
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  --------------- 06/2006            #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

# Molecule1: number of CA atoms    6 (   51),  selected    6 , name T0356TS349_4-D2
# Molecule2: number of CA atoms  192 ( 1487),  selected  192 , name T0356_D2.pdb
# PARAMETERS: T0356TS349_4-D2.T0356_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

# WARNING! The change of the parameter DIST cutoff may give you better result.

# WARNING! The change of the distance cutoff DIST may give you better result.

 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
 ERROR! 0 0 6 192
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      T     122           -
LGA    -       -      K     123           -
LGA    -       -      R     124           -
LGA    -       -      L     125           -
LGA    -       -      R     126           -
LGA    -       -      G     127           -
LGA    -       -      A     128           -
LGA    -       -      P     129           -
LGA    -       -      C     130           -
LGA    -       -      Q     131           -
LGA    -       -      Q     132           -
LGA    -       -      K     133           -
LGA    -       -      I     134           -
LGA    -       -      V     135           -
LGA    -       -      S     136           -
LGA    -       -      G     137           -
LGA    -       -      D     138           -
LGA    -       -      D     139           -
LGA    -       -      V     140           -
LGA    -       -      D     141           -
LGA    -       -      L     142           -
LGA    -       -      N     143           -
LGA    -       -      R     144           -
LGA    -       -      I     145           -
LGA    -       -      P     146           -
LGA    -       -      I     147           -
LGA    -       -      M     148           -
LGA    -       -      T     149           -
LGA    -       -      C     150           -
LGA    -       -      W     151           -
LGA    -       -      P     152           -
LGA    -       -      E     153           -
LGA    -       -      D     154           -
LGA    -       -      A     155           -
LGA    -       -      A     156           -
LGA    -       -      P     157           -
LGA    -       -      L     158           -
LGA    -       -      I     159           -
LGA    -       -      T     160           -
LGA    -       -      W     161           -
LGA    -       -      G     162           -
LGA    -       -      L     163           -
LGA    -       -      T     164           -
LGA    -       -      V     165           -
LGA    -       -      T     166           -
LGA    -       -      R     167           -
LGA    -       -      G     168           -
LGA    -       -      P     169           -
LGA    -       -      H     170           -
LGA    -       -      K     171           -
LGA    -       -      E     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      N     175           -
LGA    -       -      L     176           -
LGA    -       -      G     177           -
LGA    -       -      I     178           -
LGA    -       -      Y     179           -
LGA    -       -      R     180           -
LGA    -       -      Q     181           -
LGA    -       -      Q     182           -
LGA    -       -      L     183           -
LGA    -       -      I     184           -
LGA    -       -      G     185           -
LGA    -       -      K     186           -
LGA    -       -      N     187           -
LGA    -       -      K     188           -
LGA    -       -      L     189           -
LGA    -       -      I     190           -
LGA    -       -      M     191           -
LGA    -       -      R     192           -
LGA    -       -      W     193           -
LGA    -       -      L     194           -
LGA    -       -      S     195           -
LGA    -       -      H     196           -
LGA    -       -      R     197           -
LGA    -       -      G     198           -
LGA    -       -      G     199           -
LGA    -       -      A     200           -
LGA    -       -      L     201           -
LGA    -       -      D     202           -
LGA    -       -      Y     203           -
LGA    -       -      Q     204           -
LGA    -       -      E     205           -
LGA    -       -      W     206           -
LGA    -       -      C     207           -
LGA    -       -      A     208           -
LGA    -       -      A     209           -
LGA    -       -      H     210           -
LGA    -       -      P     211           -
LGA    -       -      G     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      F     215           -
LGA    -       -      P     216           -
LGA    -       -      V     217           -
LGA    -       -      S     218           -
LGA    -       -      V     219           -
LGA    -       -      A     220           -
LGA    -       -      L     221           -
LGA    -       -      G     222           -
LGA    -       -      A     223           -
LGA    -       -      D     224           -
LGA    -       -      P     225           -
LGA    -       -      A     226           -
LGA    -       -      T     227           -
LGA    -       -      I     228           -
LGA    -       -      L     229           -
LGA    -       -      G     230           -
LGA    -       -      A     231           -
LGA    -       -      V     232           -
LGA    -       -      T     233           -
LGA    -       -      P     234           -
LGA    -       -      V     235           -
LGA    -       -      P     236           -
LGA    -       -      D     237           -
LGA    -       -      T     238           -
LGA    -       -      L     239           -
LGA    -       -      S     240           -
LGA    -       -      E     241           -
LGA    T     122      Y     242          1.675
LGA    K     123      A     243          0.607
LGA    R     124      F     244          0.698
LGA    -       -      A     245           -
LGA    -       -      G     246           -
LGA    L     125      L     247          1.503
LGA    R     126      L     248          1.816
LGA    G     127      R     249          3.155
LGA    -       -      G     250           -
LGA    -       -      T     251           -
LGA    -       -      K     252           -
LGA    -       -      T     253           -
LGA    -       -      E     254           -
LGA    -       -      V     255           -
LGA    -       -      V     256           -
LGA    -       -      K     257           -
LGA    -       -      C     258           -
LGA    -       -      I     259           -
LGA    -       -      S     260           -
LGA    -       -      N     261           -
LGA    -       -      D     262           -
LGA    -       -      L     263           -
LGA    -       -      E     264           -
LGA    -       -      V     265           -
LGA    -       -      P     266           -
LGA    -       -      A     267           -
LGA    -       -      S     268           -
LGA    -       -      A     269           -
LGA    -       -      E     270           -
LGA    -       -      I     271           -
LGA    -       -      V     272           -
LGA    -       -      L     273           -
LGA    -       -      E     274           -
LGA    -       -      G     275           -
LGA    -       -      Y     276           -
LGA    -       -      I     277           -
LGA    -       -      E     278           -
LGA    -       -      Q     279           -
LGA    -       -      G     280           -
LGA    -       -      E     281           -
LGA    -       -      T     282           -
LGA    -       -      A     283           -
LGA    -       -      P     284           -
LGA    -       -      E     285           -
LGA    -       -      G     286           -
LGA    -       -      P     287           -
LGA    -       -      Y     288           -
LGA    -       -      G     289           -
LGA    -       -      D     290           -
LGA    -       -      H     291           -
LGA    -       -      T     292           -
LGA    -       -      G     293           -
LGA    -       -      Y     294           -
LGA    -       -      Y     295           -
LGA    -       -      N     296           -
LGA    -       -      E     297           -
LGA    -       -      V     298           -
LGA    -       -      D     299           -
LGA    -       -      S     300           -
LGA    -       -      F     301           -
LGA    -       -      P     302           -
LGA    -       -      V     303           -
LGA    -       -      F     304           -
LGA    -       -      T     305           -
LGA    -       -      V     306           -
LGA    -       -      T     307           -
LGA    -       -      H     308           -
LGA    -       -      I     309           -
LGA    -       -      T     310           -
LGA    -       -      Q     311           -
LGA    -       -      R     312           -
LGA    -       -      E     313           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  192    5.0      6    1.79    16.67      2.901     0.318

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.170071 * X  +  -0.633865 * Y  +  -0.754514 * Z  + 158.346924
  Y_new =   0.005483 * X  +  -0.766265 * Y  +   0.642501 * Z  + 150.419983
  Z_new =  -0.985416 * X  +   0.105134 * Y  +   0.133796 * Z  +  41.220413 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.666009   -2.475583  [ DEG:    38.1595   -141.8405 ]
  Theta =   1.399804    1.741788  [ DEG:    80.2029     99.7971 ]
  Phi   =   3.109362   -0.032231  [ DEG:   178.1533     -1.8467 ]
 
# END of job
REMARK  ---------------------------------------------------------- 
REMARK   Citing LGA: 
REMARK   Zemla A., LGA - a Method for Finding 3D Similarities in  
REMARK   Protein Structures, Nucleic Acids Research, 2003, V. 31, 
REMARK   No. 13, pp. 3370-3374. 
REMARK  ---------------------------------------------------------- 
REMARK   Superimposed MOLECULES (1=>2)   Output: 1 molecule      
REMARK     1: T0356TS349_4-D2                               
REMARK     2: T0356_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0356TS349_4-D2.T0356_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  192   5.0    6   1.79   16.67   2.901
REMARK  ---------------------------------------------------------- 
MOLECULE T0356TS349_4-D2
PFRMAT TS
TARGET T0356
MODEL  4  REFINED
PARENT 1FX7_D
ATOM    726  N   THR   122      80.084  71.218  72.375  1.00  0.00
ATOM    727  CA  THR   122      79.504  70.535  71.183  1.00  0.00
ATOM    728  C   THR   122      79.599  71.445  69.913  1.00  0.00
ATOM    729  O   THR   122      79.274  70.934  68.831  1.00  0.00
ATOM    730  CB  THR   122      78.053  69.992  71.247  1.00  0.00
ATOM    731  OG1 THR   122      77.631  69.555  72.533  1.00  0.00
ATOM    732  CG2 THR   122      77.893  68.792  70.241  1.00  0.00
ATOM    733  N   LYS   123      80.225  72.613  69.942  1.00  0.00
ATOM    734  CA  LYS   123      80.307  73.589  68.836  1.00  0.00
ATOM    735  C   LYS   123      78.925  73.986  68.239  1.00  0.00
ATOM    736  O   LYS   123      78.902  74.615  67.167  1.00  0.00
ATOM    737  CB  LYS   123      81.152  73.000  67.713  1.00  0.00
ATOM    738  CG  LYS   123      82.631  73.005  67.975  1.00  0.00
ATOM    739  CD  LYS   123      83.258  74.364  67.743  1.00  0.00
ATOM    740  CE  LYS   123      84.730  74.234  67.342  1.00  0.00
ATOM    741  NZ  LYS   123      85.444  75.382  67.997  1.00  0.00
ATOM    742  N   ARG   124      77.898  74.025  69.087  1.00  0.00
ATOM    743  CA  ARG   124      76.583  74.370  68.726  1.00  0.00
ATOM    744  C   ARG   124      76.329  75.763  69.219  1.00  0.00
ATOM    745  O   ARG   124      76.709  76.042  70.401  1.00  0.00
ATOM    746  CB  ARG   124      75.629  73.391  69.448  1.00  0.00
ATOM    747  CG  ARG   124      75.218  73.599  70.905  1.00  0.00
ATOM    748  CD  ARG   124      76.191  72.992  71.932  1.00  0.00
ATOM    749  NE  ARG   124      75.578  71.996  72.832  1.00  0.00
ATOM    750  CZ  ARG   124      74.567  72.258  73.682  1.00  0.00
ATOM    751  NH1 ARG   124      74.012  73.469  73.793  1.00  0.00
ATOM    752  NH2 ARG   124      74.088  71.271  74.444  1.00  0.00
ATOM    753  N   LEU   125      75.714  76.645  68.485  1.00  0.00
ATOM    754  CA  LEU   125      75.488  77.912  69.063  1.00  0.00
ATOM    755  C   LEU   125      74.357  77.956  70.135  1.00  0.00
ATOM    756  O   LEU   125      73.846  76.908  70.538  1.00  0.00
ATOM    757  CB  LEU   125      75.521  79.065  68.087  1.00  0.00
ATOM    758  CG  LEU   125      76.538  79.013  66.973  1.00  0.00
ATOM    759  CD1 LEU   125      76.256  80.089  65.926  1.00  0.00
ATOM    760  CD2 LEU   125      77.940  79.201  67.543  1.00  0.00
ATOM    761  N   ARG   126      74.495  78.950  70.927  1.00  0.00
ATOM    762  CA  ARG   126      73.673  79.271  72.063  1.00  0.00
ATOM    763  C   ARG   126      73.340  80.782  71.894  1.00  0.00
ATOM    764  O   ARG   126      73.225  81.238  70.729  1.00  0.00
ATOM    765  CB  ARG   126      74.513  78.961  73.362  1.00  0.00
ATOM    766  CG  ARG   126      73.728  79.440  74.623  1.00  0.00
ATOM    767  CD  ARG   126      74.083  78.798  75.961  1.00  0.00
ATOM    768  NE  ARG   126      73.115  79.212  76.974  1.00  0.00
ATOM    769  CZ  ARG   126      71.947  78.609  77.235  1.00  0.00
ATOM    770  NH1 ARG   126      71.584  77.536  76.575  1.00  0.00
ATOM    771  NH2 ARG   126      71.101  79.052  78.175  1.00  0.00
ATOM    772  N   GLY   127      72.560  81.338  72.790  1.00  0.00
ATOM    773  CA  GLY   127      72.120  82.750  72.735  1.00  0.00
ATOM    774  C   GLY   127      70.980  83.087  73.698  1.00  0.00
ATOM    775  O   GLY   127      70.379  84.159  73.622  1.00  0.00
ATOM    776  OXT GLY   127      70.809  82.298  74.686  1.00  0.00
TER
END
