
#######################################################
#                                                     #
#                        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    8 (   51),  selected    8 , name T0298TS268_5_1-D2
# Molecule2: number of CA atoms  186 ( 1394),  selected  186 , name T0298_D2.pdb
# PARAMETERS: T0298TS268_5_1-D2.T0298_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 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
 ERROR! 0 0 8 186
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      C     130           -
LGA    -       -      A     131           -
LGA    -       -      V     132           -
LGA    -       -      A     133           -
LGA    -       -      A     134           -
LGA    -       -      E     135           -
LGA    -       -      L     136           -
LGA    -       -      C     137           -
LGA    -       -      E     138           -
LGA    -       -      V     139           -
LGA    -       -      L     140           -
LGA    -       -      A     141           -
LGA    -       -      P     142           -
LGA    -       -      L     143           -
LGA    -       -      L     144           -
LGA    -       -      A     145           -
LGA    -       -      T     146           -
LGA    -       -      L     147           -
LGA    -       -      D     148           -
LGA    -       -      C     149           -
LGA    -       -      R     150           -
LGA    -       -      Q     151           -
LGA    -       -      L     152           -
LGA    -       -      N     153           -
LGA    -       -      L     154           -
LGA    -       -      T     155           -
LGA    -       -      A     156           -
LGA    -       -      C     157           -
LGA    -       -      L     158           -
LGA    -       -      S     159           -
LGA    -       -      V     160           -
LGA    -       -      S     161           -
LGA    -       -      S     162           -
LGA    -       -      L     163           -
LGA    -       -      G     164           -
LGA    -       -      R     165           -
LGA    -       -      E     166           -
LGA    -       -      G     167           -
LGA    -       -      V     168           -
LGA    -       -      K     169           -
LGA    -       -      E     170           -
LGA    -       -      L     171           -
LGA    -       -      A     172           -
LGA    -       -      R     173           -
LGA    -       -      Q     174           -
LGA    -       -      T     175           -
LGA    -       -      A     176           -
LGA    -       -      E     177           -
LGA    -       -      L     178           -
LGA    -       -      L     179           -
LGA    -       -      N     180           -
LGA    -       -      A     181           -
LGA    -       -      R     182           -
LGA    -       -      P     183           -
LGA    -       -      L     184           -
LGA    -       -      E     185           -
LGA    -       -      P     186           -
LGA    -       -      R     187           -
LGA    -       -      L     188           -
LGA    -       -      F     189           -
LGA    -       -      D     190           -
LGA    -       -      R     191           -
LGA    -       -      Q     192           -
LGA    -       -      I     193           -
LGA    -       -      A     194           -
LGA    -       -      F     195           -
LGA    -       -      N     196           -
LGA    -       -      L     197           -
LGA    -       -      L     198           -
LGA    -       -      A     199           -
LGA    -       -      Q     200           -
LGA    -       -      V     201           -
LGA    -       -      G     202           -
LGA    -       -      A     203           -
LGA    -       -      V     204           -
LGA    -       -      D     205           -
LGA    -       -      A     206           -
LGA    -       -      E     207           -
LGA    -       -      G     208           -
LGA    -       -      H     209           -
LGA    -       -      S     210           -
LGA    -       -      A     211           -
LGA    -       -      I     212           -
LGA    -       -      E     213           -
LGA    -       -      R     214           -
LGA    -       -      R     215           -
LGA    -       -      I     216           -
LGA    -       -      F     217           -
LGA    -       -      A     218           -
LGA    -       -      E     219           -
LGA    -       -      V     220           -
LGA    -       -      Q     221           -
LGA    -       -      A     222           -
LGA    -       -      L     223           -
LGA    -       -      L     224           -
LGA    -       -      G     225           -
LGA    -       -      E     226           -
LGA    -       -      R     227           -
LGA    -       -      I     228           -
LGA    -       -      G     229           -
LGA    -       -      P     230           -
LGA    -       -      L     231           -
LGA    -       -      N     232           -
LGA    -       -      V     233           -
LGA    -       -      T     234           -
LGA    -       -      C     235           -
LGA    -       -      I     236           -
LGA    -       -      Q     237           -
LGA    -       -      A     238           -
LGA    -       -      P     239           -
LGA    -       -      V     240           -
LGA    -       -      F     241           -
LGA    -       -      F     242           -
LGA    -       -      G     243           -
LGA    -       -      D     244           -
LGA    -       -      S     245           -
LGA    -       -      L     246           -
LGA    -       -      S     247           -
LGA    -       -      V     248           -
LGA    -       -      T     249           -
LGA    -       -      L     250           -
LGA    -       -      Q     251           -
LGA    -       -      C     252           -
LGA    -       -      A     253           -
LGA    -       -      E     254           -
LGA    -       -      P     255           -
LGA    -       -      V     256           -
LGA    -       -      D     257           -
LGA    C     130      L     258          1.148
LGA    A     131      A     259          3.090
LGA    -       -      A     260           -
LGA    -       -      V     261           -
LGA    -       -      T     262           -
LGA    V     132      R     263          0.973
LGA    A     133      V     264          4.023
LGA    A     134      L     265          1.998
LGA    -       -      D     266           -
LGA    -       -      A     267           -
LGA    E     135      T     268          1.417
LGA    L     136      K     269          2.506
LGA    -       -      G     270           -
LGA    C     137      I     271          1.837
LGA    -       -      E     272           -
LGA    -       -      W     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      E     276           -
LGA    -       -      G     277           -
LGA    -       -      D     278           -
LGA    -       -      Y     279           -
LGA    -       -      P     280           -
LGA    -       -      T     281           -
LGA    -       -      V     282           -
LGA    -       -      V     283           -
LGA    -       -      G     284           -
LGA    -       -      D     285           -
LGA    -       -      A     286           -
LGA    -       -      L     287           -
LGA    -       -      G     288           -
LGA    -       -      Q     289           -
LGA    -       -      D     290           -
LGA    -       -      E     291           -
LGA    -       -      T     292           -
LGA    -       -      Y     293           -
LGA    -       -      V     294           -
LGA    -       -      G     295           -
LGA    -       -      R     296           -
LGA    -       -      V     297           -
LGA    -       -      R     298           -
LGA    -       -      A     299           -
LGA    -       -      G     300           -
LGA    -       -      Q     301           -
LGA    -       -      A     302           -
LGA    -       -      D     303           -
LGA    -       -      P     304           -
LGA    -       -      C     305           -
LGA    -       -      Q     306           -
LGA    -       -      V     307           -
LGA    -       -      N     308           -
LGA    -       -      L     309           -
LGA    -       -      W     310           -
LGA    -       -      I     311           -
LGA    -       -      V     312           -
LGA    -       -      S     313           -
LGA    -       -      D     314           -
LGA    -       -      N     315           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  186    5.0      8    2.34    12.50      3.186     0.328

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.049558 * X  +  -0.795091 * Y  +   0.604462 * Z  +   7.866094
  Y_new =  -0.501515 * X  +  -0.543186 * Y  +  -0.673374 * Z  + 112.132217
  Z_new =   0.863729 * X  +  -0.269776 * Y  +  -0.425669 * Z  +  18.247149 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.576713    0.564880  [ DEG:  -147.6348     32.3652 ]
  Theta =  -1.042622   -2.098970  [ DEG:   -59.7379   -120.2621 ]
  Phi   =  -1.472300    1.669293  [ DEG:   -84.3566     95.6434 ]
 
# 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: T0298TS268_5_1-D2                             
REMARK     2: T0298_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0298TS268_5_1-D2.T0298_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  186   5.0    8   2.34   12.50   3.186
REMARK  ---------------------------------------------------------- 
MOLECULE T0298TS268_5_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0298
PARENT 1byi
ATOM    928  N   CYS   130     -15.549  87.562  24.025  1.00  0.00
ATOM    929  CA  CYS   130     -16.274  86.340  24.181  1.00  0.00
ATOM    930  C   CYS   130     -17.677  86.577  23.747  1.00  0.00
ATOM    931  O   CYS   130     -18.254  87.635  23.994  1.00  0.00
ATOM    932  CB  CYS   130     -16.256  85.889  25.643  1.00  0.00
ATOM    933  SG  CYS   130     -14.621  85.435  26.265  1.00  0.00
ATOM    934  N   ALA   131     -18.254  85.582  23.051  1.00  0.00
ATOM    935  CA  ALA   131     -19.609  85.687  22.610  1.00  0.00
ATOM    936  C   ALA   131     -20.083  84.294  22.393  1.00  0.00
ATOM    937  O   ALA   131     -19.283  83.364  22.288  1.00  0.00
ATOM    938  CB  ALA   131     -19.685  86.488  21.319  1.00  0.00
ATOM    939  N   VAL   132     -21.413  84.109  22.330  1.00  0.00
ATOM    940  CA  VAL   132     -21.897  82.784  22.106  1.00  0.00
ATOM    941  C   VAL   132     -21.350  82.384  20.781  1.00  0.00
ATOM    942  O   VAL   132     -21.081  83.230  19.929  1.00  0.00
ATOM    943  CB  VAL   132     -23.436  82.740  22.093  1.00  0.00
ATOM    944  CG1 VAL   132     -23.995  83.212  23.427  1.00  0.00
ATOM    945  CG2 VAL   132     -23.985  83.641  20.997  1.00  0.00
ATOM    946  N   ALA   133     -21.150  81.070  20.582  1.00  0.00
ATOM    947  CA  ALA   133     -20.578  80.617  19.353  1.00  0.00
ATOM    948  C   ALA   133     -21.467  81.086  18.254  1.00  0.00
ATOM    949  O   ALA   133     -22.625  81.434  18.476  1.00  0.00
ATOM    950  CB  ALA   133     -20.485  79.100  19.340  1.00  0.00
ATOM    951  N   ALA   134     -20.920  81.135  17.028  1.00  0.00
ATOM    952  CA  ALA   134     -21.680  81.606  15.913  1.00  0.00
ATOM    953  C   ALA   134     -22.899  80.757  15.815  1.00  0.00
ATOM    954  O   ALA   134     -22.954  79.659  16.359  1.00  0.00
ATOM    955  CB  ALA   134     -20.866  81.499  14.633  1.00  0.00
ATOM    956  N   GLU   135     -23.931  81.283  15.136  1.00  0.00
ATOM    957  CA  GLU   135     -25.201  80.630  15.015  1.00  0.00
ATOM    958  C   GLU   135     -25.030  79.321  14.316  1.00  0.00
ATOM    959  O   GLU   135     -25.632  78.321  14.706  1.00  0.00
ATOM    960  CB  GLU   135     -26.174  81.494  14.211  1.00  0.00
ATOM    961  CG  GLU   135     -26.644  82.742  14.940  1.00  0.00
ATOM    962  CD  GLU   135     -27.507  83.636  14.071  1.00  0.00
ATOM    963  OE1 GLU   135     -27.676  83.316  12.875  1.00  0.00
ATOM    964  OE2 GLU   135     -28.013  84.656  14.584  1.00  0.00
ATOM    965  N   LEU   136     -24.187  79.285  13.271  1.00  0.00
ATOM    966  CA  LEU   136     -24.063  78.078  12.510  1.00  0.00
ATOM    967  C   LEU   136     -23.604  76.983  13.414  1.00  0.00
ATOM    968  O   LEU   136     -24.182  75.896  13.429  1.00  0.00
ATOM    969  CB  LEU   136     -23.048  78.259  11.381  1.00  0.00
ATOM    970  CG  LEU   136     -22.799  77.040  10.491  1.00  0.00
ATOM    971  CD1 LEU   136     -24.076  76.628   9.774  1.00  0.00
ATOM    972  CD2 LEU   136     -21.742  77.347   9.441  1.00  0.00
ATOM    973  N   CYS   137     -22.560  77.245  14.217  1.00  0.00
ATOM    974  CA  CYS   137     -22.079  76.213  15.078  1.00  0.00
ATOM    975  C   CYS   137     -21.434  76.887  16.279  1.00  0.00
ATOM    976  O   CYS   137     -22.186  77.385  17.158  1.00  0.00
ATOM    977  CB  CYS   137     -21.052  75.343  14.351  1.00  0.00
ATOM    978  SG  CYS   137     -20.574  73.847  15.246  1.00  0.00
TER
END
