
#######################################################
#                                                     #
#                        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   20 (   20),  selected   20 , name T0330TS464_3_2-D2
# Molecule2: number of CA atoms   72 (  556),  selected   72 , name T0330_D2.pdb
# PARAMETERS: T0330TS464_3_2-D2.T0330_D2.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    V      17      V      17           -
LGA    E      18      E      18           -
LGA    S      19      S      19           -
LGA    M      20      M      20           -
LGA    N      21      N      21           -
LGA    R      22      R      22           -
LGA    -       -      R      23           -
LGA    E      36      V      24          4.926
LGA    G      37      L      25          1.424
LGA    S      38      A      26          2.522
LGA    -       -      D      27           -
LGA    -       -      A      28           -
LGA    T      39      L      29          1.020
LGA    G      40      I      30          4.087
LGA    -       -      E      31           -
LGA    S      41      V      32          1.527
LGA    -       -      Y      33           -
LGA    -       -      G      34           -
LGA    -       -      T      35           -
LGA    -       -      E      36           -
LGA    -       -      G      37           -
LGA    -       -      S      38           -
LGA    -       -      T      39           -
LGA    -       -      D      43           -
LGA    -       -      F      44           -
LGA    -       -      S      45           -
LGA    -       -      G      46           -
LGA    -       -      K      47           -
LGA    -       -      M      48           -
LGA    -       -      D      49           -
LGA    -       -      G      50           -
LGA    -       -      A      51           -
LGA    -       -      I      52           -
LGA    -       -      I      53           -
LGA    -       -      Y      54           -
LGA    -       -      E      55           -
LGA    -       -      V      56           -
LGA    -       -      L      57           -
LGA    -       -      S      58           -
LGA    -       -      N      59           -
LGA    -       -      V      60           -
LGA    -       -      G      61           -
LGA    -       -      L      62           -
LGA    -       -      E      63           -
LGA    -       -      R      64           -
LGA    -       -      A      65           -
LGA    -       -      E      66           -
LGA    -       -      I      67           -
LGA    -       -      A      68           -
LGA    -       -      D      69           -
LGA    H      42      K      70          2.815
LGA    F      44      F      71          1.594
LGA    -       -      D      72           -
LGA    S      45      K      73          4.095
LGA    G      46      A      74          1.755
LGA    -       -      K      75           -
LGA    -       -      E      76           -
LGA    K      47      T      77          3.149
LGA    M      48      Y      78          3.841
LGA    D      49      -       -           -
LGA    G      50      I      79          2.250
LGA    -       -      A      80           -
LGA    -       -      L      81           -
LGA    -       -      F      82           -
LGA    -       -      R      83           -
LGA    -       -      E      84           -
LGA    -       -      R      85           -
LGA    -       -      A      86           -
LGA    -       -      R      87           -
LGA    -       -      R      88           -
LGA    -       -      E      89           -
LGA    -       -      D      90           -
LGA    -       -      I      91           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   20   72    5.0     13    2.95     7.69     12.022     0.427

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.060962 * X  +   0.776013 * Y  +   0.627764 * Z  + -35.471550
  Y_new =  -0.993168 * X  +  -0.015540 * Y  +   0.115656 * Z  +  98.784698
  Z_new =   0.099506 * X  +  -0.630526 * Y  +   0.769763 * Z  +  -5.682200 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.686289    2.455303  [ DEG:   -39.3215    140.6785 ]
  Theta =  -0.099671   -3.041921  [ DEG:    -5.7107   -174.2893 ]
  Phi   =  -1.509492    1.632101  [ DEG:   -86.4875     93.5125 ]
 
# 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: T0330TS464_3_2-D2                             
REMARK     2: T0330_D2.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0330TS464_3_2-D2.T0330_D2.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   20   72   5.0   13   2.95    7.69  12.022
REMARK  ---------------------------------------------------------- 
MOLECULE T0330TS464_3_2-D2
REMARK PARENT number 2
PFRMAT TS
TARGET T0330
PARENT N/A
ATOM     13  CA  VAL    17      26.416  45.563 -13.188  1.00  0.00
ATOM     14  CA  GLU    18      27.871  49.077 -12.977  1.00  0.00
ATOM     15  CA  SER    19      31.166  50.265 -14.446  1.00  0.00
ATOM     16  CA  MET    20      33.366  51.638 -11.679  1.00  0.00
ATOM     17  CA  ASN    21      36.603  52.460 -13.512  1.00  0.00
ATOM     18  CA  ARG    22      36.399  56.141 -12.540  1.00  0.00
ATOM     19  CA  GLU    36      19.189  39.558   3.522  1.00  0.00
ATOM     20  CA  GLY    37      18.013  38.806   0.020  1.00  0.00
ATOM     21  CA  SER    38      18.848  39.266  -3.689  1.00  0.00
ATOM     22  CA  THR    39      20.760  42.359  -4.765  1.00  0.00
ATOM     23  CA  GLY    40      18.528  43.302  -7.688  1.00  0.00
ATOM     24  CA  SER    41      20.122  46.579  -8.697  1.00  0.00
ATOM     25  CA  HIS    42      23.503  48.260  -8.311  1.00  0.00
ATOM     26  CA  PHE    44      24.005  52.016  -4.032  1.00  0.00
ATOM     27  CA  SER    45      22.126  48.718  -3.894  1.00  0.00
ATOM     28  CA  GLY    46      18.439  47.846  -4.174  1.00  0.00
ATOM     29  CA  LYS    47      17.364  44.525  -2.697  1.00  0.00
ATOM     30  CA  MET    48      14.563  42.021  -2.399  1.00  0.00
ATOM     31  CA  ASP    49      14.919  42.525   1.329  1.00  0.00
ATOM     32  CA  GLY    50      13.031  45.819   0.799  1.00  0.00
TER
END
