
#######################################################
#                                                     #
#                        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   28 (  138),  selected   17 , name T0322TS239_5_1
# Molecule2: number of CA atoms  142 ( 1089),  selected   17 , name T0322.pdb
# PARAMETERS: T0322TS239_5_1.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:    10        19 - 37          3.86    11.40
  LCS_AVERAGE:      6.46

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        30 - 37          1.64    13.65
  LCS_AVERAGE:      4.72

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        31 - 36          0.78    12.27
  LCS_AVERAGE:      3.27

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    3    6    6    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     I      13     I      13      3    6    8     3    3    3    4    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     P      14     P      14      5    6    8     4    5    5    5    5    5    7    8    8    8   10   10   11   11   12   12   14   14   15   15 
LCS_GDT     E      15     E      15      5    6    8     4    5    5    5    6    7    7    8    8    8   10   10   10   11   12   12   14   14   15   15 
LCS_GDT     G      16     G      16      5    6    8     4    5    5    5    6    7    7    8    8    8   10   10   10   10   11   12   12   12   12   14 
LCS_GDT     F      17     F      17      5    6    8     4    5    5    5    6    7    7    8    8    8   10   10   10   10   11   12   12   14   15   15 
LCS_GDT     S      18     S      18      5    6    8     4    5    5    5    6    7    7    8    8    8   10   10   10   11   12   12   14   14   15   15 
LCS_GDT     Q      19     Q      19      3    6   10     0    3    3    4    4    7    7    8   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     Q      29     Q      29      3    4   10     3    3    3    3    4    5    5    5    9    9    9    9    9    9    9   10   10   10   13   13 
LCS_GDT     I      30     I      30      3    8   10     3    3    5    7    7    8    8    8    9   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     G      31     G      31      6    8   10     3    5    6    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     P      32     P      32      6    8   10     3    5    6    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     L      33     L      33      6    8   10     3    5    6    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     F      34     F      34      6    8   10     3    5    6    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     E      35     E      35      6    8   10     3    5    6    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     H      36     H      36      6    8   10     3    4    6    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_GDT     R      37     R      37      3    8   10     3    4    5    7    7    8    9    9   10   10   11   11   11   11   12   12   14   14   15   15 
LCS_AVERAGE  LCS_A:   4.82  (   3.27    4.72    6.46 )

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      6      7      7      8      9      9     10     10     11     11     11     11     12     12     14     14     15     15 
GDT PERCENT_CA   2.82   3.52   4.23   4.93   4.93   5.63   6.34   6.34   7.04   7.04   7.75   7.75   7.75   7.75   8.45   8.45   9.86   9.86  10.56  10.56
GDT RMS_LOCAL    0.28   0.54   0.78   1.30   1.30   1.64   2.23   2.23   2.63   2.63   3.16   3.16   3.16   3.16   3.90   3.90   5.39   5.39   5.98   5.98
GDT RMS_ALL_CA  14.32  12.21  12.27  11.95  11.95  13.65   8.48   8.48   8.25   8.25   8.35   8.35   8.35   8.35   7.99   7.99   7.46   7.46   7.35   7.35

#      Molecule1      Molecule2       DISTANCE
LGA    A      12      A      12          2.944
LGA    I      13      I      13          3.444
LGA    P      14      P      14          8.733
LGA    E      15      E      15         12.638
LGA    G      16      G      16         17.914
LGA    F      17      F      17         14.429
LGA    S      18      S      18         11.584
LGA    Q      19      Q      19          4.578
LGA    Q      29      Q      29         11.628
LGA    I      30      I      30          7.327
LGA    G      31      G      31          1.595
LGA    P      32      P      32          2.777
LGA    L      33      L      33          2.018
LGA    F      34      F      34          1.080
LGA    E      35      E      35          2.514
LGA    H      36      H      36          1.188
LGA    R      37      R      37          2.146

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   28  142    4.0      9    2.23     5.810     5.749     0.386

LGA_LOCAL      RMSD =  2.234  Number of atoms =    9  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.252  Number of atoms =   17 
Std_ALL_ATOMS  RMSD =  7.288  (standard rmsd on all 17 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.756118 * X  +  -0.604050 * Y  +   0.251812 * Z  +  29.016890
  Y_new =  -0.485809 * X  +  -0.775890 * Y  +  -0.402473 * Z  +  -4.397219
  Z_new =   0.438492 * X  +   0.181985 * Y  +  -0.880117 * Z  +  -3.866757 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.937693   -0.203900  [ DEG:   168.3174    -11.6826 ]
  Theta =  -0.453921   -2.687672  [ DEG:   -26.0077   -153.9923 ]
  Phi   =  -0.571087    2.570505  [ DEG:   -32.7209    147.2791 ]
 
# 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_5_1                                
REMARK     2: T0322.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0322TS239_5_1.T0322.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   28  142   4.0    9   2.23   5.749     7.29
REMARK  ---------------------------------------------------------- 
MOLECULE T0322TS239_5_1
REMARK PARENT number 1
PFRMAT TS
TARGET T0322
PARENT 1vh5_A
ATOM      1  N   MET     1      28.580 -24.795  -9.711  1.00  9.99
ATOM      2  CA  MET     1      27.267 -25.013  -9.096  1.00  9.99
ATOM      3  C   MET     1      27.300 -24.803  -7.586  1.00  9.99
ATOM      4  O   MET     1      27.855 -25.614  -6.850  1.00  9.99
ATOM      5  CB  MET     1      26.734 -26.417  -9.410  1.00  9.99
ATOM      6  N   SER     2      26.651 -23.748  -7.104  1.00  9.99
ATOM      7  CA  SER     2      26.736 -23.441  -5.656  1.00  9.99
ATOM      8  C   SER     2      25.634 -24.089  -4.826  1.00  9.99
ATOM      9  O   SER     2      25.769 -24.237  -3.619  1.00  9.99
ATOM     10  CB  SER     2      26.769 -21.911  -5.420  1.00  9.99
ATOM     11  N   ASP     3      20.540 -27.516  -2.660  1.00  9.99
ATOM     12  CA  ASP     3      19.167 -27.987  -2.755  1.00  9.99
ATOM     13  C   ASP     3      18.717 -27.733  -4.157  1.00  9.99
ATOM     14  O   ASP     3      19.086 -26.740  -4.771  1.00  9.99
ATOM     15  CB  ASP     3      18.232 -27.220  -1.819  1.00  9.99
ATOM     16  N   ASP     4      17.882 -28.629  -4.670  1.00  9.99
ATOM     17  CA  ASP     4      17.273 -28.396  -5.976  1.00  9.99
ATOM     18  C   ASP     4      15.876 -27.795  -5.785  1.00  9.99
ATOM     19  O   ASP     4      15.128 -28.176  -4.892  1.00  9.99
ATOM     20  CB  ASP     4      17.219 -29.703  -6.790  1.00  9.99
ATOM     21  N   LEU     5      15.555 -26.817  -6.608  1.00  9.99
ATOM     22  CA  LEU     5      14.224 -26.225  -6.622  1.00  9.99
ATOM     23  C   LEU     5      13.870 -25.808  -8.042  1.00  9.99
ATOM     24  O   LEU     5      14.741 -25.405  -8.807  1.00  9.99
ATOM     25  CB  LEU     5      14.147 -25.029  -5.602  1.00  9.99
ATOM     26  N   THR     6      12.600 -25.968  -8.411  1.00  9.99
ATOM     27  CA  THR     6      12.111 -25.421  -9.671  1.00  9.99
ATOM     28  C   THR     6      11.728 -23.967  -9.457  1.00  9.99
ATOM     29  O   THR     6      11.495 -23.550  -8.315  1.00  9.99
ATOM     30  CB  THR     6      10.862 -26.161 -10.154  1.00  9.99
ATOM     31  N   ASP     7      11.632 -23.219 -10.555  1.00  9.99
ATOM     32  CA  ASP     7      11.110 -21.855 -10.510  1.00  9.99
ATOM     33  C   ASP     7       9.694 -21.835  -9.956  1.00  9.99
ATOM     34  O   ASP     7       9.321 -20.967  -9.188  1.00  9.99
ATOM     35  CB  ASP     7      11.158 -21.186 -11.886  1.00  9.99
ATOM     36  N   ALA     8       8.904 -22.830 -10.346  1.00  9.99
ATOM     37  CA  ALA     8       7.560 -22.982  -9.827  1.00  9.99
ATOM     38  C   ALA     8       7.492 -23.043  -8.296  1.00  9.99
ATOM     39  O   ALA     8       6.683 -22.342  -7.679  1.00  9.99
ATOM     40  CB  ALA     8       6.929 -24.251 -10.415  1.00  9.99
ATOM     41  N   GLN     9       8.301 -23.909  -7.683  1.00  9.99
ATOM     42  CA  GLN     9       8.253 -24.095  -6.230  1.00  9.99
ATOM     43  C   GLN     9       8.819 -22.864  -5.496  1.00  9.99
ATOM     44  O   GLN     9       8.351 -22.510  -4.408  1.00  9.99
ATOM     45  CB  GLN     9       8.973 -25.400  -5.807  1.00  9.99
ATOM     46  N   THR    10       9.801 -22.219  -6.124  1.00  9.99
ATOM     47  CA  THR    10      10.378 -20.963  -5.631  1.00  9.99
ATOM     48  C   THR    10       9.280 -19.886  -5.579  1.00  9.99
ATOM     49  O   THR    10       9.055 -19.240  -4.555  1.00  9.99
ATOM     50  CB  THR    10      11.499 -20.518  -6.570  1.00  9.99
ATOM     51  N   ALA    11       8.554 -19.735  -6.686  1.00  9.99
ATOM     52  CA  ALA    11       7.492 -18.746  -6.770  1.00  9.99
ATOM     53  C   ALA    11       6.292 -19.047  -5.884  1.00  9.99
ATOM     54  O   ALA    11       5.607 -18.131  -5.442  1.00  9.99
ATOM     55  CB  ALA    11       7.098 -18.514  -8.222  1.00  9.99
ATOM     56  N   ALA    12       6.056 -20.335  -5.600  1.00  9.99
ATOM     57  CA  ALA    12       4.971 -20.712  -4.709  1.00  9.99
ATOM     58  C   ALA    12       5.169 -20.212  -3.281  1.00  9.99
ATOM     59  O   ALA    12       4.204 -20.026  -2.549  1.00  9.99
ATOM     60  CB  ALA    12       4.770 -22.226  -4.722  1.00  9.99
ATOM     61  N   ILE    13       6.422 -19.955  -2.894  1.00  9.99
ATOM     62  CA  ILE    13       6.724 -19.551  -1.517  1.00  9.99
ATOM     63  C   ILE    13       6.080 -18.228  -1.107  1.00  9.99
ATOM     64  O   ILE    13       5.749 -18.011   0.062  1.00  9.99
ATOM     65  CB  ILE    13       8.235 -19.397  -1.342  1.00  9.99
ATOM     66  N   PRO    14       5.926 -17.348  -2.090  1.00  9.99
ATOM     67  CA  PRO    14       5.509 -15.976  -1.874  1.00  9.99
ATOM     68  C   PRO    14       4.023 -15.784  -1.648  1.00  9.99
ATOM     69  O   PRO    14       3.595 -14.692  -1.273  1.00  9.99
ATOM     70  CB  PRO    14       5.977 -15.141  -3.078  1.00  9.99
ATOM     71  N   GLU    15       3.212 -16.823  -1.886  1.00  9.99
ATOM     72  CA  GLU    15       1.745 -16.675  -1.817  1.00  9.99
ATOM     73  C   GLU    15       1.288 -16.346  -0.414  1.00  9.99
ATOM     74  O   GLU    15       1.603 -17.075   0.534  1.00  9.99
ATOM     75  CB  GLU    15       1.022 -17.963  -2.268  1.00  9.99
ATOM     76  N   GLY    16       0.553 -15.244  -0.288  1.00  9.99
ATOM     77  CA  GLY    16       0.008 -14.837   0.986  1.00  9.99
ATOM     78  C   GLY    16       1.003 -14.117   1.890  1.00  9.99
ATOM     79  O   GLY    16       0.721 -13.918   3.073  1.00  9.99
ATOM     80  N   PHE    17       2.154 -13.725   1.337  1.00  9.99
ATOM     81  CA  PHE    17       3.148 -12.944   2.106  1.00  9.99
ATOM     82  C   PHE    17       3.668 -11.806   1.249  1.00  9.99
ATOM     83  O   PHE    17       3.177 -11.573   0.156  1.00  9.99
ATOM     84  CB  PHE    17       4.246 -13.837   2.735  1.00  9.99
ATOM     85  N   SER    18       4.691 -11.102   1.729  1.00  9.99
ATOM     86  CA  SER    18       5.085  -9.862   1.072  1.00  9.99
ATOM     87  C   SER    18       5.550 -10.085  -0.373  1.00  9.99
ATOM     88  O   SER    18       5.293  -9.255  -1.241  1.00  9.99
ATOM     89  CB  SER    18       6.175  -9.145   1.877  1.00  9.99
ATOM     90  N   GLN    19       6.273 -11.172  -0.608  1.00  9.99
ATOM     91  CA  GLN    19       6.777 -11.446  -1.946  1.00  9.99
ATOM     92  C   GLN    19       5.580 -11.524  -2.937  1.00  9.99
ATOM     93  O   GLN    19       5.615 -10.917  -4.002  1.00  9.99
ATOM     94  CB  GLN    19       7.651 -12.729  -1.992  1.00  9.99
ATOM     95  N   GLN    29       4.534 -12.243  -2.541  1.00  9.99
ATOM     96  CA  GLN    29       3.326 -12.363  -3.346  1.00  9.99
ATOM     97  C   GLN    29       2.612 -11.034  -3.487  1.00  9.99
ATOM     98  O   GLN    29       2.207 -10.654  -4.592  1.00  9.99
ATOM     99  CB  GLN    29       2.402 -13.419  -2.716  1.00  9.99
ATOM    100  N   ILE    30       2.474 -10.324  -2.379  1.00  9.99
ATOM    101  CA  ILE    30       1.806  -9.012  -2.362  1.00  9.99
ATOM    102  C   ILE    30       2.435  -8.038  -3.347  1.00  9.99
ATOM    103  O   ILE    30       1.730  -7.291  -4.009  1.00  9.99
ATOM    104  CB  ILE    30       1.824  -8.437  -0.940  1.00  9.99
ATOM    105  N   GLY    31       3.770  -8.033  -3.425  1.00  9.99
ATOM    106  CA  GLY    31       4.453  -7.104  -4.309  1.00  9.99
ATOM    107  C   GLY    31       4.694  -7.634  -5.728  1.00  9.99
ATOM    108  O   GLY    31       5.325  -6.946  -6.550  1.00  9.99
ATOM    109  N   PRO    32       4.249  -8.868  -5.995  1.00  9.99
ATOM    110  CA  PRO    32       4.466  -9.509  -7.307  1.00  9.99
ATOM    111  C   PRO    32       5.936  -9.658  -7.647  1.00  9.99
ATOM    112  O   PRO    32       6.332  -9.475  -8.788  1.00  9.99
ATOM    113  CB  PRO    32       3.737  -8.730  -8.427  1.00  9.99
ATOM    114  N   LEU    33       6.733  -9.975  -6.636  1.00  9.99
ATOM    115  CA  LEU    33       8.098 -10.388  -6.914  1.00  9.99
ATOM    116  C   LEU    33       8.057 -11.791  -7.549  1.00  9.99
ATOM    117  O   LEU    33       7.402 -12.698  -6.999  1.00  9.99
ATOM    118  CB  LEU    33       8.919 -10.326  -5.606  1.00  9.99
ATOM    119  N   PHE    34       8.754 -11.954  -8.680  1.00  9.99
ATOM    120  CA  PHE    34       8.719 -13.199  -9.441  1.00  9.99
ATOM    121  C   PHE    34      10.159 -13.650  -9.666  1.00  9.99
ATOM    122  O   PHE    34      10.945 -12.951 -10.312  1.00  9.99
ATOM    123  CB  PHE    34       8.081 -12.974 -10.825  1.00  9.99
ATOM    124  N   GLU    35      10.486 -14.850  -9.194  1.00  9.99
ATOM    125  CA  GLU    35      11.767 -15.465  -9.584  1.00  9.99
ATOM    126  C   GLU    35      11.740 -15.868 -11.067  1.00  9.99
ATOM    127  O   GLU    35      10.765 -16.454 -11.532  1.00  9.99
ATOM    128  CB  GLU    35      12.089 -16.664  -8.665  1.00  9.99
ATOM    129  N   HIS    36      12.790 -15.516 -11.785  1.00  9.99
ATOM    130  CA  HIS    36      12.854 -15.665 -13.240  1.00  9.99
ATOM    131  C   HIS    36      13.947 -16.599 -13.709  1.00  9.99
ATOM    132  O   HIS    36      13.882 -17.110 -14.840  1.00  9.99
ATOM    133  CB  HIS    36      13.165 -14.324 -13.881  1.00  9.99
ATOM    134  N   ARG    37      15.026 -16.751 -12.941  1.00  9.99
ATOM    135  CA  ARG    37      16.159 -17.516 -13.428  1.00  9.99
ATOM    136  C   ARG    37      16.967 -18.068 -12.273  1.00  9.99
ATOM    137  O   ARG    37      17.303 -17.320 -11.339  1.00  9.99
ATOM    138  CB  ARG    37      17.026 -16.633 -14.336  1.00  9.99
TER
END
