
#######################################################
#                                                     #
#                        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   46 (   46),  selected   46 , name T0363TS393_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   46 , name T0363_D1.pdb
# PARAMETERS: T0363TS393_1-D1.T0363_D1.pdb  -4  -ie  -o1  -sia  -d:5  
# Search for Atom-Atom correspondence
# Structure alignment analysis 

#      Molecule1      Molecule2       DISTANCE
LGA    N      11      N      11           #
LGA    Q      12      Q      12           #
LGA    I      13      I      13          2.830
LGA    N      14      N      14          4.814
LGA    I      15      I      15          1.956
LGA    E      16      E      16          0.477
LGA    I      17      I      17          2.043
LGA    A      18      A      18          4.488
LGA    Y      19      -       -           -
LGA    A      20      Y      19          4.620
LGA    F      21      A      20          2.866
LGA    P      22      F      21          2.688
LGA    E      23      P      22          1.449
LGA    R      24      E      23          2.849
LGA    Y      25      R      24          0.361
LGA    Y      26      Y      25          1.260
LGA    L      27      Y      26          2.759
LGA    K      28      L      27          1.953
LGA    S      29      K      28          2.593
LGA    F      30      S      29          1.273
LGA    Q      31      F      30          1.504
LGA    V      32      Q      31          2.182
LGA    D      33      -       -           -
LGA    E      34      -       -           -
LGA    G      35      -       -           -
LGA    I      36      -       -           -
LGA    T      37      V      32          4.261
LGA    V      38      D      33           #
LGA    -       -      E      34           -
LGA    -       -      G      35           -
LGA    Q      39      I      36          4.407
LGA    T      40      T      37           -
LGA    A      41      V      38           -
LGA    -       -      Q      39           -
LGA    -       -      T      40           -
LGA    I      42      A      41          1.112
LGA    -       -      I      42           -
LGA    T      43      T      43          3.324
LGA    Q      44      Q      44          1.783
LGA    -       -      S      45           -
LGA    S      45      G      46          4.656
LGA    G      46      I      47           #
LGA    I      47      -       -           -
LGA    L      48      L      48          2.411
LGA    S      49      S      49          4.011
LGA    Q      50      Q      50           #
LGA    -       -      F      51           -
LGA    F      51      P      52           #
LGA    P      52      E      53           -
LGA    E      53      I      54           #
LGA    I      54      D      55          1.808
LGA    D      55      L      56          2.129
LGA    L      56      -       -           -

#              N1   N2   DIST      N    RMSD   Seq_Id      LGA_S     LGA_Q 
SUMMARY(LGA)   46   46    5.0     29    2.87    37.93     41.609     0.975

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.000808 * X  +   0.932719 * Y  +   0.360603 * Z  +  22.707056
  Y_new =  -0.269879 * X  +  -0.347019 * Y  +   0.898189 * Z  +  12.566524
  Z_new =   0.962894 * X  +  -0.098045 * Y  +   0.251441 * Z  +   4.587351 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.371797    2.769796  [ DEG:   -21.3024    158.6976 ]
  Theta =  -1.297527   -1.844065  [ DEG:   -74.3428   -105.6572 ]
  Phi   =  -1.567803    1.573790  [ DEG:   -89.8285     90.1715 ]
 
# 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: T0363TS393_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   Structure alignment analysis
REMARK   Search for Atom-Atom correspondence
REMARK   LGA parameters: T0363TS393_1-D1.T0363_D1.pdb -4 -ie -o1 -sia -d:5 
REMARK   #CA        N1   N2  DIST    N   RMSD  Seq_Id   LGA_S
REMARK   SUMMARY:   46   46   5.0   29   2.87   37.93  41.609
REMARK  ---------------------------------------------------------- 
MOLECULE T0363TS393_1-D1
PFRMAT TS
TARGET T0363
MODEL 1
PARENT N/A
ATOM     11  CA  ASN    11      12.122   6.394  15.460  1.00 25.00           C
ATOM     12  CA  GLN    12      13.636   6.701  12.007  1.00 25.00           C
ATOM     13  CA  ILE    13      16.276   8.331   9.781  1.00 25.00           C
ATOM     14  CA  ASN    14      19.783   9.755   9.964  1.00 25.00           C
ATOM     15  CA  ILE    15      21.743  10.694   6.822  1.00 25.00           C
ATOM     16  CA  GLU    16      21.508  13.900   4.701  1.00 25.00           C
ATOM     17  CA  ILE    17      23.444  16.819   3.128  1.00 25.00           C
ATOM     18  CA  ALA    18      25.812  15.648   0.377  1.00 25.00           C
ATOM     19  CA  TYR    19      27.864  16.492  -2.760  1.00 25.00           C
ATOM     20  CA  ALA    20      30.504  18.628  -1.047  1.00 25.00           C
ATOM     21  CA  PHE    21      30.100  22.401  -1.408  1.00 25.00           C
ATOM     22  CA  PRO    22      29.368  25.966  -2.413  1.00 25.00           C
ATOM     23  CA  GLU    23      30.276  28.303  -5.218  1.00 25.00           C
ATOM     24  CA  ARG    24      32.166  25.835  -7.387  1.00 25.00           C
ATOM     25  CA  TYR    25      29.177  23.596  -6.869  1.00 25.00           C
ATOM     26  CA  TYR    26      26.178  22.575  -4.692  1.00 25.00           C
ATOM     27  CA  LEU    27      25.332  20.663  -1.474  1.00 25.00           C
ATOM     28  CA  LYS    28      22.149  18.582  -1.379  1.00 25.00           C
ATOM     29  CA  SER    29      20.962  14.956  -1.028  1.00 25.00           C
ATOM     30  CA  PHE    30      19.774  11.668   0.489  1.00 25.00           C
ATOM     31  CA  GLN    31      20.477   8.449   2.332  1.00 25.00           C
ATOM     32  CA  VAL    32      18.426   6.257   4.749  1.00 25.00           C
ATOM     33  CA  ASP    33      19.164   2.710   3.614  1.00 25.00           C
ATOM     34  CA  GLU    34      19.740   1.559   7.198  1.00 25.00           C
ATOM     35  CA  GLY    35      21.665  -1.470   5.795  1.00 25.00           C
ATOM     36  CA  ILE    36      24.652   0.871   6.129  1.00 25.00           C
ATOM     37  CA  THR    37      24.336   3.585   3.507  1.00 25.00           C
ATOM     38  CA  VAL    38      23.741   5.992   6.374  1.00 25.00           C
ATOM     39  CA  GLN    39      26.287   5.068   9.083  1.00 25.00           C
ATOM     40  CA  THR    40      28.744   3.873   6.399  1.00 25.00           C
ATOM     41  CA  ALA    41      28.279   7.153   4.477  1.00 25.00           C
ATOM     42  CA  ILE    42      28.917   9.150   7.682  1.00 25.00           C
ATOM     43  CA  THR    43      32.094   7.118   8.345  1.00 25.00           C
ATOM     44  CA  GLN    44      33.287   7.768   4.764  1.00 25.00           C
ATOM     45  CA  SER    45      32.629  11.516   5.199  1.00 25.00           C
ATOM     46  CA  GLY    46      33.613  13.488   8.284  1.00 25.00           C
ATOM     47  CA  ILE    47      33.727  17.033   6.972  1.00 25.00           C
ATOM     48  CA  LEU    48      35.990  16.270   3.999  1.00 25.00           C
ATOM     49  CA  SER    49      39.258  15.645   2.104  1.00 25.00           C
ATOM     50  CA  GLN    50      38.973  11.890   2.799  1.00 25.00           C
ATOM     51  CA  PHE    51      37.871  11.517   6.392  1.00 25.00           C
ATOM     52  CA  PRO    52      41.522  12.449   7.190  1.00 25.00           C
ATOM     53  CA  GLU    53      41.025  14.641  10.242  1.00 25.00           C
ATOM     54  CA  ILE    54      39.385  18.080   9.749  1.00 25.00           C
ATOM     55  CA  ASP    55      37.410  16.926  12.839  1.00 25.00           C
ATOM     56  CA  LEU    56      36.124  13.387  12.618  1.00 25.00           C
TER
END
