
#######################################################
#                                                     #
#                        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 (   37),  selected    5 , name T0320TS268_4_2-D2
# Molecule2: number of CA atoms   73 (  604),  selected   73 , name T0320_D2.pdb
# PARAMETERS: T0320TS268_4_2-D2.T0320_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.

#      Molecule1      Molecule2       DISTANCE
LGA    -       -      N     228           -
LGA    -       -      N     229           -
LGA    -       -      S     230           -
LGA    -       -      L     231           -
LGA    -       -      P     232           -
LGA    -       -      N     233           -
LGA    -       -      P     234           -
LGA    -       -      H     235           -
LGA    -       -      L     236           -
LGA    -       -      R     237           -
LGA    -       -      K     238           -
LGA    -       -      D     239           -
LGA    -       -      S     240           -
LGA    -       -      N     241           -
LGA    -       -      N     242           -
LGA    -       -      P     243           -
LGA    -       -      A     244           -
LGA    -       -      L     245           -
LGA    -       -      H     246           -
LGA    -       -      F     247           -
LGA    -       -      E     248           -
LGA    -       -      W     249           -
LGA    -       -      E     250           -
LGA    -       -      I     251           -
LGA    -       -      I     252           -
LGA    -       -      H     253           -
LGA    -       -      A     254           -
LGA    -       -      F     255           -
LGA    -       -      G     256           -
LGA    -       -      K     257           -
LGA    -       -      D     258           -
LGA    -       -      R     263           -
LGA    -       -      S     264           -
LGA    -       -      S     265           -
LGA    -       -      A     266           -
LGA    -       -      I     267           -
LGA    -       -      N     268           -
LGA    -       -      T     269           -
LGA    -       -      S     270           -
LGA    -       -      P     271           -
LGA    -       -      I     272           -
LGA    -       -      S     273           -
LGA    -       -      V     274           -
LGA    N     228      V     275          1.016
LGA    N     229      D     276          1.110
LGA    -       -      K     277           -
LGA    -       -      E     278           -
LGA    S     230      R     279          0.920
LGA    L     231      F     280          1.837
LGA    -       -      S     281           -
LGA    -       -      K     282           -
LGA    P     232      Y     283          2.060
LGA    -       -      H     284           -
LGA    -       -      D     285           -
LGA    -       -      N     286           -
LGA    -       -      Y     287           -
LGA    -       -      Y     288           -
LGA    -       -      P     289           -
LGA    -       -      G     290           -
LGA    -       -      W     291           -
LGA    -       -      Y     292           -
LGA    -       -      L     293           -
LGA    -       -      V     294           -
LGA    -       -      D     295           -
LGA    -       -      D     296           -
LGA    -       -      T     297           -
LGA    -       -      L     298           -
LGA    -       -      E     299           -
LGA    -       -      R     300           -
LGA    -       -      A     301           -
LGA    -       -      G     302           -
LGA    -       -      R     303           -
LGA    -       -      I     304           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   73    5.0      5    1.46     0.00      6.435     0.320

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.356228 * X  +   0.631312 * Y  +   0.688874 * Z  + -15.445713
  Y_new =  -0.504249 * X  +  -0.750555 * Y  +   0.427083 * Z  + 115.970688
  Z_new =   0.786660 * X  +  -0.195225 * Y  +   0.585707 * Z  + -11.086167 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.321735    2.819858  [ DEG:   -18.4340    161.5660 ]
  Theta =  -0.905381   -2.236212  [ DEG:   -51.8745   -128.1255 ]
  Phi   =  -2.185839    0.955754  [ DEG:  -125.2394     54.7606 ]
 
# 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: T0320TS268_4_2-D2                             
REMARK     2: T0320_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0320TS268_4_2-D2.T0320_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   73   5.0    5   1.46    0.00   6.435
REMARK  ---------------------------------------------------------- 
MOLECULE T0320TS268_4_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0320
PARENT 1ni5_A
ATOM   1861  N   ASN   228      22.256  33.053   1.001  1.00  0.00
ATOM   1862  CA  ASN   228      23.534  32.474   0.717  1.00  0.00
ATOM   1863  C   ASN   228      23.519  31.111   1.322  1.00  0.00
ATOM   1864  O   ASN   228      23.718  30.954   2.525  1.00  0.00
ATOM   1865  CB  ASN   228      24.654  33.320   1.327  1.00  0.00
ATOM   1866  CG  ASN   228      26.033  32.810   0.960  1.00  0.00
ATOM   1867  OD1 ASN   228      26.195  31.654   0.570  1.00  0.00
ATOM   1868  ND2 ASN   228      27.034  33.674   1.086  1.00  0.00
ATOM   1869  N   ASN   229      23.271  30.086   0.489  1.00  0.00
ATOM   1870  CA  ASN   229      23.240  28.745   0.989  1.00  0.00
ATOM   1871  C   ASN   229      23.731  27.861  -0.107  1.00  0.00
ATOM   1872  O   ASN   229      23.812  28.274  -1.263  1.00  0.00
ATOM   1873  CB  ASN   229      21.814  28.354   1.386  1.00  0.00
ATOM   1874  CG  ASN   229      20.866  28.332   0.204  1.00  0.00
ATOM   1875  OD1 ASN   229      20.957  27.463  -0.663  1.00  0.00
ATOM   1876  ND2 ASN   229      19.949  29.293   0.166  1.00  0.00
ATOM   1877  N   SER   230      24.101  26.616   0.241  1.00  0.00
ATOM   1878  CA  SER   230      24.530  25.706  -0.775  1.00  0.00
ATOM   1879  C   SER   230      23.291  25.237  -1.457  1.00  0.00
ATOM   1880  O   SER   230      22.198  25.317  -0.899  1.00  0.00
ATOM   1881  CB  SER   230      25.285  24.527  -0.155  1.00  0.00
ATOM   1882  OG  SER   230      24.421  23.726   0.631  1.00  0.00
ATOM   1883  N   LEU   231      23.424  24.751  -2.701  1.00  0.00
ATOM   1884  CA  LEU   231      22.259  24.293  -3.390  1.00  0.00
ATOM   1885  C   LEU   231      21.883  22.978  -2.807  1.00  0.00
ATOM   1886  O   LEU   231      22.727  22.210  -2.347  1.00  0.00
ATOM   1887  CB  LEU   231      22.546  24.139  -4.886  1.00  0.00
ATOM   1888  CG  LEU   231      22.926  25.416  -5.638  1.00  0.00
ATOM   1889  CD1 LEU   231      23.280  25.102  -7.083  1.00  0.00
ATOM   1890  CD2 LEU   231      21.771  26.405  -5.635  1.00  0.00
ATOM   1891  N   PRO   232      20.609  22.720  -2.793  1.00  0.00
ATOM   1892  CA  PRO   232      20.165  21.459  -2.273  1.00  0.00
ATOM   1893  C   PRO   232      20.421  20.393  -3.282  1.00  0.00
ATOM   1894  O   PRO   232      20.759  20.744  -4.444  1.00  0.00
ATOM   1895  CB  PRO   232      18.670  21.668  -2.020  1.00  0.00
ATOM   1896  CG  PRO   232      18.235  22.598  -3.102  1.00  0.00
ATOM   1897  CD  PRO   232      19.362  23.574  -3.293  1.00  0.00
TER
END
