
#######################################################
#                                                     #
#                        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    7 (   54),  selected    7 , name T0378TS302_3-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS302_3-D1.T0378_D1.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    -       -      M       1           -
LGA    -       -      L       2           -
LGA    -       -      S       3           -
LGA    -       -      A       4           -
LGA    -       -      N       5           -
LGA    -       -      Q       6           -
LGA    -       -      I       7           -
LGA    -       -      K       8           -
LGA    -       -      F       9           -
LGA    -       -      L      10           -
LGA    -       -      R      11           -
LGA    -       -      S      12           -
LGA    -       -      L      13           -
LGA    -       -      R      14           -
LGA    -       -      E      15           -
LGA    -       -      R      16           -
LGA    -       -      K      17           -
LGA    -       -      Y      18           -
LGA    -       -      R      19           -
LGA    -       -      L      20           -
LGA    -       -      R      21           -
LGA    -       -      E      22           -
LGA    -       -      Q      23           -
LGA    -       -      A      24           -
LGA    -       -      F      25           -
LGA    -       -      A      26           -
LGA    -       -      V      27           -
LGA    -       -      E      28           -
LGA    -       -      G      29           -
LGA    -       -      P      30           -
LGA    -       -      K      31           -
LGA    -       -      L      32           -
LGA    -       -      V      33           -
LGA    -       -      G      34           -
LGA    -       -      E      35           -
LGA    -       -      M      36           -
LGA    -       -      L      37           -
LGA    -       -      P      38           -
LGA    -       -      F      39           -
LGA    -       -      Y      40           -
LGA    P      83      R      41          1.063
LGA    L      84      C      42          2.298
LGA    M      85      R      43          2.782
LGA    A      86      M      44          0.856
LGA    V      87      L      45          2.303
LGA    F      88      V      46          2.247
LGA    -       -      G      47           -
LGA    -       -      T      48           -
LGA    -       -      A      49           -
LGA    -       -      A      50           -
LGA    -       -      M      51           -
LGA    -       -      L      52           -
LGA    -       -      R      53           -
LGA    -       -      A      54           -
LGA    -       -      V      55           -
LGA    -       -      S      56           -
LGA    -       -      T      57           -
LGA    -       -      P      58           -
LGA    -       -      H      59           -
LGA    -       -      D      60           -
LGA    -       -      A      61           -
LGA    -       -      E      62           -
LGA    -       -      V      63           -
LGA    -       -      V      64           -
LGA    -       -      E      65           -
LGA    -       -      L      66           -
LGA    -       -      P      67           -
LGA    -       -      E      68           -
LGA    -       -      S      69           -
LGA    -       -      F      70           -
LGA    -       -      D      71           -
LGA    -       -      F      72           -
LGA    -       -      K      73           -
LGA    -       -      R      74           -
LGA    -       -      I      75           -
LGA    -       -      S      76           -
LGA    -       -      T      77           -
LGA    -       -      Q      78           -
LGA    -       -      T      79           -
LGA    -       -      T      80           -
LGA    -       -      P      81           -
LGA    -       -      Q      82           -
LGA    -       -      P      83           -
LGA    -       -      L      84           -
LGA    -       -      M      85           -
LGA    D      89      A      86          1.068
LGA    -       -      V      87           -
LGA    -       -      F      88           -
LGA    -       -      D      89           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    7   89    5.0      7    1.94     0.00      7.027     0.343

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.205235 * X  +   0.850439 * Y  +   0.484389 * Z  + -112.341927
  Y_new =  -0.903203 * X  +   0.355205 * Y  +  -0.240946 * Z  +  44.837585
  Z_new =  -0.376967 * X  +  -0.388051 * Y  +   0.841019 * Z  +  70.077972 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.432298    2.709295  [ DEG:   -24.7689    155.2312 ]
  Theta =   0.386519    2.755074  [ DEG:    22.1459    157.8541 ]
  Phi   =  -1.347360    1.794232  [ DEG:   -77.1981    102.8019 ]
 
# 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: T0378TS302_3-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS302_3-D1.T0378_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    7   89   5.0    7   1.94    0.00   7.027
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS302_3-D1
PFRMAT TS
TARGET T0378
MODEL  3
PARENT 1gz0_B
ATOM   1000  N   PRO    83       7.187  13.103  57.239  1.00  0.00
ATOM   1000  CA  PRO    83       7.593  14.386  56.705  1.00  0.00
ATOM   1000  C   PRO    83       6.572  15.339  57.234  1.00  0.00
ATOM   1000  O   PRO    83       5.932  15.004  58.227  1.00  0.00
ATOM   1000  CB  PRO    83       7.578  14.208  55.170  1.00  0.00
ATOM   1000  CG  PRO    83       6.687  12.960  54.879  1.00  0.00
ATOM   1000  CD  PRO    83       6.541  12.237  56.242  1.00  0.00
ATOM   1000  N   LEU    84       6.432  16.517  56.621  1.00  0.00
ATOM   1000  CA  LEU    84       5.894  17.690  57.233  1.00  0.00
ATOM   1000  C   LEU    84       5.722  18.476  55.991  1.00  0.00
ATOM   1000  O   LEU    84       6.366  18.168  54.992  1.00  0.00
ATOM   1000  CB  LEU    84       6.821  18.492  58.174  1.00  0.00
ATOM   1000  CG  LEU    84       6.722  18.179  59.693  1.00  0.00
ATOM   1000  CD1 LEU    84       5.278  18.076  60.236  1.00  0.00
ATOM   1000  CD2 LEU    84       7.594  16.985  60.130  1.00  0.00
ATOM   1000  N   MET    85       4.843  19.479  56.000  1.00  0.00
ATOM   1000  CA  MET    85       4.140  19.823  54.804  1.00  0.00
ATOM   1000  C   MET    85       3.652  21.176  55.146  1.00  0.00
ATOM   1000  O   MET    85       3.848  21.651  56.265  1.00  0.00
ATOM   1000  CB  MET    85       2.949  18.941  54.382  1.00  0.00
ATOM   1000  CG  MET    85       3.304  17.590  53.762  1.00  0.00
ATOM   1000  SD  MET    85       4.590  17.630  52.486  1.00  0.00
ATOM   1000  CE  MET    85       5.204  15.992  52.960  1.00  0.00
ATOM   1000  N   ALA    86       3.044  21.844  54.164  1.00  0.00
ATOM   1000  CA  ALA    86       2.915  23.260  54.156  1.00  0.00
ATOM   1000  C   ALA    86       1.929  23.406  53.064  1.00  0.00
ATOM   1000  O   ALA    86       1.569  22.412  52.442  1.00  0.00
ATOM   1000  CB  ALA    86       4.175  24.036  53.729  1.00  0.00
ATOM   1000  N   VAL    87       1.534  24.646  52.738  1.00  0.00
ATOM   1000  CA  VAL    87       0.352  24.828  51.936  1.00  0.00
ATOM   1000  C   VAL    87       0.875  24.836  50.509  1.00  0.00
ATOM   1000  O   VAL    87       0.118  24.782  49.541  1.00  0.00
ATOM   1000  CB  VAL    87      -0.475  26.051  52.288  1.00  0.00
ATOM   1000  CG1 VAL    87       0.412  27.306  52.359  1.00  0.00
ATOM   1000  CG2 VAL    87      -1.717  26.202  51.376  1.00  0.00
ATOM   1000  N   PHE    88       2.209  24.802  50.348  1.00  0.00
ATOM   1000  CA  PHE    88       2.801  25.069  49.064  1.00  0.00
ATOM   1000  C   PHE    88       3.397  23.749  48.686  1.00  0.00
ATOM   1000  O   PHE    88       3.929  23.599  47.592  1.00  0.00
ATOM   1000  CB  PHE    88       3.818  26.250  48.956  1.00  0.00
ATOM   1000  CG  PHE    88       3.102  27.582  49.088  1.00  0.00
ATOM   1000  CD1 PHE    88       1.763  27.693  48.747  1.00  0.00
ATOM   1000  CD2 PHE    88       3.784  28.780  49.244  1.00  0.00
ATOM   1000  CE1 PHE    88       1.018  28.801  49.048  1.00  0.00
ATOM   1000  CE2 PHE    88       3.062  29.960  49.189  1.00  0.00
ATOM   1000  CZ  PHE    88       1.703  29.944  49.354  1.00  0.00
ATOM   1000  N   ASP    89       3.182  22.716  49.522  1.00  0.00
ATOM   1000  CA  ASP    89       4.013  21.544  49.426  1.00  0.00
ATOM   1000  C   ASP    89       3.015  20.501  49.049  1.00  0.00
ATOM   1000  O   ASP    89       3.099  19.342  49.434  1.00  0.00
ATOM   1000  CB  ASP    89       4.715  21.063  50.714  1.00  0.00
ATOM   1000  CG  ASP    89       5.965  20.261  50.315  1.00  0.00
ATOM   1000  OD1 ASP    89       6.188  20.011  49.099  1.00  0.00
ATOM   1000  OD2 ASP    89       6.747  19.931  51.247  1.00  0.00
TER
END
