
#######################################################
#                                                     #
#                        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 (   63),  selected    8 , name T0348TS622_1_2
# Molecule2: number of CA atoms   61 (  465),  selected   61 , name T0348.pdb
# PARAMETERS: T0348TS622_1_2.T0348.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    -       -      D       2           -
LGA    -       -      A       3           -
LGA    -       -      K       4           -
LGA    -       -      F       5           -
LGA    -       -      L       6           -
LGA    -       -      E       7           -
LGA    -       -      I       8           -
LGA    -       -      L       9           -
LGA    -       -      V      10           -
LGA    -       -      C      11           -
LGA    -       -      P      12           -
LGA    -       -      L      13           -
LGA    -       -      C      14           -
LGA    -       -      K      15           -
LGA    -       -      G      16           -
LGA    -       -      P      17           -
LGA    -       -      L      18           -
LGA    -       -      V      19           -
LGA    -       -      F      20           -
LGA    -       -      D      21           -
LGA    -       -      K      22           -
LGA    -       -      S      23           -
LGA    -       -      K      24           -
LGA    -       -      D      25           -
LGA    -       -      E      26           -
LGA    -       -      L      27           -
LGA    -       -      I      28           -
LGA    -       -      C      29           -
LGA    -       -      K      30           -
LGA    -       -      G      31           -
LGA    -       -      D      32           -
LGA    -       -      R      33           -
LGA    -       -      L      34           -
LGA    -       -      A      35           -
LGA    -       -      F      36           -
LGA    -       -      P      37           -
LGA    -       -      I      38           -
LGA    -       -      K      39           -
LGA    -       -      D      40           -
LGA    -       -      G      41           -
LGA    -       -      I      42           -
LGA    -       -      P      43           -
LGA    -       -      M      44           -
LGA    -       -      M      45           -
LGA    -       -      L      46           -
LGA    -       -      E      47           -
LGA    -       -      S      48           -
LGA    -       -      E      49           -
LGA    -       -      A      50           -
LGA    -       -      R      51           -
LGA    -       -      E      52           -
LGA    A      54      L      53          1.078
LGA    P      55      A      54          0.775
LGA    E      56      P      55          0.587
LGA    E      57      E      56          1.026
LGA    E      58      E      57          0.698
LGA    V      59      E      58          0.770
LGA    K      60      V      59          1.005
LGA    L      61      K      60          1.626
LGA    -       -      L      61           -
LGA    -       -      E      62           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)    8   61    5.0      8    0.99    25.00     12.985     0.732

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.999003 * X  +  -0.036229 * Y  +  -0.026096 * Z  +  50.403000
  Y_new =  -0.019759 * X  +  -0.882849 * Y  +   0.469240 * Z  +  22.238739
  Z_new =  -0.040039 * X  +  -0.468257 * Y  +  -0.882685 * Z  +  79.791023 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -2.653850    0.487742  [ DEG:  -152.0544     27.9456 ]
  Theta =   0.040049    3.101543  [ DEG:     2.2947    177.7053 ]
  Phi   =  -0.019776    3.121816  [ DEG:    -1.1331    178.8669 ]
 
# 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: T0348TS622_1_2                                
REMARK     2: T0348.pdb                                     
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0348TS622_1_2.T0348.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:    8   61   5.0    8   0.99   25.00  12.985
REMARK  ---------------------------------------------------------- 
MOLECULE T0348TS622_1_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0348
PARENT N/A
ATOM      1  N   ALA   54        8.533  16.087  55.845 1.00  0.00
ATOM      2  CA  ALA   54        9.914  16.020  56.345 1.00  0.00
ATOM      3  C   ALA   54       10.559  14.711  55.886 1.00  0.00
ATOM      4  O   ALA   54        9.949  13.632  55.854 1.00  0.00
ATOM      5  CB  ALA   54        9.931  16.074  57.865 1.00  0.00
ATOM      6  N   PRO   55       11.825  14.764  55.514 1.00  0.00
ATOM      7  CA  PRO   55       12.510  13.545  55.063 1.00  0.00
ATOM      8  C   PRO   55       13.748  13.304  55.931 1.00  0.00
ATOM      9  O   PRO   55       14.574  14.104  56.396 1.00  0.00
ATOM     10  CB  PRO   55       12.876  13.844  53.608 1.00  0.00
ATOM     11  CG  PRO   55       13.033  15.327  53.559 1.00  0.00
ATOM     12  CD  PRO   55       12.042  15.883  54.544 1.00  0.00
ATOM     13  N   GLU   56       14.013  12.054  56.260 1.00  0.00
ATOM     14  CA  GLU   56       15.186  11.747  57.093 1.00  0.00
ATOM     15  C   GLU   56       16.452  12.244  56.393 1.00  0.00
ATOM     16  O   GLU   56       17.298  12.957  56.952 1.00  0.00
ATOM     17  CB  GLU   56       15.302  10.238  57.319 1.00  0.00
ATOM     18  CG  GLU   56       16.464   9.831  58.210 1.00  0.00
ATOM     19  CD  GLU   56       16.528   8.334  58.438 1.00  0.00
ATOM     20  OE1 GLU   56       15.653   7.615  57.909 1.00  0.00
ATOM     21  OE2 GLU   56       17.451   7.880  59.146 1.00  0.00
ATOM     22  N   GLU   57       16.624  11.880  55.136 1.00  0.00
ATOM     23  CA  GLU   57       17.818  12.320  54.400 1.00  0.00
ATOM     24  C   GLU   57       17.865  13.848  54.372 1.00  0.00
ATOM     25  O   GLU   57       18.779  14.632  54.669 1.00  0.00
ATOM     26  CB  GLU   57       17.784  11.797  52.962 1.00  0.00
ATOM     27  CG  GLU   57       19.006  12.167  52.138 1.00  0.00
ATOM     28  CD  GLU   57       18.953  11.605  50.732 1.00  0.00
ATOM     29  OE1 GLU   57       17.965  10.913  50.406 1.00  0.00
ATOM     30  OE2 GLU   57       19.899  11.854  49.955 1.00  0.00
ATOM     31  N   GLU   58       16.774  14.474  53.972 1.00  0.00
ATOM     32  CA  GLU   58       16.746  15.944  53.920 1.00  0.00
ATOM     33  C   GLU   58       17.031  16.508  55.313 1.00  0.00
ATOM     34  O   GLU   58       17.892  17.376  55.527 1.00  0.00
ATOM     35  CB  GLU   58       15.375  16.437  53.455 1.00  0.00
ATOM     36  CG  GLU   58       15.270  17.948  53.328 1.00  0.00
ATOM     37  CD  GLU   58       13.908  18.398  52.834 1.00  0.00
ATOM     38  OE1 GLU   58       13.052  17.526  52.577 1.00  0.00
ATOM     39  OE2 GLU   58       13.699  19.622  52.702 1.00  0.00
ATOM     40  N   VAL   59       16.313  16.032  56.313 1.00  0.00
ATOM     41  CA  VAL   59       16.532  16.528  57.679 1.00  0.00
ATOM     42  C   VAL   59       17.985  16.272  58.087 1.00  0.00
ATOM     43  O   VAL   59       18.835  17.040  58.563 1.00  0.00
ATOM     44  CB  VAL   59       15.610  15.822  58.691 1.00  0.00
ATOM     45  CG1 VAL   59       15.989  16.203  60.113 1.00  0.00
ATOM     46  CG2 VAL   59       14.160  16.219  58.456 1.00  0.00
ATOM     47  N   LYS   60       18.446  15.047  57.922 1.00  0.00
ATOM     48  CA  LYS   60       19.833  14.728  58.292 1.00  0.00
ATOM     49  C   LYS   60       20.791  15.617  57.496 1.00  0.00
ATOM     50  O   LYS   60       21.696  16.279  58.026 1.00  0.00
ATOM     51  CB  LYS   60       20.145  13.262  57.987 1.00  0.00
ATOM     52  CG  LYS   60       21.550  12.832  58.378 1.00  0.00
ATOM     53  CD  LYS   60       21.768  11.351  58.113 1.00  0.00
ATOM     54  CE  LYS   60       23.188  10.932  58.458 1.00  0.00
ATOM     55  NZ  LYS   60       23.424   9.488  58.180 1.00  0.00
ATOM     56  N   LEU   61       20.621  15.659  56.188 1.00  0.00
ATOM     57  CA  LEU   61       21.504  16.492  55.358 1.00  0.00
ATOM     58  C   LEU   61       21.405  17.950  55.812 1.00  0.00
ATOM     59  O   LEU   61       22.292  18.764  56.107 1.00  0.00
ATOM     60  CB  LEU   61       21.099  16.402  53.886 1.00  0.00
ATOM     61  CG  LEU   61       21.118  15.004  53.262 1.00  0.00
ATOM     62  CD1 LEU   61       20.579  15.043  51.841 1.00  0.00
ATOM     63  CD2 LEU   61       22.535  14.454  53.218 1.00  0.00
TER
END
