
#######################################################
#                                                     #
#                        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 (   24),  selected    6 , name T0316AL333_2-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL333_2-D2.T0316_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    -       -      G     220           -
LGA    -       -      R     221           -
LGA    -       -      M     222           -
LGA    -       -      M     223           -
LGA    -       -      T     224           -
LGA    -       -      V     225           -
LGA    -       -      D     226           -
LGA    -       -      G     227           -
LGA    -       -      R     228           -
LGA    -       -      D     229           -
LGA    -       -      M     230           -
LGA    -       -      G     231           -
LGA    -       -      E     232           -
LGA    -       -      H     233           -
LGA    -       -      A     234           -
LGA    G     220      G     235          0.901
LGA    R     221      L     236          0.413
LGA    M     222      M     237          0.774
LGA    M     223      Y     238          0.260
LGA    T     224      Y     239          1.048
LGA    L     283      T     240          1.705
LGA    -       -      I     241           -
LGA    -       -      G     242           -
LGA    -       -      Q     243           -
LGA    -       -      R     244           -
LGA    -       -      G     245           -
LGA    -       -      G     246           -
LGA    -       -      L     247           -
LGA    -       -      G     248           -
LGA    -       -      I     249           -
LGA    -       -      G     250           -
LGA    -       -      G     251           -
LGA    -       -      D     256           -
LGA    -       -      N     257           -
LGA    -       -      A     258           -
LGA    -       -      P     259           -
LGA    -       -      W     260           -
LGA    -       -      F     261           -
LGA    -       -      V     262           -
LGA    -       -      V     263           -
LGA    -       -      G     264           -
LGA    -       -      K     265           -
LGA    -       -      D     266           -
LGA    -       -      L     267           -
LGA    -       -      S     268           -
LGA    -       -      K     269           -
LGA    -       -      N     270           -
LGA    -       -      I     271           -
LGA    -       -      L     272           -
LGA    -       -      Y     273           -
LGA    -       -      V     274           -
LGA    -       -      G     275           -
LGA    -       -      Q     276           -
LGA    -       -      G     277           -
LGA    -       -      F     278           -
LGA    -       -      Y     279           -
LGA    -       -      H     280           -
LGA    -       -      D     281           -
LGA    -       -      S     282           -
LGA    -       -      L     283           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6   60    5.0      6    0.97    33.33      9.868     0.560

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.210161 * X  +   0.952148 * Y  +  -0.221917 * Z  + -36.591885
  Y_new =  -0.840436 * X  +   0.059976 * Y  +  -0.538582 * Z  +  43.006889
  Z_new =  -0.499500 * X  +   0.299696 * Y  +   0.812824 * Z  + -11.740843 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.353245   -2.788348  [ DEG:    20.2394   -159.7606 ]
  Theta =   0.523022    2.618571  [ DEG:    29.9669    150.0331 ]
  Phi   =  -1.325759    1.815834  [ DEG:   -75.9604    104.0396 ]
 
# 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: T0316AL333_2-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL333_2-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6   60   5.0    6   0.97   33.33   9.868
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL333_2-D2
REMARK Aligment from pdb entry: 1ni5_A
ATOM    781  N   GLY   220      43.246  24.080 -15.954  1.00  0.00              
ATOM    782  CA  GLY   220      42.226  24.845 -15.249  1.00  0.00              
ATOM    783  C   GLY   220      41.063  23.956 -14.792  1.00  0.00              
ATOM    784  O   GLY   220      39.924  24.411 -14.673  1.00  0.00              
ATOM    785  N   ARG   221      41.353  22.692 -14.523  1.00  0.00              
ATOM    786  CA  ARG   221      40.308  21.783 -14.091  1.00  0.00              
ATOM    787  C   ARG   221      39.554  22.310 -12.883  1.00  0.00              
ATOM    788  O   ARG   221      38.324  22.311 -12.861  1.00  0.00              
ATOM    789  N   MET   222      40.292  22.746 -11.871  1.00  0.00              
ATOM    790  CA  MET   222      39.661  23.247 -10.659  1.00  0.00              
ATOM    791  C   MET   222      38.747  24.443 -10.919  1.00  0.00              
ATOM    792  O   MET   222      37.788  24.670 -10.183  1.00  0.00              
ATOM    793  N   MET   223      39.041  25.202 -11.967  1.00  0.00              
ATOM    794  CA  MET   223      38.242  26.368 -12.299  1.00  0.00              
ATOM    795  C   MET   223      36.932  25.916 -12.941  1.00  0.00              
ATOM    796  O   MET   223      35.868  26.475 -12.680  1.00  0.00              
ATOM    797  N   THR   224      37.017  24.887 -13.772  1.00  0.00              
ATOM    798  CA  THR   224      35.842  24.350 -14.446  1.00  0.00              
ATOM    799  C   THR   224      34.856  23.768 -13.437  1.00  0.00              
ATOM    800  O   THR   224      33.639  23.856 -13.615  1.00  0.00              
ATOM    801  N   LEU   283      35.398  23.178 -12.375  1.00  0.00              
ATOM    802  CA  LEU   283      34.600  22.548 -11.338  1.00  0.00              
ATOM    803  C   LEU   283      33.789  23.536 -10.517  1.00  0.00              
ATOM    804  O   LEU   283      32.655  23.248 -10.136  1.00  0.00              
END
