
#######################################################
#                                                     #
#                        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 (   99),  selected    9 , name T0322TS239_4_2
# Molecule2: number of CA atoms  142 ( 1089),  selected    9 , name T0322.pdb
# PARAMETERS: T0322TS239_4_2.T0322.pdb  -3  -ie  -o1  -sda  -d:4  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        12 - 19          2.40    12.73
  LONGEST_CONTINUOUS_SEGMENT:     8        13 - 142         4.68     5.79
  LCS_AVERAGE:      5.63

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        13 - 18          1.88    12.69
  LONGEST_CONTINUOUS_SEGMENT:     6        14 - 19          1.98    11.47
  LCS_AVERAGE:      3.99

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5        14 - 18          0.64    12.16
  LCS_AVERAGE:      2.90

LCS_GDT    MOLECULE-1    MOLECULE-2    LENGTH_OF_THE
LCS_GDT     RESIDUE       RESIDUE         CONTINUOUS
LCS_GDT   NAME NUMBER   NAME NUMBER          SEGMENT     GLOBAL DISTANCE TEST - GDT_DATA_COLUMNS                             NUMBER OF THE RESIDUES:  142
LCS_GDT     A      12     A      12      3    4    8     3    3    4    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     I      13     I      13      3    6    8     3    3    3    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     P      14     P      14      5    6    8     4    5    5    5    5    5    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     E      15     E      15      5    6    8     4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     G      16     G      16      5    6    8     4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     F      17     F      17      5    6    8     4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     S      18     S      18      5    6    8     4    5    5    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     Q      19     Q      19      3    6    8     2    3    4    5    6    7    7    8    8    8    8    8    8    8    8    8    9    9    9    9 
LCS_GDT     S     142     S     142      3    5    8     0    3    3    4    5    5    5    6    6    6    7    7    7    8    8    8    9    9    9    9 
LCS_AVERAGE  LCS_A:   4.17  (   2.90    3.99    5.63 )

GLOBAL_DISTANCE_TEST (the largest set of residues that can fit under specified DISTANCE_CUTOFF)
GDT DIST_CUTOFF  0.50   1.00   1.50   2.00   2.50   3.00   3.50   4.00   4.50   5.00   5.50   6.00   6.50   7.00   7.50   8.00   8.50   9.00   9.50  10.00
GDT NUMBER_CA      4      5      5      5      6      7      7      8      8      8      8      8      8      8      8      8      9      9      9      9 
GDT PERCENT_CA   2.82   3.52   3.52   3.52   4.23   4.93   4.93   5.63   5.63   5.63   5.63   5.63   5.63   5.63   5.63   5.63   6.34   6.34   6.34   6.34
GDT RMS_LOCAL    0.28   0.64   0.64   0.64   1.66   1.98   1.98   2.40   2.40   2.40   2.40   2.40   2.40   2.40   2.40   2.40   5.48   5.48   5.48   5.48
GDT RMS_ALL_CA  12.72  12.16  12.16  12.16  12.85  12.67  12.67  12.73  12.73  12.73  12.73  12.73  12.73  12.73  12.73  12.73   5.48   5.48   5.48   5.48

#      Molecule1      Molecule2       DISTANCE
LGA    A      12      A      12          1.874
LGA    I      13      I      13          2.255
LGA    P      14      P      14          3.988
LGA    E      15      E      15          2.431
LGA    G      16      G      16          0.676
LGA    F      17      F      17          1.464
LGA    S      18      S      18          3.153
LGA    Q      19      Q      19          2.475
LGA    S     142      S     142         39.094

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   20  142    4.0      8    2.40     4.577     4.593     0.320

LGA_LOCAL      RMSD =  2.399  Number of atoms =    8  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 13.239  Number of atoms =    9 
Std_ALL_ATOMS  RMSD =  5.484  (standard rmsd on all 9 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.927241 * X  +  -0.236421 * Y  +  -0.290396 * Z  +   1.999850
  Y_new =   0.316664 * X  +  -0.908974 * Y  +  -0.271090 * Z  +   4.971493
  Z_new =  -0.199871 * X  +  -0.343324 * Y  +   0.917704 * Z  +   2.738247 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -0.357992    2.783601  [ DEG:   -20.5114    159.4886 ]
  Theta =   0.201226    2.940366  [ DEG:    11.5294    168.4706 ]
  Phi   =   2.812499   -0.329093  [ DEG:   161.1443    -18.8557 ]
 
# 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: T0322TS239_4_2                                
REMARK     2: T0322.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_4_2.T0322.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   20  142   4.0    8   2.40   4.593     5.48
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_4_2
REMARK PARENT number 2
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM      1  N   MET     1     -11.904 -10.056   8.330  1.00  9.99
ATOM      2  CA  MET     1     -11.358 -11.015   7.365  1.00  9.99
ATOM      3  C   MET     1     -11.514 -10.533   5.927  1.00  9.99
ATOM      4  O   MET     1     -12.617 -10.512   5.386  1.00  9.99
ATOM      5  CB  MET     1     -12.014 -12.393   7.521  1.00  9.99
ATOM      6  N   SER     2     -10.406 -10.201   5.272  1.00  9.99
ATOM      7  CA  SER     2     -10.511  -9.629   3.908  1.00  9.99
ATOM      8  C   SER     2     -10.462 -10.676   2.801  1.00  9.99
ATOM      9  O   SER     2     -10.893 -10.421   1.684  1.00  9.99
ATOM     10  CB  SER     2      -9.428  -8.546   3.683  1.00  9.99
ATOM     11  N   ASP     3     -10.239 -16.149  -0.718  1.00  9.99
ATOM     12  CA  ASP     3      -9.707 -17.469  -1.019  1.00  9.99
ATOM     13  C   ASP     3      -8.960 -17.923   0.194  1.00  9.99
ATOM     14  O   ASP     3      -8.329 -17.131   0.882  1.00  9.99
ATOM     15  CB  ASP     3      -8.723 -17.437  -2.188  1.00  9.99
ATOM     16  N   ASP     4      -9.006 -19.225   0.451  1.00  9.99
ATOM     17  CA  ASP     4      -8.193 -19.787   1.525  1.00  9.99
ATOM     18  C   ASP     4      -6.897 -20.355   0.937  1.00  9.99
ATOM     19  O   ASP     4      -6.884 -20.956  -0.132  1.00  9.99
ATOM     20  CB  ASP     4      -8.982 -20.861   2.297  1.00  9.99
ATOM     21  N   LEU     5      -5.800 -20.114   1.627  1.00  9.99
ATOM     22  CA  LEU     5      -4.513 -20.685   1.255  1.00  9.99
ATOM     23  C   LEU     5      -3.701 -20.966   2.511  1.00  9.99
ATOM     24  O   LEU     5      -3.799 -20.234   3.491  1.00  9.99
ATOM     25  CB  LEU     5      -3.764 -19.734   0.249  1.00  9.99
ATOM     26  N   THR     6      -2.947 -22.064   2.500  1.00  9.99
ATOM     27  CA  THR     6      -1.984 -22.322   3.563  1.00  9.99
ATOM     28  C   THR     6      -0.692 -21.592   3.240  1.00  9.99
ATOM     29  O   THR     6      -0.452 -21.243   2.076  1.00  9.99
ATOM     30  CB  THR     6      -1.657 -23.813   3.671  1.00  9.99
ATOM     31  N   ASP     7       0.144 -21.400   4.259  1.00  9.99
ATOM     32  CA  ASP     7       1.489 -20.866   4.058  1.00  9.99
ATOM     33  C   ASP     7       2.290 -21.754   3.121  1.00  9.99
ATOM     34  O   ASP     7       3.029 -21.287   2.272  1.00  9.99
ATOM     35  CB  ASP     7       2.228 -20.682   5.386  1.00  9.99
ATOM     36  N   ALA     8       2.118 -23.064   3.272  1.00  9.99
ATOM     37  CA  ALA     8       2.752 -24.022   2.390  1.00  9.99
ATOM     38  C   ALA     8       2.452 -23.786   0.905  1.00  9.99
ATOM     39  O   ALA     8       3.369 -23.776   0.078  1.00  9.99
ATOM     40  CB  ALA     8       2.311 -25.440   2.780  1.00  9.99
ATOM     41  N   GLN     9       1.172 -23.646   0.555  1.00  9.99
ATOM     42  CA  GLN     9       0.781 -23.496  -0.849  1.00  9.99
ATOM     43  C   GLN     9       1.205 -22.119  -1.397  1.00  9.99
ATOM     44  O   GLN     9       1.555 -21.991  -2.576  1.00  9.99
ATOM     45  CB  GLN     9      -0.736 -23.749  -1.040  1.00  9.99
ATOM     46  N   THR    10       1.191 -21.119  -0.516  1.00  9.99
ATOM     47  CA  THR    10       1.674 -19.769  -0.831  1.00  9.99
ATOM     48  C   THR    10       3.166 -19.838  -1.202  1.00  9.99
ATOM     49  O   THR    10       3.595 -19.356  -2.251  1.00  9.99
ATOM     50  CB  THR    10       1.482 -18.867   0.388  1.00  9.99
ATOM     51  N   ALA    11       3.952 -20.496  -0.351  1.00  9.99
ATOM     52  CA  ALA    11       5.382 -20.625  -0.582  1.00  9.99
ATOM     53  C   ALA    11       5.741 -21.500  -1.774  1.00  9.99
ATOM     54  O   ALA    11       6.776 -21.295  -2.399  1.00  9.99
ATOM     55  CB  ALA    11       6.086 -21.064   0.694  1.00  9.99
ATOM     56  N   ALA    12       4.869 -22.461  -2.106  1.00  9.99
ATOM     57  CA  ALA    12       5.097 -23.302  -3.268  1.00  9.99
ATOM     58  C   ALA    12       5.071 -22.526  -4.583  1.00  9.99
ATOM     59  O   ALA    12       5.678 -22.943  -5.562  1.00  9.99
ATOM     60  CB  ALA    12       4.090 -24.450  -3.305  1.00  9.99
ATOM     61  N   ILE    13       4.398 -21.372  -4.594  1.00  9.99
ATOM     62  CA  ILE    13       4.243 -20.596  -5.829  1.00  9.99
ATOM     63  C   ILE    13       5.563 -20.100  -6.415  1.00  9.99
ATOM     64  O   ILE    13       5.709 -19.946  -7.631  1.00  9.99
ATOM     65  CB  ILE    13       3.371 -19.369  -5.563  1.00  9.99
ATOM     66  N   PRO    14       6.512 -19.837  -5.523  1.00  9.99
ATOM     67  CA  PRO    14       7.764 -19.185  -5.857  1.00  9.99
ATOM     68  C   PRO    14       8.803 -20.081  -6.502  1.00  9.99
ATOM     69  O   PRO    14       9.819 -19.589  -6.991  1.00  9.99
ATOM     70  CB  PRO    14       8.329 -18.552  -4.575  1.00  9.99
ATOM     71  N   GLU    15       8.581 -21.402  -6.501  1.00  9.99
ATOM     72  CA  GLU    15       9.604 -22.346  -6.990  1.00  9.99
ATOM     73  C   GLU    15       9.868 -22.161  -8.466  1.00  9.99
ATOM     74  O   GLU    15       8.937 -22.214  -9.280  1.00  9.99
ATOM     75  CB  GLU    15       9.181 -23.813  -6.758  1.00  9.99
ATOM     76  N   GLY    16      11.134 -21.935  -8.805  1.00  9.99
ATOM     77  CA  GLY    16      11.537 -21.788 -10.184  1.00  9.99
ATOM     78  C   GLY    16      11.273 -20.405 -10.769  1.00  9.99
ATOM     79  O   GLY    16      11.372 -20.226 -11.983  1.00  9.99
ATOM     80  N   PHE    17      10.949 -19.434  -9.910  1.00  9.99
ATOM     81  CA  PHE    17      10.759 -18.039 -10.366  1.00  9.99
ATOM     82  C   PHE    17      11.451 -17.094  -9.402  1.00  9.99
ATOM     83  O   PHE    17      12.148 -17.526  -8.497  1.00  9.99
ATOM     84  CB  PHE    17       9.273 -17.705 -10.648  1.00  9.99
ATOM     85  N   SER    18      11.240 -15.791  -9.572  1.00  9.99
ATOM     86  CA  SER    18      12.050 -14.828  -8.837  1.00  9.99
ATOM     87  C   SER    18      11.870 -14.946  -7.318  1.00  9.99
ATOM     88  O   SER    18      12.823 -14.767  -6.565  1.00  9.99
ATOM     89  CB  SER    18      11.744 -13.398  -9.298  1.00  9.99
ATOM     90  N   GLN    19      10.642 -15.193  -6.879  1.00  9.99
ATOM     91  CA  GLN    19      10.377 -15.295  -5.451  1.00  9.99
ATOM     92  C   GLN    19      11.267 -16.419  -4.845  1.00  9.99
ATOM     93  O   GLN    19      11.908 -16.219  -3.819  1.00  9.99
ATOM     94  CB  GLN    19       8.871 -15.523  -5.148  1.00  9.99
ATOM    639  N   SER   142     -11.412  -9.966 -14.983  1.00  9.99
ATOM    640  CA  SER   142     -12.597 -10.782 -14.812  1.00  9.99
ATOM    641  C   SER   142     -12.430 -12.059 -15.593  1.00  9.99
ATOM    642  O   SER   142     -12.938 -13.098 -15.195  1.00  9.99
ATOM    643  CB  SER   142     -13.869  -9.996 -15.243  1.00  9.99
TER
END
