
#######################################################
#                                                     #
#                        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 T0378TS247_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS247_5-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.

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

 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
 ERROR! 0 0 7 89
#      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    -       -      R      41           -
LGA    -       -      C      42           -
LGA    P      83      R      43          1.795
LGA    L      84      M      44          0.742
LGA    M      85      L      45          0.389
LGA    A      86      V      46          0.439
LGA    V      87      G      47          0.809
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    F      88      P      83          2.177
LGA    D      89      L      84          1.482
LGA    -       -      M      85           -
LGA    -       -      A      86           -
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    1.29     0.00      7.441     0.503

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.291569 * X  +  -0.949263 * Y  +   0.117843 * Z  +   5.594720
  Y_new =  -0.861285 * X  +   0.314127 * Y  +   0.399390 * Z  +  20.527397
  Z_new =  -0.416144 * X  +   0.014953 * Y  +  -0.909176 * Z  +  56.539570 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.125147   -0.016445  [ DEG:   179.0578     -0.9422 ]
  Theta =   0.429201    2.712392  [ DEG:    24.5914    155.4086 ]
  Phi   =  -1.897214    1.244378  [ DEG:  -108.7024     71.2976 ]
 
# 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: T0378TS247_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS247_5-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   1.29    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS247_5-D1
PFRMAT TS
TARGET T0378
MODEL  5
PARENT 1zjr_A 1gz0_A 1gz0_B 1gz0_C 1gz0_D 1gz0_F 1gz0_H 1v2x_A 1x7p_A 1ipa_A
ATOM      1  N   PRO    83       5.595  20.527  56.540  1.00 0.00         0
ATOM      2  CA  PRO    83       5.766  21.107  55.221  1.00 0.00         0
ATOM      3  C   PRO    83       4.403  21.712  54.922  1.00 0.00         0
ATOM      4  O   PRO    83       3.408  20.989  54.978  1.00 0.00         0
ATOM      5  CB  PRO    83       6.139  19.914  54.339  1.00 0.00         0
ATOM      6  CG  PRO    83       6.735  18.923  55.282  1.00 0.00         0
ATOM      7  CD  PRO    83       5.959  19.049  56.563  1.00 0.00         0
ATOM      8  N   LEU    84       4.352  23.005  54.611  1.00 0.00         0
ATOM      9  CA  LEU    84       3.091  23.674  54.340  1.00 0.00         0
ATOM     10  C   LEU    84       2.793  23.589  52.850  1.00 0.00         0
ATOM     11  O   LEU    84       3.588  24.028  52.018  1.00 0.00         0
ATOM     12  CB  LEU    84       3.167  25.146  54.753  1.00 0.00         0
ATOM     13  CG  LEU    84       1.913  25.986  54.497  1.00 0.00         0
ATOM     14  CD1 LEU    84       0.749  25.486  55.339  1.00 0.00         0
ATOM     15  CD2 LEU    84       2.163  27.444  54.851  1.00 0.00         0
ATOM     16  N   MET    85       1.636  23.018  52.522  1.00 0.00         0
ATOM     17  CA  MET    85       1.192  22.945  51.140  1.00 0.00         0
ATOM     18  C   MET    85       0.594  24.275  50.690  1.00 0.00         0
ATOM     19  O   MET    85      -0.137  24.942  51.425  1.00 0.00         0
ATOM     20  CB  MET    85       0.125  21.861  50.976  1.00 0.00         0
ATOM     21  CG  MET    85       0.616  20.456  51.286  1.00 0.00         0
ATOM     22  SD  MET    85       1.993  19.952  50.238  1.00 0.00         0
ATOM     23  CE  MET    85       1.182  19.836  48.646  1.00 0.00         0
ATOM     24  N   ALA    86       0.917  24.655  49.455  1.00 0.00         0
ATOM     25  CA  ALA    86       0.419  25.873  48.839  1.00 0.00         0
ATOM     26  C   ALA    86      -0.212  25.548  47.488  1.00 0.00         0
ATOM     27  O   ALA    86      -0.029  24.440  46.978  1.00 0.00         0
ATOM     28  CB  ALA    86       1.555  26.862  48.626  1.00 0.00         0
ATOM     29  N   VAL    87      -0.955  26.497  46.898  1.00 0.00         0
ATOM     30  CA  VAL    87      -1.744  26.303  45.672  1.00 0.00         0
ATOM     31  C   VAL    87      -0.969  25.641  44.533  1.00 0.00         0
ATOM     32  O   VAL    87      -1.455  24.711  43.884  1.00 0.00         0
ATOM     33  CB  VAL    87      -2.260  27.642  45.114  1.00 0.00         0
ATOM     34  CG1 VAL    87      -2.887  27.442  43.743  1.00 0.00         0
ATOM     35  CG2 VAL    87      -3.309  28.237  46.040  1.00 0.00         0
ATOM     36  N   PHE    88       0.252  26.116  44.276  1.00 0.00         0
ATOM     37  CA  PHE    88       1.103  25.567  43.227  1.00 0.00         0
ATOM     38  C   PHE    88       1.572  24.128  43.447  1.00 0.00         0
ATOM     39  O   PHE    88       2.074  23.487  42.523  1.00 0.00         0
ATOM     40  CB  PHE    88       2.376  26.403  43.078  1.00 0.00         0
ATOM     41  CG  PHE    88       2.148  27.750  42.455  1.00 0.00         0
ATOM     42  CD1 PHE    88       2.076  28.888  43.239  1.00 0.00         0
ATOM     43  CD2 PHE    88       2.005  27.880  41.084  1.00 0.00         0
ATOM     44  CE1 PHE    88       1.866  30.128  42.665  1.00 0.00         0
ATOM     45  CE2 PHE    88       1.794  29.119  40.511  1.00 0.00         0
ATOM     46  CZ  PHE    88       1.725  30.241  41.295  1.00 0.00         0
ATOM     47  N   ASP    89       1.422  23.589  44.662  1.00 0.00         0
ATOM     48  CA  ASP    89       1.742  22.192  44.947  1.00 0.00         0
ATOM     49  C   ASP    89       0.610  21.254  44.538  1.00 0.00         0
ATOM     50  O   ASP    89       0.807  20.040  44.500  1.00 0.00         0
ATOM     51  CB  ASP    89       1.992  21.995  46.444  1.00 0.00         0
ATOM     52  CG  ASP    89       3.299  22.609  46.902  1.00 0.00         0
ATOM     53  OD1 ASP    89       4.137  22.940  46.036  1.00 0.00         0
ATOM     54  OD2 ASP    89       3.486  22.760  48.128  1.00 0.00         0
TER
END
