
#######################################################
#                                                     #
#                        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 T0358TS102_2
# Molecule2: number of CA atoms   66 ( 1047),  selected   66 , name T0358.pdb
# PARAMETERS: T0358TS102_2.T0358.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    -       -      G      10           -
LGA    -       -      P      11           -
LGA    -       -      F      12           -
LGA    -       -      T      13           -
LGA    -       -      R      14           -
LGA    -       -      R      15           -
LGA    -       -      Q      16           -
LGA    -       -      A      17           -
LGA    -       -      Q      18           -
LGA    -       -      A      19           -
LGA    -       -      V      20           -
LGA    -       -      T      21           -
LGA    -       -      T      22           -
LGA    -       -      T      23           -
LGA    -       -      Y      24           -
LGA    -       -      S      25           -
LGA    -       -      N      26           -
LGA    -       -      I      27           -
LGA    -       -      T      28           -
LGA    -       -      L      29           -
LGA    -       -      E      30           -
LGA    -       -      D      31           -
LGA    -       -      D      32           -
LGA    -       -      Q      33           -
LGA    -       -      G      34           -
LGA    -       -      S      35           -
LGA    -       -      H      36           -
LGA    -       -      F      37           -
LGA    -       -      R      38           -
LGA    -       -      L      39           -
LGA    -       -      V      40           -
LGA    -       -      V      41           -
LGA    -       -      R      42           -
LGA    -       -      D      43           -
LGA    -       -      T      44           -
LGA    -       -      E      45           -
LGA    -       -      G      46           -
LGA    -       -      R      47           -
LGA    -       -      M      48           -
LGA    -       -      V      49           -
LGA    -       -      W      50           -
LGA    -       -      R      51           -
LGA    -       -      A      52           -
LGA    -       -      W      53           -
LGA    -       -      N      54           -
LGA    -       -      F      55           -
LGA    -       -      E      56           -
LGA    -       -      P      57           -
LGA    -       -      D      58           -
LGA    -       -      A      59           -
LGA    -       -      G      60           -
LGA    -       -      E      61           -
LGA    H      83      G      62          1.321
LGA    H      84      L      63          0.761
LGA    H      85      N      64          1.036
LGA    -       -      R      65           -
LGA    -       -      Y      66           -
LGA    H      86      I      67          0.701
LGA    H      87      R      68          0.664
LGA    -       -      T      69           -
LGA    -       -      S      70           -
LGA    -       -      G      71           -
LGA    -       -      I      72           -
LGA    -       -      R      73           -
LGA    -       -      T      74           -
LGA    -       -      D      75           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    5   66    5.0      5    0.93     0.00      7.456     0.485

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.466578 * X  +  -0.833406 * Y  +  -0.296207 * Z  +  -4.645539
  Y_new =  -0.735060 * X  +  -0.551626 * Y  +   0.394203 * Z  +  41.404537
  Z_new =  -0.491927 * X  +   0.033804 * Y  +  -0.869980 * Z  +  44.161037 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   3.102757   -0.038836  [ DEG:   177.7749     -2.2251 ]
  Theta =   0.514302    2.627291  [ DEG:    29.4673    150.5327 ]
  Phi   =  -1.005217    2.136375  [ DEG:   -57.5947    122.4053 ]
 
# 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: T0358TS102_2                                  
REMARK     2: T0358.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0358TS102_2.T0358.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    5   66   5.0    5   0.93    0.00   7.456
REMARK  ---------------------------------------------------------- 
MOLECULE T0358TS102_2
PFRMAT TS
TARGET T0358
MODEL 2
PARENT 2aml_A
ATOM      1  N   HIS    83       1.907   2.582   9.374  1.00  1.00
ATOM      2  CA  HIS    83       2.929   1.980   8.455  1.00  1.00
ATOM      3  C   HIS    83       2.496   0.527   8.214  1.00  1.00
ATOM      4  O   HIS    83       2.372  -0.259   9.159  1.00  1.00
ATOM      5  CB  HIS    83       4.352   1.984   9.070  1.00  1.00
ATOM      6  N   HIS    84       2.231   0.170   6.953  1.00  1.00
ATOM      7  CA  HIS    84       1.866  -1.195   6.579  1.00  1.00
ATOM      8  C   HIS    84       3.110  -2.062   6.687  1.00  1.00
ATOM      9  O   HIS    84       4.125  -1.832   5.982  1.00  1.00
ATOM     10  CB  HIS    84       1.321  -1.199   5.147  1.00  1.00
ATOM     11  N   HIS    85       3.050  -3.013   7.617  1.00  1.00
ATOM     12  CA  HIS    85       4.076  -4.049   7.713  1.00  1.00
ATOM     13  C   HIS    85       3.356  -5.376   7.558  1.00  1.00
ATOM     14  O   HIS    85       2.580  -5.761   8.432  1.00  1.00
ATOM     15  CB  HIS    85       4.838  -3.990   9.045  1.00  1.00
ATOM     16  N   HIS    86       3.552  -6.012   6.387  1.00  1.00
ATOM     17  CA  HIS    86       2.816  -7.242   5.986  1.00  1.00
ATOM     18  C   HIS    86       2.776  -8.327   7.089  1.00  1.00
ATOM     19  O   HIS    86       1.739  -8.947   7.294  1.00  1.00
ATOM     20  CB  HIS    86       3.470  -7.783   4.689  1.00  1.00
ATOM     21  N   HIS    87       3.890  -8.527   7.790  1.00  1.00
ATOM     22  CA  HIS    87       3.952  -9.592   8.784  1.00  1.00
ATOM     23  C   HIS    87       3.422  -9.147  10.149  1.00  1.00
ATOM     24  O   HIS    87       3.288  -9.980  11.035  1.00  1.00
ATOM     25  CB  HIS    87       5.362 -10.176   8.880  1.00  1.00
TER
END
