
#######################################################
#                                                     #
#                        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   23 (  115),  selected   23 , name T0378TS239_3_2-D1
# Molecule2: number of CA atoms   89 (  716),  selected   23 , name T0378_D1.pdb
# PARAMETERS: T0378TS239_3_2-D1.T0378_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:    23         1 - 23          2.27     2.27
  LCS_AVERAGE:     25.84

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21         3 - 23          1.75     2.50
  LCS_AVERAGE:     21.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19         5 - 23          0.88     2.90
  LCS_AVERAGE:     18.91

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:   89
LCS_GDT     M       1     M       1      3    3   23     0    3    3    3    9   19   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L       2     L       2      3    4   23     1    3    3    4    6   10   14   19   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S       3     S       3      3   21   23     3    3    3    4    5   10   12   19   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     A       4     A       4     17   21   23     8   12   15   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     N       5     N       5     19   21   23     8   12   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q       6     Q       6     19   21   23     8   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     I       7     I       7     19   21   23     8   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K       8     K       8     19   21   23     8   14   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     F       9     F       9     19   21   23     8   14   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      10     L      10     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      11     R      11     19   21   23    11   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     S      12     S      12     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      13     L      13     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      14     R      14     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      15     E      15     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      16     R      16     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     K      17     K      17     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Y      18     Y      18     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      19     R      19     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     L      20     L      20     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     R      21     R      21     19   21   23    11   14   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     E      22     E      22     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_GDT     Q      23     Q      23     19   21   23    12   15   18   20   20   20   21   21   23   23   23   23   23   23   23   23   23   23   23   23 
LCS_AVERAGE  LCS_A:  22.21  (  18.91   21.89   25.84 )

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     12     15     18     20     20     20     21     21     23     23     23     23     23     23     23     23     23     23     23     23 
GDT PERCENT_CA  13.48  16.85  20.22  22.47  22.47  22.47  23.60  23.60  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84  25.84
GDT RMS_LOCAL    0.30   0.58   0.73   1.01   1.01   1.01   1.70   1.70   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27
GDT RMS_ALL_CA   3.38   3.10   3.04   2.88   2.88   2.88   2.45   2.45   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27   2.27

#      Molecule1      Molecule2       DISTANCE
LGA    M       1      M       1          3.723
LGA    L       2      L       2          4.872
LGA    S       3      S       3          4.474
LGA    A       4      A       4          3.270
LGA    N       5      N       5          1.775
LGA    Q       6      Q       6          2.260
LGA    I       7      I       7          2.849
LGA    K       8      K       8          2.024
LGA    F       9      F       9          1.556
LGA    L      10      L      10          2.259
LGA    R      11      R      11          1.915
LGA    S      12      S      12          0.950
LGA    L      13      L      13          0.874
LGA    R      14      R      14          1.449
LGA    E      15      E      15          1.208
LGA    R      16      R      16          1.208
LGA    K      17      K      17          0.742
LGA    Y      18      Y      18          0.442
LGA    R      19      R      19          0.374
LGA    L      20      L      20          1.345
LGA    R      21      R      21          1.966
LGA    E      22      E      22          1.920
LGA    Q      23      Q      23          1.328

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   23   89    4.0     21    1.70    22.191    22.813     1.169

LGA_LOCAL      RMSD =  1.696  Number of atoms =   21  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.271  Number of atoms =   23 
Std_ALL_ATOMS  RMSD =  2.271  (standard rmsd on all 23 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.585113 * X  +  -0.791517 * Y  +   0.176478 * Z  +  18.313086
  Y_new =   0.799019 * X  +   0.525492 * Y  +  -0.292280 * Z  +   5.490513
  Z_new =   0.138607 * X  +   0.312026 * Y  +   0.939909 * Z  +  25.539347 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.320527   -2.821066  [ DEG:    18.3648   -161.6351 ]
  Theta =  -0.139055   -3.002538  [ DEG:    -7.9672   -172.0328 ]
  Phi   =   0.938727   -2.202866  [ DEG:    53.7851   -126.2149 ]
 
# 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: T0378TS239_3_2-D1                             
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378TS239_3_2-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   23   89   4.0   21   1.70  22.813     2.27
REMARK  ---------------------------------------------------------- 
MOLECULE T0378TS239_3_2-D1
REMARK PARENT number 2
PFRMAT TS
TARGET T0378
PARENT 1ipa_A
ATOM      1  N   MET     1      -0.116  36.017  49.229  1.00  9.99
ATOM      2  CA  MET     1       1.009  36.932  49.102  1.00  9.99
ATOM      3  C   MET     1       2.348  36.233  49.258  1.00  9.99
ATOM      4  O   MET     1       2.569  35.497  50.220  1.00  9.99
ATOM      5  CB  MET     1       0.893  38.048  50.140  1.00  9.99
ATOM      6  N   LEU     2       3.242  36.476  48.309  1.00  9.99
ATOM      7  CA  LEU     2       4.567  35.876  48.340  1.00  9.99
ATOM      8  C   LEU     2       5.405  36.533  49.439  1.00  9.99
ATOM      9  O   LEU     2       6.460  36.026  49.819  1.00  9.99
ATOM     10  CB  LEU     2       5.279  36.030  46.973  1.00  9.99
ATOM     11  N   SER     3       4.912  37.660  49.951  1.00  9.99
ATOM     12  CA  SER     3       5.596  38.403  51.002  1.00  9.99
ATOM     13  C   SER     3       5.258  37.831  52.372  1.00  9.99
ATOM     14  O   SER     3       5.911  38.156  53.364  1.00  9.99
ATOM     15  CB  SER     3       5.203  39.875  50.941  1.00  9.99
ATOM     16  N   ALA     4       4.231  36.987  52.418  1.00  9.99
ATOM     17  CA  ALA     4       3.801  36.347  53.656  1.00  9.99
ATOM     18  C   ALA     4       5.029  35.688  54.294  1.00  9.99
ATOM     19  O   ALA     4       5.694  34.863  53.671  1.00  9.99
ATOM     20  CB  ALA     4       2.724  35.305  53.339  1.00  9.99
ATOM     21  N   ASN     5       5.340  36.046  55.550  1.00  9.99
ATOM     22  CA  ASN     5       6.497  35.498  56.275  1.00  9.99
ATOM     23  C   ASN     5       6.661  33.981  56.204  1.00  9.99
ATOM     24  O   ASN     5       7.785  33.476  56.170  1.00  9.99
ATOM     25  CB  ASN     5       6.287  36.012  57.704  1.00  9.99
ATOM     26  N   GLN     6       5.548  33.257  56.181  1.00  9.99
ATOM     27  CA  GLN     6       5.611  31.809  56.098  1.00  9.99
ATOM     28  C   GLN     6       6.159  31.397  54.741  1.00  9.99
ATOM     29  O   GLN     6       6.920  30.437  54.633  1.00  9.99
ATOM     30  CB  GLN     6       4.223  31.195  56.294  1.00  9.99
ATOM     31  N   ILE     7       5.770  32.134  53.709  1.00  9.99
ATOM     32  CA  ILE     7       6.214  31.852  52.359  1.00  9.99
ATOM     33  C   ILE     7       7.661  32.290  52.150  1.00  9.99
ATOM     34  O   ILE     7       8.387  31.707  51.348  1.00  9.99
ATOM     35  CB  ILE     7       5.309  32.548  51.320  1.00  9.99
ATOM     36  N   LYS     8       8.084  33.317  52.870  1.00  9.99
ATOM     37  CA  LYS     8       9.458  33.778  52.752  1.00  9.99
ATOM     38  C   LYS     8      10.390  32.741  53.379  1.00  9.99
ATOM     39  O   LYS     8      11.518  32.547  52.922  1.00  9.99
ATOM     40  CB  LYS     8       9.616  35.134  53.447  1.00  9.99
ATOM     41  N   PHE     9       9.908  32.064  54.418  1.00  9.99
ATOM     42  CA  PHE     9      10.704  31.046  55.090  1.00  9.99
ATOM     43  C   PHE     9      10.838  29.802  54.216  1.00  9.99
ATOM     44  O   PHE     9      11.900  29.203  54.141  1.00  9.99
ATOM     45  CB  PHE     9      10.073  30.668  56.431  1.00  9.99
ATOM     46  N   LEU    10       9.762  29.415  53.547  1.00  9.99
ATOM     47  CA  LEU    10       9.815  28.244  52.685  1.00  9.99
ATOM     48  C   LEU    10      10.656  28.490  51.421  1.00  9.99
ATOM     49  O   LEU    10      11.361  27.594  50.955  1.00  9.99
ATOM     50  CB  LEU    10       8.398  27.813  52.315  1.00  9.99
ATOM     51  N   ARG    11      10.600  29.706  50.883  1.00  9.99
ATOM     52  CA  ARG    11      11.362  30.045  49.674  1.00  9.99
ATOM     53  C   ARG    11      12.873  29.873  49.859  1.00  9.99
ATOM     54  O   ARG    11      13.591  29.559  48.909  1.00  9.99
ATOM     55  CB  ARG    11      11.046  31.485  49.226  1.00  9.99
ATOM     56  N   SER    12      13.356  30.083  51.079  1.00  9.99
ATOM     57  CA  SER    12      14.774  29.937  51.366  1.00  9.99
ATOM     58  C   SER    12      15.241  28.507  51.097  1.00  9.99
ATOM     59  O   SER    12      16.417  28.264  50.832  1.00  9.99
ATOM     60  CB  SER    12      15.049  30.298  52.830  1.00  9.99
ATOM     61  N   LEU    13      14.313  27.561  51.166  1.00  9.99
ATOM     62  CA  LEU    13      14.652  26.164  50.946  1.00  9.99
ATOM     63  C   LEU    13      15.043  25.881  49.495  1.00  9.99
ATOM     64  O   LEU    13      15.466  24.770  49.168  1.00  9.99
ATOM     65  CB  LEU    13      13.487  25.266  51.382  1.00  9.99
ATOM     66  N   ARG    14      14.914  26.881  48.621  1.00  9.99
ATOM     67  CA  ARG    14      15.306  26.681  47.227  1.00  9.99
ATOM     68  C   ARG    14      16.827  26.662  47.115  1.00  9.99
ATOM     69  O   ARG    14      17.379  26.169  46.135  1.00  9.99
ATOM     70  CB  ARG    14      14.716  27.759  46.315  1.00  9.99
ATOM     71  N   GLU    15      17.498  27.177  48.141  1.00  9.99
ATOM     72  CA  GLU    15      18.953  27.196  48.164  1.00  9.99
ATOM     73  C   GLU    15      19.484  26.077  49.068  1.00  9.99
ATOM     74  O   GLU    15      18.889  25.773  50.104  1.00  9.99
ATOM     75  CB  GLU    15      19.426  28.573  48.617  1.00  9.99
ATOM     76  N   ARG    16      20.596  25.459  48.675  1.00  9.99
ATOM     77  CA  ARG    16      21.139  24.341  49.442  1.00  9.99
ATOM     78  C   ARG    16      21.554  24.589  50.884  1.00  9.99
ATOM     79  O   ARG    16      21.200  23.807  51.757  1.00  9.99
ATOM     80  CB  ARG    16      22.321  23.691  48.713  1.00  9.99
ATOM     81  N   LYS    17      22.315  25.644  51.143  1.00  9.99
ATOM     82  CA  LYS    17      22.756  25.917  52.509  1.00  9.99
ATOM     83  C   LYS    17      21.588  25.965  53.501  1.00  9.99
ATOM     84  O   LYS    17      21.697  25.470  54.619  1.00  9.99
ATOM     85  CB  LYS    17      23.535  27.240  52.568  1.00  9.99
ATOM     86  N   TYR    18      20.478  26.562  53.082  1.00  9.99
ATOM     87  CA  TYR    18      19.298  26.680  53.925  1.00  9.99
ATOM     88  C   TYR    18      18.616  25.348  54.180  1.00  9.99
ATOM     89  O   TYR    18      18.072  25.127  55.257  1.00  9.99
ATOM     90  CB  TYR    18      18.323  27.669  53.296  1.00  9.99
ATOM     91  N   ARG    19      18.641  24.457  53.198  1.00  9.99
ATOM     92  CA  ARG    19      18.035  23.147  53.371  1.00  9.99
ATOM     93  C   ARG    19      18.867  22.342  54.352  1.00  9.99
ATOM     94  O   ARG    19      18.337  21.660  55.225  1.00  9.99
ATOM     95  CB  ARG    19      17.984  22.389  52.044  1.00  9.99
ATOM     96  N   LEU    20      20.183  22.427  54.204  1.00  9.99
ATOM     97  CA  LEU    20      21.085  21.673  55.060  1.00  9.99
ATOM     98  C   LEU    20      21.076  22.104  56.518  1.00  9.99
ATOM     99  O   LEU    20      21.056  21.264  57.414  1.00  9.99
ATOM    100  CB  LEU    20      22.519  21.745  54.522  1.00  9.99
ATOM    101  N   ARG    21      21.076  23.407  56.764  1.00  9.99
ATOM    102  CA  ARG    21      21.108  23.874  58.134  1.00  9.99
ATOM    103  C   ARG    21      19.794  23.613  58.846  1.00  9.99
ATOM    104  O   ARG    21      19.789  23.286  60.027  1.00  9.99
ATOM    105  CB  ARG    21      21.462  25.363  58.189  1.00  9.99
ATOM    106  N   GLU    22      18.681  23.732  58.132  1.00  9.99
ATOM    107  CA  GLU    22      17.371  23.505  58.744  1.00  9.99
ATOM    108  C   GLU    22      16.865  22.078  58.593  1.00  9.99
ATOM    109  O   GLU    22      15.827  21.728  59.142  1.00  9.99
ATOM    110  CB  GLU    22      16.335  24.446  58.150  1.00  9.99
ATOM    111  N   GLN    23      17.600  21.259  57.853  1.00  9.99
ATOM    112  CA  GLN    23      17.209  19.875  57.627  1.00  9.99
ATOM    113  C   GLN    23      15.795  19.748  57.076  1.00  9.99
ATOM    114  O   GLN    23      15.027  18.882  57.497  1.00  9.99
ATOM    115  CB  GLN    23      17.344  19.067  58.913  1.00  9.99
TER
END
