
#######################################################
#                                                     #
#                        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 (   53),  selected    6 , name T0372TS022_1_1-D2
# Molecule2: number of CA atoms  172 ( 1400),  selected  172 , name T0372_D2.pdb
# PARAMETERS: T0372TS022_1_1-D2.T0372_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.

# WARNING! The change of the distance cutoff DIST may give you better result.

 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
 ERROR! 0 0 6 172
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      R     118           -
LGA    -       -      A     119           -
LGA    -       -      Y     120           -
LGA    -       -      A     121           -
LGA    -       -      D     122           -
LGA    -       -      Y     123           -
LGA    -       -      I     124           -
LGA    -       -      Y     125           -
LGA    -       -      L     126           -
LGA    -       -      R     127           -
LGA    -       -      S     128           -
LGA    -       -      D     129           -
LGA    -       -      L     130           -
LGA    -       -      A     131           -
LGA    -       -      T     132           -
LGA    -       -      L     133           -
LGA    -       -      K     134           -
LGA    R     118      G     135          0.251
LGA    A     119      K     136          0.191
LGA    Y     120      K     137          0.814
LGA    A     121      F     138          0.696
LGA    -       -      Q     139           -
LGA    -       -      A     140           -
LGA    D     122      K     141          0.923
LGA    Y     123      R     142          0.318
LGA    -       -      N     143           -
LGA    -       -      H     144           -
LGA    -       -      I     145           -
LGA    -       -      N     146           -
LGA    -       -      R     147           -
LGA    -       -      F     148           -
LGA    -       -      R     149           -
LGA    -       -      N     150           -
LGA    -       -      T     151           -
LGA    -       -      Y     152           -
LGA    -       -      P     153           -
LGA    -       -      D     154           -
LGA    -       -      Y     155           -
LGA    -       -      E     156           -
LGA    -       -      Y     157           -
LGA    -       -      T     158           -
LGA    -       -      P     159           -
LGA    -       -      I     160           -
LGA    -       -      T     161           -
LGA    -       -      P     162           -
LGA    -       -      D     163           -
LGA    -       -      R     164           -
LGA    -       -      I     165           -
LGA    -       -      Q     166           -
LGA    -       -      E     167           -
LGA    -       -      C     168           -
LGA    -       -      L     169           -
LGA    -       -      D     170           -
LGA    -       -      L     171           -
LGA    -       -      E     172           -
LGA    -       -      A     173           -
LGA    -       -      E     174           -
LGA    -       -      W     175           -
LGA    -       -      C     176           -
LGA    -       -      K     177           -
LGA    -       -      V     178           -
LGA    -       -      N     179           -
LGA    -       -      N     180           -
LGA    -       -      C     181           -
LGA    -       -      D     182           -
LGA    -       -      Q     183           -
LGA    -       -      Q     184           -
LGA    -       -      E     185           -
LGA    -       -      G     186           -
LGA    -       -      T     187           -
LGA    -       -      G     188           -
LGA    -       -      N     189           -
LGA    -       -      E     190           -
LGA    -       -      R     191           -
LGA    -       -      R     192           -
LGA    -       -      A     193           -
LGA    -       -      L     194           -
LGA    -       -      I     195           -
LGA    -       -      Y     196           -
LGA    -       -      A     197           -
LGA    -       -      L     198           -
LGA    -       -      H     199           -
LGA    -       -      N     200           -
LGA    -       -      F     201           -
LGA    -       -      E     202           -
LGA    -       -      A     203           -
LGA    -       -      L     204           -
LGA    -       -      G     205           -
LGA    -       -      L     206           -
LGA    -       -      T     207           -
LGA    -       -      G     208           -
LGA    -       -      G     209           -
LGA    -       -      I     210           -
LGA    -       -      L     211           -
LGA    -       -      H     212           -
LGA    -       -      V     213           -
LGA    -       -      N     214           -
LGA    -       -      G     215           -
LGA    -       -      K     216           -
LGA    -       -      I     217           -
LGA    -       -      V     218           -
LGA    -       -      A     219           -
LGA    -       -      F     220           -
LGA    -       -      T     221           -
LGA    -       -      F     222           -
LGA    -       -      G     223           -
LGA    -       -      M     224           -
LGA    -       -      P     225           -
LGA    -       -      I     226           -
LGA    -       -      N     227           -
LGA    -       -      H     228           -
LGA    -       -      E     229           -
LGA    -       -      T     230           -
LGA    -       -      F     231           -
LGA    -       -      G     232           -
LGA    -       -      V     233           -
LGA    -       -      H     234           -
LGA    -       -      V     235           -
LGA    -       -      E     236           -
LGA    -       -      K     237           -
LGA    -       -      A     238           -
LGA    -       -      D     239           -
LGA    -       -      T     240           -
LGA    -       -      S     241           -
LGA    -       -      I     242           -
LGA    -       -      D     243           -
LGA    -       -      G     244           -
LGA    -       -      A     245           -
LGA    -       -      Y     246           -
LGA    -       -      A     247           -
LGA    -       -      M     248           -
LGA    -       -      I     249           -
LGA    -       -      N     250           -
LGA    -       -      Y     251           -
LGA    -       -      E     252           -
LGA    -       -      F     253           -
LGA    -       -      A     254           -
LGA    -       -      N     255           -
LGA    -       -      R     256           -
LGA    -       -      I     257           -
LGA    -       -      P     258           -
LGA    -       -      E     259           -
LGA    -       -      Q     260           -
LGA    -       -      Y     261           -
LGA    -       -      I     262           -
LGA    -       -      Y     263           -
LGA    -       -      I     264           -
LGA    -       -      N     265           -
LGA    -       -      R     266           -
LGA    -       -      E     267           -
LGA    -       -      E     268           -
LGA    -       -      D     269           -
LGA    -       -      L     270           -
LGA    -       -      G     271           -
LGA    -       -      I     272           -
LGA    -       -      E     273           -
LGA    -       -      G     274           -
LGA    -       -      L     275           -
LGA    -       -      R     276           -
LGA    -       -      K     277           -
LGA    -       -      A     278           -
LGA    -       -      K     279           -
LGA    -       -      L     280           -
LGA    -       -      S     281           -
LGA    -       -      Y     282           -
LGA    -       -      Q     283           -
LGA    -       -      P     284           -
LGA    -       -      V     285           -
LGA    -       -      T     286           -
LGA    -       -      I     287           -
LGA    -       -      L     288           -
LGA    -       -      E     289           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    6  172    5.0      6    0.61     0.00      3.488     0.850

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.889106 * X  +   0.446822 * Y  +   0.099202 * Z  + -23.304724
  Y_new =  -0.336839 * X  +   0.492029 * Y  +   0.802775 * Z  +  43.184490
  Z_new =   0.309888 * X  +  -0.747166 * Y  +   0.587973 * Z  +  49.958614 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.904072    2.237521  [ DEG:   -51.7995    128.2005 ]
  Theta =  -0.315075   -2.826518  [ DEG:   -18.0525   -161.9475 ]
  Phi   =  -0.362144    2.779449  [ DEG:   -20.7493    159.2507 ]
 
# 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: T0372TS022_1_1-D2                             
REMARK     2: T0372_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS022_1_1-D2.T0372_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    6  172   5.0    6   0.61    0.00   3.488
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS022_1_1-D2
REMARK PARENT number 1
PFRMAT TS
TARGET T0372
PARENT 1qst_A
ATOM    945  N   ARG   118      17.519  47.555  36.624  1.00  0.00
ATOM    946  CA  ARG   118      18.315  46.543  35.985  1.00  0.00
ATOM    947  C   ARG   118      17.793  45.152  36.168  1.00  0.00
ATOM    948  O   ARG   118      18.478  44.266  36.679  1.00  0.00
ATOM    949  CB  ARG   118      19.741  46.552  36.542  1.00  0.00
ATOM    950  CG  ARG   118      20.453  47.888  36.402  1.00  0.00
ATOM    951  CD  ARG   118      20.557  48.308  34.945  1.00  0.00
ATOM    952  NE  ARG   118      21.333  47.355  34.155  1.00  0.00
ATOM    953  CZ  ARG   118      21.431  47.390  32.830  1.00  0.00
ATOM    954  NH1 ARG   118      22.159  46.481  32.196  1.00  0.00
ATOM    955  NH2 ARG   118      20.801  48.333  32.143  1.00  0.00
ATOM    956  N   ALA   119      16.537  44.939  35.728  1.00  0.00
ATOM    957  CA  ALA   119      15.923  43.646  35.744  1.00  0.00
ATOM    958  C   ALA   119      16.706  42.750  34.833  1.00  0.00
ATOM    959  O   ALA   119      16.937  41.583  35.146  1.00  0.00
ATOM    960  CB  ALA   119      14.484  43.737  35.261  1.00  0.00
ATOM    961  N   TYR   120      17.148  43.273  33.672  1.00  0.00
ATOM    962  CA  TYR   120      17.878  42.425  32.776  1.00  0.00
ATOM    963  C   TYR   120      19.326  42.782  32.840  1.00  0.00
ATOM    964  O   TYR   120      19.733  43.908  32.563  1.00  0.00
ATOM    965  CB  TYR   120      17.378  42.606  31.341  1.00  0.00
ATOM    966  CG  TYR   120      15.962  42.125  31.121  1.00  0.00
ATOM    967  CD1 TYR   120      14.884  42.987  31.285  1.00  0.00
ATOM    968  CD2 TYR   120      15.706  40.812  30.749  1.00  0.00
ATOM    969  CE1 TYR   120      13.587  42.557  31.085  1.00  0.00
ATOM    970  CE2 TYR   120      14.415  40.364  30.545  1.00  0.00
ATOM    971  CZ  TYR   120      13.352  41.250  30.717  1.00  0.00
ATOM    972  OH  TYR   120      12.060  40.819  30.519  1.00  0.00
ATOM    973  N   ALA   121      20.153  41.810  33.258  1.00  0.00
ATOM    974  CA  ALA   121      21.564  42.021  33.300  1.00  0.00
ATOM    975  C   ALA   121      22.149  40.775  33.868  1.00  0.00
ATOM    976  O   ALA   121      21.473  40.035  34.583  1.00  0.00
ATOM    977  CB  ALA   121      21.896  43.220  34.175  1.00  0.00
ATOM    978  N   ASP   122      23.431  40.508  33.563  1.00  0.00
ATOM    979  CA  ASP   122      24.026  39.319  34.092  1.00  0.00
ATOM    980  C   ASP   122      24.699  39.700  35.364  1.00  0.00
ATOM    981  O   ASP   122      25.747  40.343  35.351  1.00  0.00
ATOM    982  CB  ASP   122      25.045  38.746  33.106  1.00  0.00
ATOM    983  CG  ASP   122      25.674  37.459  33.600  1.00  0.00
ATOM    984  OD1 ASP   122      25.406  37.073  34.757  1.00  0.00
ATOM    985  OD2 ASP   122      26.436  36.835  32.832  1.00  0.00
ATOM    986  N   TYR   123      24.103  39.325  36.512  1.00  0.00
ATOM    987  CA  TYR   123      24.755  39.651  37.740  1.00  0.00
ATOM    988  C   TYR   123      25.281  38.359  38.334  1.00  0.00
ATOM    989  O   TYR   123      26.531  38.218  38.403  1.00  0.00
ATOM    990  CB  TYR   123      23.771  40.310  38.710  1.00  0.00
ATOM    991  CG  TYR   123      23.168  41.596  38.191  1.00  0.00
ATOM    992  CD1 TYR   123      21.872  41.625  37.697  1.00  0.00
ATOM    993  CD2 TYR   123      23.900  42.777  38.196  1.00  0.00
ATOM    994  CE1 TYR   123      21.312  42.795  37.220  1.00  0.00
ATOM    995  CE2 TYR   123      23.357  43.957  37.725  1.00  0.00
ATOM    996  CZ  TYR   123      22.052  43.958  37.234  1.00  0.00
ATOM    997  OH  TYR   123      21.498  45.125  36.762  1.00  0.00
TER
END
