
#######################################################
#                                                     #
#                        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   16 (  126),  selected   16 , name T0329TS490_1_1-D1
# Molecule2: number of CA atoms  141 ( 1070),  selected   16 , name T0329_D1.pdb
# PARAMETERS: T0329TS490_1_1-D1.T0329_D1.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:    16         1 - 16          1.35     1.35
  LCS_AVERAGE:     11.35

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16         1 - 16          1.35     1.35
  LCS_AVERAGE:     11.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14         3 - 16          0.83     1.61
  LCS_AVERAGE:      9.49

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:  141
LCS_GDT     M       1     M       1      9   16   16     3    7    9   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     K       2     K       2      9   16   16     3    6    9   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     Y       3     Y       3     14   16   16     3   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     K       4     K       4     14   16   16     6   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     A       5     A       5     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     A       6     A       6     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     I       7     I       7     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     F       8     F       8     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     D       9     D       9     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     M      10     M      10     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     D      11     D      11     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     G      12     G      12     14   16   16     5   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     T      13     T      13     14   16   16     8   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     I      14     I      14     14   16   16     5   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     L      15     L      15     14   16   16     3    4    5   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_GDT     D      16     D      16     14   16   16     3   12   13   14   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16   16 
LCS_AVERAGE  LCS_A:  10.73  (   9.49   11.35   11.35 )

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      8     12     13     14     16     16     16     16     16     16     16     16     16     16     16     16     16     16     16     16 
GDT PERCENT_CA   5.67   8.51   9.22   9.93  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35  11.35
GDT RMS_LOCAL    0.33   0.55   0.63   0.83   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35
GDT RMS_ALL_CA   1.89   1.80   1.66   1.61   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35   1.35

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          2.271
LGA    K       2      K       2          2.689
LGA    Y       3      Y       3          1.041
LGA    K       4      K       4          0.707
LGA    A       5      A       5          0.807
LGA    A       6      A       6          0.728
LGA    I       7      I       7          1.141
LGA    F       8      F       8          0.843
LGA    D       9      D       9          0.995
LGA    M      10      M      10          0.359
LGA    D      11      D      11          0.489
LGA    G      12      G      12          0.588
LGA    T      13      T      13          0.920
LGA    I      14      I      14          1.333
LGA    L      15      L      15          1.830
LGA    D      16      D      16          2.038

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   16  141    4.0     16    1.35    10.284    10.865     1.106

LGA_LOCAL      RMSD =  1.346  Number of atoms =   16  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  1.346  Number of atoms =   16 
Std_ALL_ATOMS  RMSD =  1.346  (standard rmsd on all 16 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.351153 * X  +  -0.933853 * Y  +  -0.067904 * Z  +  44.561329
  Y_new =  -0.554634 * X  +   0.149030 * Y  +   0.818640 * Z  +   2.822814
  Z_new =  -0.754369 * X  +   0.325130 * Y  +  -0.570279 * Z  +  49.925777 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   2.623431   -0.518162  [ DEG:   150.3115    -29.6885 ]
  Theta =   0.854692    2.286900  [ DEG:    48.9703    131.0297 ]
  Phi   =  -2.135217    1.006376  [ DEG:  -122.3389     57.6611 ]
 
# 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: T0329TS490_1_1-D1                             
REMARK     2: T0329_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0329TS490_1_1-D1.T0329_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   16  141   4.0   16   1.35  10.865     1.35
REMARK  ---------------------------------------------------------- 
MOLECULE T0329TS490_1_1-D1
REMARK PARENT number 1
PFRMAT     TS
TARGET     T0329
PARENT     2ah5A
ATOM      1  N   MET     1      22.996  -1.519  34.051  1.00  0.47
ATOM      2  CA  MET     1      22.596  -2.365  32.904  1.00  0.47
ATOM      3  C   MET     1      21.366  -1.819  32.266  1.00  0.47
ATOM      4  O   MET     1      21.163  -0.606  32.249  1.00  0.47
ATOM      5  CB  MET     1      22.288  -3.797  33.369  1.00  0.47
ATOM      6  CG  MET     1      21.051  -3.885  34.263  1.00  0.47
ATOM      7  SD  MET     1      20.562  -5.576  34.717  1.00  0.47
ATOM      8  CE  MET     1      21.999  -5.881  35.785  1.00  0.47
ATOM      9  N   LYS     2      20.558  -2.734  31.685  1.00  0.58
ATOM     10  CA  LYS     2      19.304  -2.462  31.040  1.00  0.58
ATOM     11  C   LYS     2      18.593  -1.360  31.756  1.00  0.58
ATOM     12  O   LYS     2      18.787  -0.183  31.460  1.00  0.58
ATOM     13  CB  LYS     2      18.371  -3.684  31.006  1.00  0.58
ATOM     14  CG  LYS     2      18.903  -4.825  30.138  1.00  0.58
ATOM     15  CD  LYS     2      20.170  -5.477  30.696  1.00  0.58
ATOM     16  CE  LYS     2      20.703  -6.618  29.827  1.00  0.58
ATOM     17  NZ  LYS     2      21.924  -7.190  30.436  1.00  0.58
ATOM     18  N   TYR     3      17.754  -1.731  32.740  1.00  0.74
ATOM     19  CA  TYR     3      17.010  -0.775  33.505  1.00  0.74
ATOM     20  C   TYR     3      17.970   0.143  34.181  1.00  0.74
ATOM     21  O   TYR     3      18.716  -0.264  35.069  1.00  0.74
ATOM     22  CB  TYR     3      16.156  -1.455  34.590  1.00  0.74
ATOM     23  CG  TYR     3      15.763  -0.442  35.607  1.00  0.74
ATOM     24  CD1 TYR     3      14.649   0.349  35.450  1.00  0.74
ATOM     25  CD2 TYR     3      16.535  -0.295  36.737  1.00  0.74
ATOM     26  CE1 TYR     3      14.316   1.274  36.412  1.00  0.74
ATOM     27  CE2 TYR     3      16.206   0.626  37.700  1.00  0.74
ATOM     28  CZ  TYR     3      15.094   1.412  37.538  1.00  0.74
ATOM     29  OH  TYR     3      14.757   2.359  38.527  1.00  0.74
ATOM     30  N   LYS     4      17.991   1.421  33.751  1.00  0.58
ATOM     31  CA  LYS     4      18.859   2.368  34.377  1.00  0.58
ATOM     32  C   LYS     4      18.024   3.326  35.170  1.00  0.58
ATOM     33  O   LYS     4      18.358   3.649  36.307  1.00  0.58
ATOM     34  CB  LYS     4      19.679   3.188  33.366  1.00  0.58
ATOM     35  CG  LYS     4      18.827   4.032  32.417  1.00  0.58
ATOM     36  CD  LYS     4      19.640   5.052  31.616  1.00  0.58
ATOM     37  CE  LYS     4      18.795   5.902  30.665  1.00  0.58
ATOM     38  NZ  LYS     4      18.031   6.909  31.432  1.00  0.58
ATOM     39  N   ALA     5      16.895   3.794  34.598  1.00  0.23
ATOM     40  CA  ALA     5      16.105   4.776  35.289  1.00  0.23
ATOM     41  C   ALA     5      14.702   4.280  35.455  1.00  0.23
ATOM     42  O   ALA     5      14.235   3.422  34.709  1.00  0.23
ATOM     43  CB  ALA     5      16.022   6.121  34.548  1.00  0.23
ATOM     44  N   ALA     6      13.992   4.821  36.472  1.00  0.21
ATOM     45  CA  ALA     6      12.636   4.416  36.723  1.00  0.21
ATOM     46  C   ALA     6      11.753   5.622  36.637  1.00  0.21
ATOM     47  O   ALA     6      12.075   6.680  37.177  1.00  0.21
ATOM     48  CB  ALA     6      12.419   3.814  38.121  1.00  0.21
ATOM     49  N   ILE     7      10.599   5.486  35.948  1.00  0.31
ATOM     50  CA  ILE     7       9.690   6.592  35.832  1.00  0.31
ATOM     51  C   ILE     7       8.405   6.222  36.506  1.00  0.31
ATOM     52  O   ILE     7       7.956   5.078  36.436  1.00  0.31
ATOM     53  CB  ILE     7       9.414   7.009  34.414  1.00  0.31
ATOM     54  CG1 ILE     7       8.758   5.878  33.608  1.00  0.31
ATOM     55  CG2 ILE     7      10.735   7.514  33.810  1.00  0.31
ATOM     56  CD1 ILE     7       8.311   6.326  32.218  1.00  0.31
ATOM     57  N   PHE     8       7.785   7.198  37.203  1.00  0.22
ATOM     58  CA  PHE     8       6.586   6.914  37.936  1.00  0.22
ATOM     59  C   PHE     8       5.486   7.821  37.484  1.00  0.22
ATOM     60  O   PHE     8       5.715   8.960  37.083  1.00  0.22
ATOM     61  CB  PHE     8       6.705   7.183  39.448  1.00  0.22
ATOM     62  CG  PHE     8       7.676   6.236  40.061  1.00  0.22
ATOM     63  CD1 PHE     8       9.028   6.471  39.973  1.00  0.22
ATOM     64  CD2 PHE     8       7.231   5.127  40.741  1.00  0.22
ATOM     65  CE1 PHE     8       9.926   5.602  40.547  1.00  0.22
ATOM     66  CE2 PHE     8       8.125   4.255  41.315  1.00  0.22
ATOM     67  CZ  PHE     8       9.475   4.491  41.218  1.00  0.22
ATOM     68  N   ASP     9       4.245   7.299  37.529  1.00  0.26
ATOM     69  CA  ASP     9       3.078   8.092  37.282  1.00  0.26
ATOM     70  C   ASP     9       2.875   8.772  38.598  1.00  0.26
ATOM     71  O   ASP     9       3.471   8.353  39.586  1.00  0.26
ATOM     72  CB  ASP     9       1.827   7.245  36.981  1.00  0.26
ATOM     73  CG  ASP     9       0.760   8.129  36.348  1.00  0.26
ATOM     74  OD1 ASP     9       0.955   9.372  36.314  1.00  0.26
ATOM     75  OD2 ASP     9      -0.266   7.563  35.884  1.00  0.26
ATOM     76  N   MET    10       2.038   9.824  38.668  1.00  0.48
ATOM     77  CA  MET    10       1.891  10.556  39.896  1.00  0.48
ATOM     78  C   MET    10       0.622  10.142  40.558  1.00  0.48
ATOM     79  O   MET    10       0.620   9.284  41.439  1.00  0.48
ATOM     80  CB  MET    10       1.811  12.076  39.682  1.00  0.48
ATOM     81  CG  MET    10       1.624  12.860  40.982  1.00  0.48
ATOM     82  SD  MET    10       3.057  12.851  42.096  1.00  0.48
ATOM     83  CE  MET    10       2.146  13.654  43.446  1.00  0.48
ATOM     84  N   ASP    11      -0.497  10.782  40.176  1.00  0.45
ATOM     85  CA  ASP    11      -1.734  10.436  40.801  1.00  0.45
ATOM     86  C   ASP    11      -2.103   9.026  40.459  1.00  0.45
ATOM     87  O   ASP    11      -1.941   8.575  39.326  1.00  0.45
ATOM     88  CB  ASP    11      -2.887  11.417  40.489  1.00  0.45
ATOM     89  CG  ASP    11      -3.088  11.573  38.986  1.00  0.45
ATOM     90  OD1 ASP    11      -2.079  11.556  38.233  1.00  0.45
ATOM     91  OD2 ASP    11      -4.264  11.753  38.574  1.00  0.45
ATOM     92  N   GLY    12      -2.566   8.273  41.482  1.00  0.22
ATOM     93  CA  GLY    12      -2.997   6.912  41.295  1.00  0.22
ATOM     94  C   GLY    12      -1.837   5.975  41.508  1.00  0.22
ATOM     95  O   GLY    12      -2.032   4.765  41.615  1.00  0.22
ATOM     96  N   THR    13      -0.596   6.509  41.554  1.00  0.24
ATOM     97  CA  THR    13       0.600   5.715  41.737  1.00  0.24
ATOM     98  C   THR    13       1.247   6.111  43.045  1.00  0.24
ATOM     99  O   THR    13       1.216   5.352  44.015  1.00  0.24
ATOM    100  CB  THR    13       1.603   5.921  40.643  1.00  0.24
ATOM    101  OG1 THR    13       1.036   5.564  39.390  1.00  0.24
ATOM    102  CG2 THR    13       2.835   5.046  40.940  1.00  0.24
ATOM    103  N   ILE    14       1.944   7.279  43.064  1.00  0.59
ATOM    104  CA  ILE    14       2.468   7.809  44.303  1.00  0.59
ATOM    105  C   ILE    14       1.255   8.065  45.101  1.00  0.59
ATOM    106  O   ILE    14       1.252   7.896  46.322  1.00  0.59
ATOM    107  CB  ILE    14       3.163   9.137  44.208  1.00  0.59
ATOM    108  CG1 ILE    14       4.545   8.991  43.560  1.00  0.59
ATOM    109  CG2 ILE    14       3.211   9.732  45.627  1.00  0.59
ATOM    110  CD1 ILE    14       4.513   8.556  42.102  1.00  0.59
ATOM    111  N   LEU    15       0.254   8.612  44.382  1.00  0.89
ATOM    112  CA  LEU    15      -1.101   8.463  44.783  1.00  0.89
ATOM    113  C   LEU    15      -2.033   9.533  44.953  1.00  0.89
ATOM    114  O   LEU    15      -2.284  10.346  44.070  1.00  0.89
ATOM    115  CB  LEU    15      -1.400   7.441  45.880  1.00  0.89
ATOM    116  CG  LEU    15      -2.231   6.232  45.395  1.00  0.89
ATOM    117  CD1 LEU    15      -3.618   6.691  44.904  1.00  0.89
ATOM    118  CD2 LEU    15      -1.492   5.365  44.370  1.00  0.89
ATOM    119  N   ASP    16      -2.688   9.298  46.100  1.00  0.88
ATOM    120  CA  ASP    16      -3.623  10.000  46.895  1.00  0.88
ATOM    121  C   ASP    16      -4.821  10.560  46.257  1.00  0.88
ATOM    122  O   ASP    16      -5.899  10.439  46.824  1.00  0.88
ATOM    123  CB  ASP    16      -3.157  11.358  47.326  1.00  0.88
ATOM    124  CG  ASP    16      -1.709  11.557  47.027  1.00  0.88
ATOM    125  OD1 ASP    16      -0.825  10.769  47.452  1.00  0.88
ATOM    126  OD2 ASP    16      -1.497  12.547  46.288  1.00  0.88
TER
END
