
#######################################################
#                                                     #
#                        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    5 (   25),  selected    5 , name T0350TS102_1
# Molecule2: number of CA atoms  109 ( 1798),  selected  109 , name T0350.pdb
# PARAMETERS: T0350TS102_1.T0350.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 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
 ERROR! 0 0 5 109
#      Molecule1      Molecule2       DISTANCE
LGA    -       -      M       1           -
LGA    -       -      N       2           -
LGA    -       -      I       3           -
LGA    -       -      E       4           -
LGA    -       -      R       5           -
LGA    -       -      L       6           -
LGA    -       -      T       7           -
LGA    H     113      T       8          1.928
LGA    H     114      L       9          1.861
LGA    H     115      Q      10          0.627
LGA    -       -      P      11           -
LGA    -       -      V      12           -
LGA    H     116      W      13          1.310
LGA    H     117      D      14          1.407
LGA    -       -      R      15           -
LGA    -       -      Y      16           -
LGA    -       -      D      17           -
LGA    -       -      T      18           -
LGA    -       -      Q      19           -
LGA    -       -      I      20           -
LGA    -       -      H      21           -
LGA    -       -      N      22           -
LGA    -       -      Q      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      N      26           -
LGA    -       -      D      27           -
LGA    -       -      N      28           -
LGA    -       -      E      29           -
LGA    -       -      V      30           -
LGA    -       -      P      31           -
LGA    -       -      V      32           -
LGA    -       -      H      33           -
LGA    -       -      Q      34           -
LGA    -       -      V      35           -
LGA    -       -      S      36           -
LGA    -       -      Y      37           -
LGA    -       -      T      38           -
LGA    -       -      N      39           -
LGA    -       -      L      40           -
LGA    -       -      A      41           -
LGA    -       -      E      42           -
LGA    -       -      M      43           -
LGA    -       -      V      44           -
LGA    -       -      G      45           -
LGA    -       -      E      46           -
LGA    -       -      M      47           -
LGA    -       -      N      48           -
LGA    -       -      K      49           -
LGA    -       -      L      50           -
LGA    -       -      L      51           -
LGA    -       -      E      52           -
LGA    -       -      P      53           -
LGA    -       -      S      54           -
LGA    -       -      Q      55           -
LGA    -       -      V      56           -
LGA    -       -      H      57           -
LGA    -       -      L      58           -
LGA    -       -      K      59           -
LGA    -       -      F      60           -
LGA    -       -      E      61           -
LGA    -       -      L      62           -
LGA    -       -      H      63           -
LGA    -       -      D      64           -
LGA    -       -      K      65           -
LGA    -       -      L      66           -
LGA    -       -      N      67           -
LGA    -       -      E      68           -
LGA    -       -      Y      69           -
LGA    -       -      Y      70           -
LGA    -       -      V      71           -
LGA    -       -      K      72           -
LGA    -       -      V      73           -
LGA    -       -      I      74           -
LGA    -       -      E      75           -
LGA    -       -      D      76           -
LGA    -       -      S      77           -
LGA    -       -      T      78           -
LGA    -       -      N      79           -
LGA    -       -      E      80           -
LGA    -       -      V      81           -
LGA    -       -      I      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      I      85           -
LGA    -       -      P      86           -
LGA    -       -      P      87           -
LGA    -       -      K      88           -
LGA    -       -      R      89           -
LGA    -       -      W      90           -
LGA    -       -      L      91           -
LGA    -       -      D      92           -
LGA    -       -      F      93           -
LGA    -       -      Y      94           -
LGA    -       -      A      95           -
LGA    -       -      A      96           -
LGA    -       -      M      97           -
LGA    -       -      T      98           -
LGA    -       -      E      99           -
LGA    -       -      F     100           -
LGA    -       -      L     101           -
LGA    -       -      G     102           -
LGA    -       -      L     103           -
LGA    -       -      F     104           -
LGA    -       -      V     105           -
LGA    -       -      D     106           -
LGA    -       -      E     107           -
LGA    -       -      K     108           -
LGA    -       -      K     109           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5  109    5.0      5    1.50     0.00      4.374     0.312

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.624182 * X  +   0.335057 * Y  +   0.705786 * Z  + -29.120575
  Y_new =  -0.685095 * X  +   0.668976 * Y  +   0.288300 * Z  + -29.517948
  Z_new =  -0.375556 * X  +  -0.663482 * Y  +   0.647108 * Z  + -35.573063 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.797891    2.343702  [ DEG:   -45.7158    134.2842 ]
  Theta =   0.384997    2.756596  [ DEG:    22.0587    157.9413 ]
  Phi   =  -0.831889    2.309704  [ DEG:   -47.6637    132.3363 ]
 
# 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: T0350TS102_1                                  
REMARK     2: T0350.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0350TS102_1.T0350.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5  109   5.0    5   1.50    0.00   4.374
REMARK  ---------------------------------------------------------- 
MOLECULE T0350TS102_1
PFRMAT TS
TARGET T0350
MODEL 1
PARENT 1zko_A
ATOM      1  N   HIS   113      12.503   0.117  -8.814  1.00  1.00
ATOM      2  CA  HIS   113      12.056  -0.804  -9.896  1.00  1.00
ATOM      3  C   HIS   113      11.431  -2.052  -9.309  1.00  1.00
ATOM      4  O   HIS   113      11.900  -2.579  -8.300  1.00  1.00
ATOM      5  CB  HIS   113      13.224  -1.169 -10.808  1.00  1.00
ATOM      6  N   HIS   114      10.374  -2.515  -9.960  1.00  1.00
ATOM      7  CA  HIS   114       9.572  -3.618  -9.459  1.00  1.00
ATOM      8  C   HIS   114       9.707  -4.833 -10.359  1.00  1.00
ATOM      9  O   HIS   114       9.963  -4.693 -11.556  1.00  1.00
ATOM     10  CB  HIS   114       8.121  -3.171  -9.317  1.00  1.00
ATOM     11  N   HIS   115       9.570  -6.018  -9.766  1.00  1.00
ATOM     12  CA  HIS   115       9.725  -7.278 -10.488  1.00  1.00
ATOM     13  C   HIS   115       8.791  -7.345 -11.694  1.00  1.00
ATOM     14  O   HIS   115       7.575  -7.192 -11.565  1.00  1.00
ATOM     15  CB  HIS   115       9.473  -8.449  -9.532  1.00  1.00
ATOM     16  N   HIS   116       9.370  -7.562 -12.869  1.00  1.00
ATOM     17  CA  HIS   116       8.595  -7.642 -14.097  1.00  1.00
ATOM     18  C   HIS   116       7.759  -8.912 -14.117  1.00  1.00
ATOM     19  O   HIS   116       8.263  -9.989 -13.816  1.00  1.00
ATOM     20  CB  HIS   116       9.540  -7.631 -15.296  1.00  1.00
ATOM     21  N   HIS   117       6.483  -8.767 -14.460  1.00  1.00
ATOM     22  CA  HIS   117       5.622  -9.912 -14.717  1.00  1.00
ATOM     23  C   HIS   117       6.000 -10.532 -16.053  1.00  1.00
ATOM     24  O   HIS   117       6.551  -9.861 -16.925  1.00  1.00
ATOM     25  CB  HIS   117       4.162  -9.500 -14.801  1.00  1.00
TER
END
