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[modeller_usage] non expected atoms !


Dear Modeller community,
I am trying to model a protein (i.e. a polymerase) with magnesium and a nucleotide in its active site. The problem is that after calculations, unless metals and ligand are well localized in the active site , a meaningless fragment -SCC(N)CO(O) like a cystein- is linked to the last aminoacid ( a cystein)of my protein. 
the last part of my sequence alignment looks like that:


P1;unknown

sequence:UL54:   1: :1000: :: : 0.00: 0.00
AKKRARKPPSVVCNYEVAEDPSYVREHGVPIHADKYFE-QVLKAVTNVLSPVFPGGETARKDKFLHMVLPRRLHLEPAFLPYSVKAHECC/
....*

P1;template1

structureX:template1:  60:B: 2020:B: : :-1.00:-1.00
ARLAALRELDKLLVSELAEDPAYAIAHGVALNTDYYFS-HLLGAACVTFKALF-GNNAKITESLLKRFIPEVWH----------------/
....*


P1;template2

structureX:template2:1223:B:1242:B: : :-1.00:-1.00
----------------------------------------------------------------------RRLHLEPAFLPYSVKAHECC/
----*

"...." are for the BLK residues nucleotide and the 3 Mg2+, respectively

the end of the PDB file of template2 which BLK residues belongs to:

[...]
ATOM   8153  N   TRP B1196      65.776  26.703   9.332  1.00 58.52           N
ATOM   8154  CA  TRP B1196      64.810  27.441  10.157  1.00 58.00           C
ATOM   8155  C   TRP B1196      63.752  28.162   9.304  1.00 58.04           C
ATOM   8156  O   TRP B1196      62.939  28.970   9.795  1.00 56.87           O
ATOM   8157  CB  TRP B1196      65.546  28.462  11.019  1.00 57.75           C
ATOM   8158  CG  TRP B1196      66.438  27.901  12.067  1.00 56.58           C
ATOM   8159  CD1 TRP B1196      66.411  26.651  12.577  1.00 56.98           C
ATOM   8160  CD2 TRP B1196      67.457  28.604  12.773  1.00 55.70           C
ATOM   8161  CE2 TRP B1196      68.016  27.709  13.699  1.00 56.89           C
ATOM   8162  CE3 TRP B1196      67.959  29.909  12.707  1.00 57.14           C
ATOM   8163  NE1 TRP B1196      67.363  26.516  13.550  1.00 57.61           N
ATOM   8164  CZ2 TRP B1196      69.070  28.063  14.552  1.00 56.64           C
ATOM   8165  CZ3 TRP B1196      68.999  30.278  13.572  1.00 57.29           C
ATOM   8166  CH2 TRP B1196      69.538  29.349  14.485  1.00 57.02           C
ATOM   8167  N   HIS B1197      63.763  27.835   8.020  1.00 58.43           N
ATOM   8168  CA  HIS B1197      62.788  28.344   7.087  1.00 58.51           C
ATOM   8169  C   HIS B1197      61.503  27.591   7.340  1.00 59.34           C
ATOM   8170  O   HIS B1197      60.736  28.030   8.189  1.00 60.44           O
ATOM   8171  CB  HIS B1197      63.284  28.126   5.657  1.00 58.57           C
ATOM   8172  CG  HIS B1197      64.495  28.937   5.314  1.00 57.60           C
ATOM   8173  CD2 HIS B1197      65.285  29.727   6.080  1.00 57.68           C
ATOM   8174  ND1 HIS B1197      64.992  29.031   4.036  1.00 57.71           N
ATOM   8175  CE1 HIS B1197      66.042  29.834   4.032  1.00 57.32           C
ATOM   8176  NE2 HIS B1197      66.250  30.258   5.263  1.00 54.79           N
TER    8177      HIS B1197
HETATM 8178  PA  BLK B2017      52.886  71.468  10.308  1.00 21.91           P
HETATM 8179  PB  BLK B2017      52.583  74.293  10.892  1.00 21.14           P
HETATM 8180  PG  BLK B2017      54.870  74.729  12.687  1.00 21.92           P
HETATM 8181  C5' BLK B2017      51.878  71.976   7.940  1.00 18.42           C
HETATM 8182  O5' BLK B2017      51.853  71.173   9.113  1.00 20.44           O
HETATM 8183  C4' BLK B2017      50.438  72.342   7.584  1.00 18.78           C
HETATM 8184  O4' BLK B2017      49.619  71.166   7.552  1.00 17.55           O
HETATM 8185  C3' BLK B2017      49.744  73.248   8.586  1.00 17.53           C
HETATM 8186  O3' BLK B2017      50.110  74.645   8.523  1.00 16.04           O
HETATM 8187  C2' BLK B2017      48.281  72.991   8.232  1.00 15.82           C
HETATM 8188  C1' BLK B2017      48.276  71.490   7.958  1.00 17.68           C
HETATM 8189  N1  BLK B2017      47.947  70.834   9.243  1.00 19.13           N
HETATM 8190 O1A BLK B2017 54.256 71.815 9.770 1.00 20.91 O1- HETATM 8191 O1B BLK B2017 51.239 74.950 10.958 1.00 21.71 O1- 
HETATM 8192  O1G BLK B2017      54.925  74.009  14.011  1.00 20.37           O
HETATM 8193  C2  BLK B2017      46.600  70.860   9.679  1.00 20.99           C
HETATM 8194  O2  BLK B2017      45.732  71.415   8.949  1.00 18.60           O
HETATM 8195  O2A BLK B2017      52.799  70.342  11.279  1.00 21.10           O
HETATM 8196  O2B BLK B2017      53.419  74.703   9.682  1.00 20.26           O
HETATM 8197 O2G BLK B2017 55.058 76.214 12.843 1.00 20.21 O1- 
HETATM 8198  N3  BLK B2017      46.249  70.310  10.877  1.00 20.67           N
HETATM 8199  O3A BLK B2017      52.247  72.737  11.034  1.00 21.93           O
HETATM 8200  O3B BLK B2017      53.302  74.613  12.284  1.00 21.91           O
HETATM 8201  O3G BLK B2017      55.666  74.057  11.600  1.00 22.00           O
HETATM 8202  C4  BLK B2017      47.185  69.723  11.660  1.00 22.30           C
HETATM 8203  N4  BLK B2017      46.816  69.177  12.845  1.00 21.81           N
HETATM 8204  C5  BLK B2017      48.526  69.686  11.242  1.00 22.38           C
HETATM 8205  C6  BLK B2017      48.883  70.260  10.012  1.00 19.16           C
HETATM 8206 MG MG B2018 55.475 73.776 9.310 1.00 20.18 MG2+ HETATM 8207 MG MG B2019 55.986 70.196 8.530 1.00 43.33 MG2+ HETATM 8208 MG MG B2020 39.276 55.436 40.480 1.00 55.02 MG2+ 
END
and the end of the .pdb of one of the generated model (non expected atoms are highlighted by "<<<<<<<"): 

[...]
ATOM  16741  N   CYS D1055      67.146  39.478  18.616  1.00217.11           N
ATOM  16742  H   CYS D1055      66.718  39.397  17.719  1.00217.11           H
ATOM  16743  CA  CYS D1055      67.047  40.695  19.336  1.00217.11           C
ATOM  16744  HA  CYS D1055      67.914  40.758  19.976  1.00217.11           H
ATOM  16745  CB  CYS D1055      66.972  41.938  18.439  1.00217.11           C
ATOM  16746  HB3 CYS D1055      66.744  42.815  19.083  1.00217.11           H
ATOM  16747  HB2 CYS D1055      66.136  41.824  17.716  1.00217.11           H
ATOM  16748  SG  CYS D1055      68.544  42.217  17.575  1.00217.11           S
ATOM  16749  HG  CYS D1055      68.158  43.350  17.007  1.00217.11           H
ATOM  16750  C   CYS D1055      65.855  40.722  20.171  1.00217.11           C
ATOM  16751  O   CYS D1055      64.729  40.723  19.679  1.00217.11           O
ATOM  16752  N   CYS D1056      66.137  40.806  21.477  1.00115.72           N
ATOM  16753  H   CYS D1056      67.077  40.820  21.811  1.00115.72           H
ATOM  16754  CA  CYS D1056      65.129  40.891  22.465  1.00115.72           C
ATOM  16755  HA  CYS D1056      65.583  40.633  23.404  1.00115.72           H
ATOM  16756  CB  CYS D1056      64.539  42.290  22.571  1.00115.72           C
ATOM  16757  HB3 CYS D1056      65.305  42.969  22.999  1.00115.72           H
ATOM  16758  HB2 CYS D1056      63.717  42.241  23.317  1.00115.72           H
ATOM  16759  SG  CYS D1056      63.907  43.004  21.019  1.00115.72           S
ATOM  16760  HG  CYS D1056      63.496  44.140  21.564  1.00115.72           H
ATOM  16761  C   CYS D1056      64.051  39.882  22.170  1.00115.72           C
ATOM  16762  O   CYS D1056      64.442  38.722  21.891  1.00115.72           O
ATOM  16763  OXT CYS D1056      62.846  40.235  22.229  1.00115.72           O
TER   16764      CYS D1056
HETATM16765 N BLK E1057 67.782 36.707 25.725 1.00216.72 N <<<<<<< HETATM16766 CA BLK E1057 67.537 35.764 26.809 1.00216.72 C <<<<<<< HETATM16767 C BLK E1057 68.587 34.650 27.038 1.00216.72 C <<<<<<< HETATM16768 O BLK E1057 69.332 34.143 26.193 1.00216.72 O <<<<<<< HETATM16769 CB BLK E1057 66.140 35.141 26.779 1.00216.72 C <<<<<<< HETATM16770 SG BLK E1057 64.838 36.192 27.419 1.00216.72 S <<<<<<< HETATM16771 OXT BLK E1057 68.789 34.157 28.153 1.00216.72 O <<<<<<< 
HETATM16772  PA  BLK E1057      58.705  76.985  10.592  1.00216.72           P
HETATM16773  PB  BLK E1057      58.489  79.812  11.194  1.00216.72           P
HETATM16774  PG  BLK E1057      60.725  80.154  13.073  1.00216.72           P
HETATM16775  C5' BLK E1057      57.796  77.547   8.203  1.00216.72           C
HETATM16776  O5' BLK E1057      57.704  76.739   9.365  1.00216.72           O
HETATM16777  C4' BLK E1057      56.386  77.969   7.800  1.00216.72           C
HETATM16778  O4' BLK E1057      55.526  76.827   7.730  1.00216.72           O
HETATM16779  C3' BLK E1057      55.694  78.895   8.784  1.00216.72           C
HETATM16780  O3' BLK E1057      56.116  80.277   8.750  1.00216.72           O
HETATM16781  C2' BLK E1057      54.237  78.701   8.378  1.00216.72           C
HETATM16782  C1' BLK E1057      54.183  77.201   8.094  1.00216.72           C
HETATM16783  N1  BLK E1057      53.784  76.548   9.361  1.00216.72           N
HETATM16784  O1A BLK E1057      60.097  77.267  10.138  1.00216.72           O
HETATM16785  O1B BLK E1057      57.169  80.521  11.219  1.00216.72           O
HETATM16786  O1G BLK E1057      60.705  79.423  14.394  1.00216.72           O
HETATM16787  C2  BLK E1057      52.421  76.623   9.750  1.00216.72           C
HETATM16788  O2  BLK E1057      51.606  77.216   8.995  1.00216.72           O
HETATM16789  O2A BLK E1057      58.537  75.854  11.560  1.00216.72           O
HETATM16790  O2B BLK E1057      59.381  80.198  10.018  1.00216.72           O
HETATM16791  O2G BLK E1057      60.968  81.626  13.239  1.00216.72           O
HETATM16792  N3  BLK E1057      52.012  76.082  10.932  1.00216.72           N
HETATM16793  O3A BLK E1057      58.087  78.270  11.312  1.00216.72           O
HETATM16794  O3B BLK E1057      59.172  80.099  12.615  1.00216.72           O
HETATM16795  O3G BLK E1057      61.531  79.449  12.025  1.00216.72           O
HETATM16796  C4  BLK E1057      52.894  75.450  11.741  1.00216.72           C
HETATM16797  N4  BLK E1057      52.464  74.912  12.908  1.00216.72           N
HETATM16798  C5  BLK E1057      54.250  75.364  11.367  1.00216.72           C
HETATM16799  C6  BLK E1057      54.668  75.934  10.156  1.00216.72           C
HETATM16800 MG    MG E1058      61.402  79.397   9.419  1.00 32.87          MG
HETATM16801 MG    MG E1059      61.943  75.542   9.040  1.00 19.54          MG
HETATM16802 MG    MG E1060      45.100  60.452  39.519  1.00  3.68          MG
END

I precise that the .py works well.


By advance, Thanks for your help.

Anthony
--
Anthony Couvreux, postdoc
UMR Inserm 1092
Anti-infectieux: Supports moléculaires des résistances et innovations thérapeutiques - FR CNRS 3503 GEIST 
Faculté de Médecine, Université de Limoges
87000 Limoges
tel:05.55.43.59.74