
#######################################################
#                                                     #
#                        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    8 (   40),  selected    8 , name T0372TS261_1_3-D1
# Molecule2: number of CA atoms  126 ( 1027),  selected  126 , name T0372_D1.pdb
# PARAMETERS: T0372TS261_1_3-D1.T0372_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    -       -      I       2           -
LGA    -       -      P       3           -
LGA    -       -      F       4           -
LGA    -       -      K       5           -
LGA    -       -      D       6           -
LGA    -       -      I       7           -
LGA    -       -      T       8           -
LGA    -       -      L       9           -
LGA    -       -      A      10           -
LGA    -       -      D      11           -
LGA    -       -      R      12           -
LGA    -       -      D      13           -
LGA    -       -      T      14           -
LGA    -       -      I      15           -
LGA    -       -      T      16           -
LGA    -       -      A      17           -
LGA    -       -      F      18           -
LGA    -       -      T      19           -
LGA    -       -      M      20           -
LGA    -       -      K      21           -
LGA    -       -      S      22           -
LGA    -       -      D      23           -
LGA    -       -      R      24           -
LGA    -       -      R      25           -
LGA    -       -      N      26           -
LGA    -       -      C      27           -
LGA    -       -      D      28           -
LGA    -       -      L      29           -
LGA    -       -      S      30           -
LGA    -       -      F      31           -
LGA    -       -      S      32           -
LGA    -       -      N      33           -
LGA    -       -      L      34           -
LGA    -       -      C      35           -
LGA    -       -      S      36           -
LGA    -       -      W      37           -
LGA    -       -      R      38           -
LGA    -       -      F      39           -
LGA    -       -      L      40           -
LGA    -       -      Y      41           -
LGA    -       -      D      42           -
LGA    -       -      T      43           -
LGA    -       -      Q      44           -
LGA    -       -      F      45           -
LGA    -       -      A      46           -
LGA    -       -      V      47           -
LGA    -       -      I      48           -
LGA    -       -      D      49           -
LGA    -       -      D      50           -
LGA    -       -      F      51           -
LGA    -       -      L      52           -
LGA    -       -      V      53           -
LGA    -       -      F      54           -
LGA    -       -      K      55           -
LGA    -       -      F      56           -
LGA    -       -      W      57           -
LGA    -       -      A      58           -
LGA    -       -      G      59           -
LGA    -       -      E      60           -
LGA    -       -      Q      61           -
LGA    -       -      L      62           -
LGA    -       -      A      63           -
LGA    -       -      Y      64           -
LGA    -       -      M      65           -
LGA    -       -      M      66           -
LGA    -       -      P      67           -
LGA    -       -      V      68           -
LGA    -       -      G      69           -
LGA    -       -      N      70           -
LGA    -       -      G      71           -
LGA    -       -      D      72           -
LGA    -       -      L      73           -
LGA    -       -      K      74           -
LGA    -       -      A      75           -
LGA    -       -      V      76           -
LGA    K     290      L      77          1.293
LGA    Y     291      R      78          2.268
LGA    M     292      K      79          1.368
LGA    -       -      L      80           -
LGA    -       -      I      81           -
LGA    A     293      E      82          1.354
LGA    C     294      D      83          0.960
LGA    K     296      A      84          2.384
LGA    D     297      D      85          1.935
LGA    -       -      K      86           -
LGA    -       -      E      87           -
LGA    -       -      K      88           -
LGA    -       -      H      89           -
LGA    -       -      N      90           -
LGA    H     298      F      91          2.622
LGA    -       -      C      92           -
LGA    -       -      M      93           -
LGA    -       -      L      94           -
LGA    -       -      G      95           -
LGA    -       -      V      96           -
LGA    -       -      C      97           -
LGA    -       -      S      98           -
LGA    -       -      N      99           -
LGA    -       -      M     100           -
LGA    -       -      R     101           -
LGA    -       -      A     102           -
LGA    -       -      D     103           -
LGA    -       -      L     104           -
LGA    -       -      E     105           -
LGA    -       -      A     106           -
LGA    -       -      I     107           -
LGA    -       -      L     108           -
LGA    -       -      P     109           -
LGA    -       -      E     110           -
LGA    -       -      R     111           -
LGA    -       -      F     112           -
LGA    -       -      I     113           -
LGA    -       -      F     114           -
LGA    -       -      T     115           -
LGA    -       -      E     116           -
LGA    -       -      D     117           -
LGA    -       -      K     290           -
LGA    -       -      Y     291           -
LGA    -       -      M     292           -
LGA    -       -      A     293           -
LGA    -       -      C     294           -
LGA    -       -      L     295           -
LGA    -       -      K     296           -
LGA    -       -      D     297           -
LGA    -       -      H     298           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8  126    5.0      8    1.86    12.50      5.757     0.408

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.139836 * X  +  -0.988947 * Y  +   0.049301 * Z  +  80.185982
  Y_new =  -0.941082 * X  +  -0.148221 * Y  +  -0.303965 * Z  + 104.942917
  Z_new =   0.307913 * X  +  -0.003891 * Y  +  -0.951407 * Z  +  -4.908119 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.137503    0.004090  [ DEG:  -179.7657      0.2343 ]
  Theta =  -0.312999   -2.828594  [ DEG:   -17.9335   -162.0665 ]
  Phi   =  -1.423285    1.718307  [ DEG:   -81.5482     98.4518 ]
 
# 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: T0372TS261_1_3-D1                             
REMARK     2: T0372_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0372TS261_1_3-D1.T0372_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8  126   5.0    8   1.86   12.50   5.757
REMARK  ---------------------------------------------------------- 
MOLECULE T0372TS261_1_3-D1
REMARK PARENT number 3
PFRMAT TS
TARGET T0372
PARENT 2fck_A
ATOM   1019  N   LYS   290      31.763  58.347  -5.114  1.00  1.00
ATOM   1020  CA  LYS   290      31.789  57.771  -6.463  1.00  1.00
ATOM   1021  C   LYS   290      32.500  58.630  -7.500  1.00  1.00
ATOM   1022  O   LYS   290      32.153  58.678  -8.688  1.00  1.00
ATOM   1023  CB  LYS   290      30.327  57.469  -6.920  1.00  1.00
ATOM   1024  N   TYR   291      33.552  59.341  -7.076  1.00  1.00
ATOM   1025  CA  TYR   291      34.174  60.288  -7.974  1.00  1.00
ATOM   1026  C   TYR   291      35.182  59.697  -9.008  1.00  1.00
ATOM   1027  O   TYR   291      35.486  60.308 -10.025  1.00  1.00
ATOM   1028  CB  TYR   291      34.796  61.431  -7.133  1.00  1.00
ATOM   1029  N   MET   292      35.739  58.506  -8.748  1.00  3.25
ATOM   1030  CA  MET   292      36.646  57.925  -9.754  1.00  3.25
ATOM   1031  C   MET   292      36.514  56.404  -9.758  1.00  3.25
ATOM   1032  O   MET   292      35.942  55.847  -8.845  1.00  3.25
ATOM   1033  CB  MET   292      38.130  58.372  -9.559  1.00  3.25
ATOM   1034  N   ALA   293      37.033  55.755 -10.804  1.00  4.83
ATOM   1035  CA  ALA   293      37.005  54.289 -10.856  1.00  4.83
ATOM   1036  C   ALA   293      38.372  53.681 -10.495  1.00  4.83
ATOM   1037  O   ALA   293      39.396  54.149 -10.989  1.00  4.83
ATOM   1038  CB  ALA   293      36.598  53.818 -12.254  1.00  4.83
ATOM   1039  N   CYS   294      38.353  52.660  -9.637  1.00  5.25
ATOM   1040  CA  CYS   294      39.498  51.751  -9.466  1.00  5.25
ATOM   1041  C   CYS   294      39.072  50.301  -9.647  1.00  5.25
ATOM   1042  O   CYS   294      38.238  49.794  -8.878  1.00  5.25
ATOM   1043  CB  CYS   294      40.179  51.926  -8.114  1.00  5.25
ATOM   1044  N   LYS   296      39.649  49.647 -10.665  1.00  4.72
ATOM   1045  CA  LYS   296      39.323  48.250 -11.012  1.00  4.72
ATOM   1046  C   LYS   296      37.856  48.115 -11.451  1.00  4.72
ATOM   1047  O   LYS   296      37.166  47.164 -11.066  1.00  4.72
ATOM   1048  CB  LYS   296      39.635  47.298  -9.833  1.00  4.72
ATOM   1049  N   ASP   297      37.403  49.079 -12.263  1.00  4.58
ATOM   1050  CA  ASP   297      36.008  49.183 -12.701  1.00  4.58
ATOM   1051  C   ASP   297      34.940  49.466 -11.637  1.00  4.58
ATOM   1052  O   ASP   297      33.759  49.442 -11.956  1.00  4.58
ATOM   1053  CB  ASP   297      35.666  47.877 -13.438  1.00  4.58
ATOM   1054  N   HIS   298      35.330  49.726 -10.382  1.00  4.16
ATOM   1055  CA  HIS   298      34.374  50.080  -9.289  1.00  4.16
ATOM   1056  C   HIS   298      34.564  51.517  -8.780  1.00  4.16
ATOM   1057  O   HIS   298      35.692  52.019  -8.784  1.00  4.16
ATOM   1058  CB  HIS   298      34.541  49.159  -8.109  1.00  4.16
TER
END
