CG', '1574X-HSP218:NE2', '1575X-HSP218:ND1', '1576X-HSP218:CE1', '1577X-HSP218:C', '1578X-HSP218:O', '1470X-HSE206:N', '1471X-HSE206:CA', '1472X-HSE206:CB', '1473X-HSE206:ND1', '1474X-HSE206:CG', '1475X-HSE206:CE1', '1476X-HSE206:NE2', '1477X-HSE206:CD2', '1478X-HSE206:C', '1479X-HSE206:O', '1391X-HSD196:N', '1392X-HSD196:CA', '1393X-HSD196:CB', '1394X-HSD196:ND1', '1395X-HSD196:CG', '1396X-HSD196:CE1', '1397X-HSD196:NE2', '1398X-HSD196:CD2', '1399X-HSD196:C', '1400X-HSD196:O']
   INFO - step - vermouth - Averaging the coordinates.
   INFO - step - vermouth - Applying the links.
   INFO - step - vermouth - Placing the charge dummies.
   INFO - step - vermouth - Applying position restraints.
   INFO - step - vermouth - Writing output.
   DEBUG - step - vermouth - Writing molecule molecule_0 with 510 atoms, 539 edges, 232 position_restraints, 536 bonds, 165 constraints, 483 angles, 14 impropers, 77 exclusions, and 3 virtual_sitesn.
   INFO - general - vermouth - Please cite: Souza, P C T; Alessandri, R; Barnoud, J; Thallmair, S; Faustino, I; Grünewald, F; Patmanidis, I; Abdizadeh, H; Bruininks, B M H; Wassenaar, T A; Kroon, P C; Melcr, J; Nieto, V; Corradi, V; Khan, H M; Domański, J; Javanainen, M; Martinez-Seara, H; Reuter, N; Best, R B; Vattulainen, I; Monticelli, L; Periole, X; Tieleman, D P; de Vries, A H; Marrink, S J;  Nature Methods 2021; 10.1038/s41592-021-01098-3
   ERROR - general - vermouth - 1 warnings were encountered after accounting for the -maxwarn flag. No output files will be written. Consider fixing the warnings, or if you are sure they are harmless, use the -maxwarn flag.

4. I have looked at the termini modifications before. But I was not able to figure out how to write it for the histidines.

[Oishika-1]

If in the input pdb, i replace the histidine names as HSE | HSD | HSP then two cases

1. HSE | HSD | HSP has corresponding hydrogens (other residues do not have hydrogens)
2. HSE | HSD | HSP do not contain hydrogens

in both these cases i am getting the mapping errors for hydrogens.

[pckroon]

Progress :) I found an issue with your HSE mapping: The mapping describes a HD1 atom, but that atom is not present in the HSE block in the universal FF (https://github.com/marrink-lab/vermouth-martinize/blob/master/vermouth/data/force_fields/universal/aminoacids.rtp#L499). The parser is a little lax, and simply throws away the mapping rather than raising errors (run with -vv and look at the beginning of the output if you're curious).

You should probably just remove the HD1 from the mapping. I expect something similar is happening with the other two mappings.

[Oishika-1]

i removed the HD1 containing line under [atoms] section and [out] section in the his.charmm36.map file, but same error is coming. i tried out some combinations to introduce modification for only one HIS as HSE ------ like, input pdb with or without hydrogens | input pdb with name "HIS" or 'HSE" | under [molecule] section in mapping file changing the name to "HIS" or "HSE" ----- error remains same.

I have a feeling that i have to introduce modification mapping for HSE | HSD | HSP explicitly in the following file : vermouth-martinize-master/vermouth/data/mappings/martini30/martini3001/modifications.mapping because of the following lines (where vermouth.processors.do_mapping is common) INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('C-ter',) INFO - general - vermouth.processors.do_mapping - Applying modification mapping ('N-ter',) DEBUG - unmapped-atom - vermouth.processors.do_mapping - These hydrogen atoms are not covered by a mapping.

But i am not able to understand this modifications.mapping file...how to do this blocks mapping..could you please suggest me something

[pckroon]

I'm rather surprised your HSE mapping doesn't work after you remove the HD1 atom from the HSE mapping. (You did remove it from the HSE mapping, not the HIS one, right?) As a debugging option you can try removing all hydrogens from your HSE mapping, and then progressively remove atoms from the mapping (not the block in universal) until it works. That should narrow things down. You can also safely remove/ignore the out and chiral sections. Martinize2 doesn't use them anyway.

If you rename your residues to HSE/HSP/... you can ignore modifications and their mappings. You can do this renaming either in your input pdb file, or using the -mutate flag. Mapping by block/residue should work.

[Oishika-1]

I removed from the HSE mapping only. The file (his.charmm36.map) is in folder (/vermouth/data/mappings/martini30/martini3001/).

If the Input PDB has HSE name with and without hydrogens, same mapping error is coming.

Martinize2 is not reading "his.charmm36.map" file (from neither of the below folders: /data/mappings/martini30/martini3001/. /data/mappings/martini30/. /data/mappings/. Because, i commented out some of lines (C/N/H) in [atoms] section of the his.charmm36.map from the above folders, and the input PDB has a particular Histidine molecule with HSE-hydrogens and name as HIS. I did not use mutate flag. But it successfully generated output with that Histidine residue named as HIS (not HSE) in the top file. With this generated pdb file and itp file, I can manually change particular histidine to HSE or HSP and can use as GROMACS input.

my coarse-grained topology(.top) file looks like this:

include "martini_v3.0.0.itp"

include "molecule_0_t2.itp" [the output itp modified by me under [atoms] section :: HIS as HSP or HSE]

[ system ] Title of the system

[ molecules ] molecule_0 1

For HSP, I used, TQ2p having +1.0 charge like HIH. Do i have to use +0.5 charge each TP3dq (SC3 | SC4). Do i have to modify any other section (other than [atoms] section) in the output itp file (molecule_0_t2.itp) Though it is working, please let me this is correct or not.

[fgrunewald]

Pronated HIS parameters are now implemented and available either as charmm or amber based residue names HIP/HSP resepctively.