
#######################################################
#                                                     #
#                        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 T0378TS050_5-D1
# Molecule2: number of CA atoms   89 (  716),  selected   89 , name T0378_D1.pdb
# PARAMETERS: T0378TS050_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          1.821
LGA    L      84      M      44          0.745
LGA    M      85      L      45          0.391
LGA    A      86      V      46          0.449
LGA    V      87      G      47          0.814
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          2.182
LGA    D      89      L      84          1.497
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    1.30     0.00      7.441     0.499

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.308819 * X  +  -0.946811 * Y  +   0.090442 * Z  +   5.621220
  Y_new =  -0.881954 * X  +   0.320662 * Y  +   0.345446 * Z  +  20.600643
  Z_new =  -0.356074 * X  +   0.026915 * Y  +  -0.934070 * Z  +  56.547604 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.112786   -0.028807  [ DEG:   178.3495     -1.6505 ]
  Theta =   0.364063    2.777530  [ DEG:    20.8593    159.1407 ]
  Phi   =  -1.907607    1.233986  [ DEG:  -109.2978     70.7022 ]
 
# 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: T0378TS050_5-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0378TS050_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   1.30    0.00   7.441
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS050_5-D1
PFRMAT TS
TARGET T0378
MODEL 5
PARENT 1zjr_A
ATOM      1  N   PRO    83       5.621  20.601  56.548  1.00 15.00
ATOM      2  CA  PRO    83       5.753  21.102  55.191  1.00 15.00
ATOM      3  C   PRO    83       4.395  21.709  54.866  1.00 15.00
ATOM      4  O   PRO    83       3.398  20.987  54.850  1.00 15.00
ATOM      5  CB  PRO    83       6.091  19.858  54.368  1.00 15.00
ATOM      6  CG  PRO    83       6.713  18.919  55.347  1.00 15.00
ATOM      7  CD  PRO    83       5.980  19.125  56.643  1.00 15.00
ATOM      8  N   LEU    84       4.357  23.014  54.609  1.00 15.00
ATOM      9  CA  LEU    84       3.105  23.697  54.322  1.00 15.00
ATOM     10  C   LEU    84       2.793  23.607  52.836  1.00 15.00
ATOM     11  O   LEU    84       3.568  24.062  51.996  1.00 15.00
ATOM     12  CB  LEU    84       3.197  25.173  54.715  1.00 15.00
ATOM     13  CG  LEU    84       1.956  26.026  54.441  1.00 15.00
ATOM     14  CD1 LEU    84       0.782  25.551  55.284  1.00 15.00
ATOM     15  CD2 LEU    84       2.223  27.485  54.775  1.00 15.00
ATOM     16  N   MET    85       1.643  23.012  52.519  1.00 15.00
ATOM     17  CA  MET    85       1.185  22.934  51.142  1.00 15.00
ATOM     18  C   MET    85       0.576  24.257  50.688  1.00 15.00
ATOM     19  O   MET    85      -0.174  24.916  51.414  1.00 15.00
ATOM     20  CB  MET    85       0.120  21.845  50.993  1.00 15.00
ATOM     21  CG  MET    85       0.619  20.443  51.302  1.00 15.00
ATOM     22  SD  MET    85       1.988  19.941  50.239  1.00 15.00
ATOM     23  CE  MET    85       1.160  19.818  48.656  1.00 15.00
ATOM     24  N   ALA    86       0.914  24.642  49.458  1.00 15.00
ATOM     25  CA  ALA    86       0.410  25.854  48.835  1.00 15.00
ATOM     26  C   ALA    86      -0.227  25.527  47.488  1.00 15.00
ATOM     27  O   ALA    86      -0.060  24.416  46.982  1.00 15.00
ATOM     28  CB  ALA    86       1.543  26.845  48.609  1.00 15.00
ATOM     29  N   VAL    87      -0.958  26.486  46.899  1.00 15.00
ATOM     30  CA  VAL    87      -1.740  26.308  45.667  1.00 15.00
ATOM     31  C   VAL    87      -0.965  25.639  44.531  1.00 15.00
ATOM     32  O   VAL    87      -1.453  24.705  43.890  1.00 15.00
ATOM     33  CB  VAL    87      -2.231  27.657  45.110  1.00 15.00
ATOM     34  CG1 VAL    87      -2.851  27.472  43.734  1.00 15.00
ATOM     35  CG2 VAL    87      -3.278  28.264  46.032  1.00 15.00
ATOM     36  N   PHE    88       0.257  26.112  44.270  1.00 15.00
ATOM     37  CA  PHE    88       1.114  25.553  43.229  1.00 15.00
ATOM     38  C   PHE    88       1.574  24.116  43.468  1.00 15.00
ATOM     39  O   PHE    88       2.057  23.451  42.550  1.00 15.00
ATOM     40  CB  PHE    88       2.390  26.384  43.081  1.00 15.00
ATOM     41  CG  PHE    88       2.173  27.717  42.424  1.00 15.00
ATOM     42  CD1 PHE    88       2.108  28.875  43.178  1.00 15.00
ATOM     43  CD2 PHE    88       2.034  27.812  41.050  1.00 15.00
ATOM     44  CE1 PHE    88       1.907  30.101  42.572  1.00 15.00
ATOM     45  CE2 PHE    88       1.834  29.038  40.444  1.00 15.00
ATOM     46  CZ  PHE    88       1.771  30.180  41.199  1.00 15.00
ATOM     47  N   ASP    89       1.434  23.608  44.699  1.00 15.00
ATOM     48  CA  ASP    89       1.742  22.213  45.002  1.00 15.00
ATOM     49  C   ASP    89       0.612  21.273  44.607  1.00 15.00
ATOM     50  O   ASP    89       0.808  20.056  44.602  1.00 15.00
ATOM     51  CB  ASP    89       1.989  22.033  46.500  1.00 15.00
ATOM     52  CG  ASP    89       3.300  22.643  46.954  1.00 15.00
ATOM     53  OD1 ASP    89       4.141  22.956  46.083  1.00 15.00
ATOM     54  OD2 ASP    89       3.488  22.807  48.177  1.00 15.00
TER
END
