
#######################################################
#                                                     #
#                        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    5 (   40),  selected    5 , name T0316TS277_1-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS277_1-D3.T0316_D3.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.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    -       -      A     290           -
LGA    -       -      S     291           -
LGA    -       -      Q     292           -
LGA    -       -      V     293           -
LGA    -       -      H     294           -
LGA    -       -      F     295           -
LGA    -       -      T     296           -
LGA    -       -      R     297           -
LGA    -       -      E     298           -
LGA    -       -      M     299           -
LGA    -       -      P     300           -
LGA    -       -      E     301           -
LGA    -       -      E     302           -
LGA    -       -      F     303           -
LGA    M     284      T     304          0.756
LGA    S     285      L     305          0.650
LGA    T     286      E     306          0.781
LGA    S     287      C     307          0.661
LGA    L     288      T     308          0.452
LGA    -       -      A     309           -
LGA    -       -      K     310           -
LGA    -       -      F     311           -
LGA    -       -      R     312           -
LGA    -       -      Y     313           -
LGA    -       -      R     314           -
LGA    -       -      Q     315           -
LGA    -       -      P     316           -
LGA    -       -      D     317           -
LGA    -       -      S     318           -
LGA    -       -      K     319           -
LGA    -       -      V     320           -
LGA    -       -      T     321           -
LGA    -       -      V     322           -
LGA    -       -      H     323           -
LGA    -       -      V     324           -
LGA    -       -      K     325           -
LGA    -       -      G     326           -
LGA    -       -      E     327           -
LGA    -       -      K     328           -
LGA    -       -      T     329           -
LGA    -       -      E     330           -
LGA    -       -      V     331           -
LGA    -       -      I     332           -
LGA    -       -      F     333           -
LGA    -       -      A     334           -
LGA    -       -      E     335           -
LGA    -       -      P     336           -
LGA    -       -      Q     337           -
LGA    -       -      R     338           -
LGA    -       -      A     339           -
LGA    -       -      I     340           -
LGA    -       -      T     341           -
LGA    -       -      P     342           -
LGA    -       -      G     343           -
LGA    -       -      Q     344           -
LGA    -       -      A     345           -
LGA    -       -      V     346           -
LGA    -       -      V     347           -
LGA    -       -      F     348           -
LGA    -       -      Y     349           -
LGA    -       -      D     350           -
LGA    -       -      G     351           -
LGA    -       -      E     352           -
LGA    -       -      E     353           -
LGA    -       -      C     354           -
LGA    -       -      L     355           -
LGA    -       -      G     356           -
LGA    -       -      G     357           -
LGA    -       -      G     358           -
LGA    -       -      L     359           -
LGA    -       -      I     360           -
LGA    -       -      D     361           -
LGA    -       -      N     362           -
LGA    -       -      A     363           -
LGA    -       -      Y     364           -
LGA    -       -      R     365           -
LGA    -       -      D     366           -
LGA    -       -      G     367           -
LGA    -       -      Q     368           -
LGA    -       -      V     369           -
LGA    -       -      C     370           -
LGA    -       -      Q     371           -
LGA    -       -      Y     372           -
LGA    -       -      I     373           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   90    5.0      5    0.67     0.00      5.556     0.649

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.447625 * X  +   0.876416 * Y  +  -0.177557 * Z  +  17.665848
  Y_new =  -0.061106 * X  +  -0.228075 * Y  +  -0.971724 * Z  +  68.325226
  Z_new =  -0.892131 * X  +  -0.424118 * Y  +   0.155646 * Z  +  46.520100 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.219069    1.922524  [ DEG:   -69.8475    110.1525 ]
  Theta =   1.102041    2.039552  [ DEG:    63.1423    116.8577 ]
  Phi   =  -3.005921    0.135672  [ DEG:  -172.2266      7.7734 ]
 
# 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: T0316TS277_1-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS277_1-D3.T0316_D3.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   90   5.0    5   0.67    0.00   5.556
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS277_1-D3
PFRMAT TS 
TARGET T0316
MODEL 1
PARENT 1K92_A
ATOM   5135  H   MET   284      19.834  -1.387   6.355  1.00  0.00                              
ATOM   5137  N   MET   284      20.656  -0.920   6.381  1.00  0.00                              
ATOM   5139  CA  MET   284      20.835   0.289   5.554  1.00  0.00                              
ATOM   5141  CB  MET   284      20.636   0.009   4.082  1.00  0.00                              
ATOM   5143  C   MET   284      19.953   1.442   5.963  1.00  0.00                              
ATOM   5145  O   MET   284      18.728   1.304   6.078  1.00  0.00                              
ATOM   5147  CG  MET   284      20.689   1.278   3.236  1.00  0.00                              
ATOM   5149  SD  MET   284      20.198   1.003   1.534  1.00  0.00                              
ATOM   5151  CE  MET   284      21.522  -0.053   0.988  1.00  0.00                              
ATOM   5153  H   SER   285      21.491   2.654   6.038  1.00  0.00                              
ATOM   5155  N   SER   285      20.561   2.590   6.132  1.00  0.00                              
ATOM   5157  CA  SER   285      19.828   3.777   6.437  1.00  0.00                              
ATOM   5159  CB  SER   285      20.756   4.818   7.058  1.00  0.00                              
ATOM   5161  C   SER   285      19.247   4.337   5.177  1.00  0.00                              
ATOM   5163  O   SER   285      19.999   4.845   4.320  1.00  0.00                              
ATOM   5165  OG  SER   285      20.206   6.120   6.936  1.00  0.00                              
ATOM   5167  H   THR   286      17.395   3.838   5.701  1.00  0.00                              
ATOM   5169  N   THR   286      17.912   4.213   5.013  1.00  0.00                              
ATOM   5171  CA  THR   286      17.226   4.686   3.779  1.00  0.00                              
ATOM   5173  CB  THR   286      15.791   4.075   3.667  1.00  0.00                              
ATOM   5175  C   THR   286      17.125   6.216   3.762  1.00  0.00                              
ATOM   5177  O   THR   286      18.103   6.909   3.446  1.00  0.00                              
ATOM   5179  CG2 THR   286      14.978   4.721   2.529  1.00  0.00                              
ATOM   5181  OG1 THR   286      15.900   2.662   3.423  1.00  0.00                              
ATOM   5183  H   SER   287      15.213   6.184   4.277  1.00  0.00                              
ATOM   5185  N   SER   287      15.933   6.743   4.069  1.00  0.00                              
ATOM   5187  CA  SER   287      15.729   8.190   4.126  1.00  0.00                              
ATOM   5189  CB  SER   287      16.483   8.783   5.318  1.00  0.00                              
ATOM   5191  C   SER   287      16.174   8.880   2.835  1.00  0.00                              
ATOM   5193  O   SER   287      16.155   8.277   1.760  1.00  0.00                              
ATOM   5195  OG  SER   287      16.349  10.176   5.349  1.00  0.00                              
ATOM   5197  H   LEU   288      16.544  10.561   3.794  1.00  0.00                              
ATOM   5199  N   LEU   288      16.545  10.152   2.943  1.00  0.00                              
ATOM   5201  CA  LEU   288      16.942  10.942   1.779  1.00  0.00                              
ATOM   5203  CB  LEU   288      15.979  10.683   0.612  1.00  0.00                              
ATOM   5205  C   LEU   288      16.931  12.408   2.125  1.00  0.00                              
ATOM   5207  O   LEU   288      16.220  12.801   3.024  1.00  0.00                              
ATOM   5209  CG  LEU   288      16.128  11.596  -0.611  1.00  0.00                              
ATOM   5211  CD1 LEU   288      17.490  11.384  -1.260  1.00  0.00                              
ATOM   5213  CD2 LEU   288      15.012  11.317  -1.610  1.00  0.00                              
TER 
END
