
#######################################################
#                                                     #
#                        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 (   41),  selected    5 , name T0316TS276_2-D3
# Molecule2: number of CA atoms   90 (  711),  selected   90 , name T0316_D3.pdb
# PARAMETERS: T0316TS276_2-D3.T0316_D3.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M     284           -
LGA    -       -      S     285           -
LGA    -       -      T     286           -
LGA    -       -      S     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -
LGA    M     284      A     290          0.559
LGA    S     285      S     291          0.995
LGA    T     286      Q     292          1.218
LGA    S     287      V     293          0.885
LGA    L     288      H     294          0.826
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    -       -      T     304           -
LGA    -       -      L     305           -
LGA    -       -      E     306           -
LGA    -       -      C     307           -
LGA    -       -      T     308           -
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    0.92    20.00      5.468     0.489

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.125177 * X  +   0.960335 * Y  +   0.249172 * Z  +  -9.969439
  Y_new =   0.925741 * X  +   0.022728 * Y  +   0.377474 * Z  + -50.400467
  Z_new =   0.356838 * X  +   0.277920 * Y  +  -0.891867 * Z  +  31.167200 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.839514   -0.302079  [ DEG:   162.6921    -17.3079 ]
  Theta =  -0.364881   -2.776711  [ DEG:   -20.9061   -159.0939 ]
  Phi   =   1.705200   -1.436393  [ DEG:    97.7007    -82.2993 ]
 
# 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: T0316TS276_2-D3                               
REMARK     2: T0316_D3.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316TS276_2-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   0.92   20.00   5.468
REMARK  ---------------------------------------------------------- 
MOLECULE T0316TS276_2-D3
PFRMAT TS 
TARGET T0316
MODEL 2
PARENT 1K92_A
ATOM   5133  H   MET   284      33.129   8.517  -1.430  1.00  0.00               
ATOM   5135  N   MET   284      32.843   9.308  -1.001  1.00  0.00               
ATOM   5137  CA  MET   284      31.881   9.157   0.105  1.00  0.00               
ATOM   5139  CB  MET   284      30.914   8.029  -0.152  1.00  0.00               
ATOM   5141  C   MET   284      32.500   9.037   1.484  1.00  0.00               
ATOM   5143  O   MET   284      31.838   9.281   2.485  1.00  0.00               
ATOM   5145  CG  MET   284      29.841   7.922   0.912  1.00  0.00               
ATOM   5147  SD  MET   284      28.608   6.665   0.520  1.00  0.00               
ATOM   5149  CE  MET   284      27.679   7.510  -0.752  1.00  0.00               
ATOM   5151  H   SER   285      34.252   8.559   0.761  1.00  0.00               
ATOM   5153  N   SER   285      33.729   8.580   1.534  1.00  0.00               
ATOM   5155  CA  SER   285      34.328   8.121   2.783  1.00  0.00               
ATOM   5157  CB  SER   285      35.720   7.600   2.539  1.00  0.00               
ATOM   5159  C   SER   285      34.350   9.116   3.933  1.00  0.00               
ATOM   5161  O   SER   285      34.458   8.677   5.081  1.00  0.00               
ATOM   5163  OG  SER   285      36.335   7.272   3.765  1.00  0.00               
ATOM   5165  H   THR   286      34.340  10.785   2.864  1.00  0.00               
ATOM   5167  N   THR   286      34.267  10.412   3.722  1.00  0.00               
ATOM   5169  CA  THR   286      34.135  11.250   4.900  1.00  0.00               
ATOM   5171  CB  THR   286      34.409  12.728   4.556  1.00  0.00               
ATOM   5173  C   THR   286      32.694  11.097   5.397  1.00  0.00               
ATOM   5175  O   THR   286      31.745  11.286   4.635  1.00  0.00               
ATOM   5177  CG2 THR   286      35.812  12.911   3.990  1.00  0.00               
ATOM   5179  OG1 THR   286      33.453  13.158   3.583  1.00  0.00               
ATOM   5181  H   SER   287      33.256  10.874   7.270  1.00  0.00               
ATOM   5183  N   SER   287      32.527  10.857   6.688  1.00  0.00               
ATOM   5185  CA  SER   287      31.209  10.510   7.217  1.00  0.00               
ATOM   5187  CB  SER   287      30.858   9.047   6.883  1.00  0.00               
ATOM   5189  C   SER   287      31.061  10.789   8.709  1.00  0.00               
ATOM   5191  O   SER   287      32.039  11.112   9.388  1.00  0.00               
ATOM   5193  OG  SER   287      31.777   8.144   7.486  1.00  0.00               
ATOM   5195  H   LEU   288      29.131  10.371   8.656  1.00  0.00               
ATOM   5197  N   LEU   288      29.847  10.604   9.229  1.00  0.00               
ATOM   5199  CA  LEU   288      29.604  10.706  10.666  1.00  0.00               
ATOM   5201  CB  LEU   288      28.395  11.600  10.939  1.00  0.00               
ATOM   5203  C   LEU   288      29.370   9.330  11.291  1.00  0.00               
ATOM   5205  O   LEU   288      30.294   8.493  11.235  1.00  0.00               
ATOM   5207  OXT LEU   288      28.219   9.052  11.685  1.00  0.00               
ATOM   5209  CG  LEU   288      28.576  13.089  10.659  1.00  0.00               
ATOM   5211  CD1 LEU   288      27.245  13.810  10.808  1.00  0.00               
ATOM   5213  CD2 LEU   288      29.607  13.677  11.614  1.00  0.00               
TER 
END
