
#######################################################
#                                                     #
#                        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   11 (   44),  selected   11 , name T0316AL380_4-D2
# Molecule2: number of CA atoms   60 (  457),  selected   60 , name T0316_D2.pdb
# PARAMETERS: T0316AL380_4-D2.T0316_D2.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      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     220      G     231          1.886
LGA    R     221      E     232          1.849
LGA    M     222      H     233          1.268
LGA    -       -      A     234           -
LGA    M     223      G     235           #
LGA    -       -      L     236           -
LGA    -       -      M     237           -
LGA    -       -      Y     238           -
LGA    -       -      Y     239           -
LGA    -       -      T     240           -
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    T     224      L     272          1.127
LGA    V     225      Y     273          1.181
LGA    D     226      V     274          1.188
LGA    G     227      G     275          1.212
LGA    R     228      Q     276          1.587
LGA    D     229      G     277          1.734
LGA    M     230      F     278          4.181
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)   11   60    5.0     10    1.93    20.00     13.941     0.493

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.749280 * X  +  -0.007382 * Y  +   0.662212 * Z  + -74.279221
  Y_new =  -0.597758 * X  +  -0.437968 * Y  +   0.671468 * Z  + 102.777344
  Z_new =   0.285071 * X  +  -0.898960 * Y  +  -0.332573 * Z  +  23.924267 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.925135    1.216458  [ DEG:  -110.3021     69.6979 ]
  Theta =  -0.289081   -2.852512  [ DEG:   -16.5631   -163.4369 ]
  Phi   =  -0.673384    2.468209  [ DEG:   -38.5820    141.4180 ]
 
# 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: T0316AL380_4-D2                               
REMARK     2: T0316_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0316AL380_4-D2.T0316_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   11   60   5.0   10   1.93   20.00  13.941
REMARK  ---------------------------------------------------------- 
MOLECULE T0316AL380_4-D2
REMARK Aligment from pdb entry: 1gpmB
ATOM    693  N   GLY   220      38.942  26.139 -25.798  1.00  0.00              
ATOM    694  CA  GLY   220      38.677  24.709 -25.984  1.00  0.00              
ATOM    695  C   GLY   220      39.728  23.790 -25.343  1.00  0.00              
ATOM    696  O   GLY   220      39.390  22.754 -24.757  1.00  0.00              
ATOM    697  N   ARG   221      40.996  24.166 -25.484  1.00  0.00              
ATOM    698  CA  ARG   221      42.106  23.394 -24.935  1.00  0.00              
ATOM    699  C   ARG   221      42.266  23.638 -23.439  1.00  0.00              
ATOM    700  O   ARG   221      43.084  22.993 -22.786  1.00  0.00              
ATOM    701  N   MET   222      41.507  24.594 -22.909  1.00  0.00              
ATOM    702  CA  MET   222      41.581  24.948 -21.492  1.00  0.00              
ATOM    703  C   MET   222      40.739  24.041 -20.591  1.00  0.00              
ATOM    704  O   MET   222      41.051  23.880 -19.408  1.00  0.00              
ATOM    705  N   MET   223      39.675  23.463 -21.147  1.00  0.00              
ATOM    706  CA  MET   223      38.782  22.580 -20.392  1.00  0.00              
ATOM    707  C   MET   223      38.994  21.094 -20.686  1.00  0.00              
ATOM    708  O   MET   223      39.282  20.715 -21.826  1.00  0.00              
ATOM    709  N   THR   224      38.819  20.257 -19.663  1.00  0.00              
ATOM    710  CA  THR   224      38.966  18.807 -19.808  1.00  0.00              
ATOM    711  C   THR   224      37.803  18.241 -20.620  1.00  0.00              
ATOM    712  O   THR   224      37.981  17.358 -21.470  1.00  0.00              
ATOM    713  N   VAL   225      36.612  18.772 -20.368  1.00  0.00              
ATOM    714  CA  VAL   225      35.422  18.330 -21.068  1.00  0.00              
ATOM    715  C   VAL   225      34.404  19.458 -21.060  1.00  0.00              
ATOM    716  O   VAL   225      34.370  20.255 -20.127  1.00  0.00              
ATOM    717  N   ASP   226      33.596  19.544 -22.110  1.00  0.00              
ATOM    718  CA  ASP   226      32.605  20.604 -22.211  1.00  0.00              
ATOM    719  C   ASP   226      31.428  20.210 -23.088  1.00  0.00              
ATOM    720  O   ASP   226      31.592  19.943 -24.284  1.00  0.00              
ATOM    721  N   GLY   227      30.239  20.195 -22.501  1.00  0.00              
ATOM    722  CA  GLY   227      29.045  19.843 -23.245  1.00  0.00              
ATOM    723  C   GLY   227      27.813  20.639 -22.856  1.00  0.00              
ATOM    724  O   GLY   227      27.856  21.491 -21.972  1.00  0.00              
ATOM    725  N   ARG   228      26.720  20.370 -23.548  1.00  0.00              
ATOM    726  CA  ARG   228      25.461  21.028 -23.287  1.00  0.00              
ATOM    727  C   ARG   228      24.455  19.937 -22.942  1.00  0.00              
ATOM    728  O   ARG   228      24.451  18.869 -23.558  1.00  0.00              
ATOM    729  N   ASP   229      23.672  20.178 -21.895  1.00  0.00              
ATOM    730  CA  ASP   229      22.651  19.238 -21.438  1.00  0.00              
ATOM    731  C   ASP   229      21.310  19.898 -21.744  1.00  0.00              
ATOM    732  O   ASP   229      21.167  21.119 -21.630  1.00  0.00              
ATOM    733  N   MET   230      20.343  19.115 -22.191  1.00  0.00              
ATOM    734  CA  MET   230      19.039  19.665 -22.505  1.00  0.00              
ATOM    735  C   MET   230      18.097  19.422 -21.327  1.00  0.00              
ATOM    736  O   MET   230      17.980  18.302 -20.840  1.00  0.00              
END
