
#######################################################
#                                                     #
#                        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   25 (  100),  selected   25 , name T0378AL509_1-D1
# Molecule2: number of CA atoms   89 (  716),  selected   25 , name T0378_D1.pdb
# PARAMETERS: T0378AL509_1-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:    25         5 - 29          0.90     0.90
  LCS_AVERAGE:     28.09

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25         5 - 29          0.90     0.90
  LCS_AVERAGE:     28.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25         5 - 29          0.90     0.90
  LCS_AVERAGE:     28.09

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     N       5     N       5     25   25   25     7   11   19   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     Q       6     Q       6     25   25   25     7   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     I       7     I       7     25   25   25     7   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     K       8     K       8     25   25   25     7   18   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     F       9     F       9     25   25   25     7   18   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     L      10     L      10     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R      11     R      11     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     S      12     S      12     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     L      13     L      13     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R      14     R      14     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     E      15     E      15     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R      16     R      16     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     K      17     K      17     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     Y      18     Y      18     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R      19     R      19     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     L      20     L      20     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     R      21     R      21     25   25   25    12   18   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     E      22     E      22     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     Q      23     Q      23     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     A      24     A      24     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     F      25     F      25     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     A      26     A      26     25   25   25    15   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     V      27     V      27     25   25   25    13   19   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     E      28     E      28     25   25   25     3   18   23   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_GDT     G      29     G      29     25   25   25     3    4   14   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25   25 
LCS_AVERAGE  LCS_A:  28.09  (  28.09   28.09   28.09 )

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     15     19     23     25     25     25     25     25     25     25     25     25     25     25     25     25     25     25     25     25 
GDT PERCENT_CA  16.85  21.35  25.84  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09  28.09
GDT RMS_LOCAL    0.32   0.55   0.72   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90
GDT RMS_ALL_CA   1.41   1.01   0.96   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90   0.90

#      Molecule1      Molecule2       DISTANCE
LGA    N       5      N       5          1.927
LGA    Q       6      Q       6          0.930
LGA    I       7      I       7          0.680
LGA    K       8      K       8          0.990
LGA    F       9      F       9          1.253
LGA    L      10      L      10          1.152
LGA    R      11      R      11          0.496
LGA    S      12      S      12          0.386
LGA    L      13      L      13          0.486
LGA    R      14      R      14          0.653
LGA    E      15      E      15          0.378
LGA    R      16      R      16          0.528
LGA    K      17      K      17          0.906
LGA    Y      18      Y      18          0.443
LGA    R      19      R      19          0.090
LGA    L      20      L      20          1.044
LGA    R      21      R      21          1.557
LGA    E      22      E      22          1.025
LGA    Q      23      Q      23          0.545
LGA    A      24      A      24          0.327
LGA    F      25      F      25          0.582
LGA    A      26      A      26          0.438
LGA    V      27      V      27          0.358
LGA    E      28      E      28          0.683
LGA    G      29      G      29          1.710

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   25   89    4.0     25    0.90    26.404    27.390     2.490

LGA_LOCAL      RMSD =  0.904  Number of atoms =   25  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  0.904  Number of atoms =   25 
Std_ALL_ATOMS  RMSD =  0.904  (standard rmsd on all 25 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.662717 * X  +  -0.748713 * Y  +   0.015315 * Z  +  19.133444
  Y_new =   0.718664 * X  +   0.630104 * Y  +  -0.294093 * Z  +   4.893569
  Z_new =   0.210541 * X  +   0.205907 * Y  +   0.955654 * Z  +  25.851946 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.212218   -2.929375  [ DEG:    12.1592   -167.8408 ]
  Theta =  -0.212129   -2.929464  [ DEG:   -12.1541   -167.8459 ]
  Phi   =   0.825877   -2.315716  [ DEG:    47.3193   -132.6807 ]
 
# 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: T0378AL509_1-D1                               
REMARK     2: T0378_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0378AL509_1-D1.T0378_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   25   89   4.0   25   0.90  27.390     0.90
REMARK  ---------------------------------------------------------- 
MOLECULE T0378AL509_1-D1
REMARK Aligment from pdb entry: 1ipaA_
ATOM      1  N   ASN     5       6.579  37.465  53.852  1.00  0.00              
ATOM      2  CA  ASN     5       7.551  36.786  54.722  1.00  0.00              
ATOM      3  C   ASN     5       7.523  35.259  54.677  1.00  0.00              
ATOM      4  O   ASN     5       8.565  34.612  54.789  1.00  0.00              
ATOM      5  N   GLN     6       6.336  34.686  54.513  1.00  0.00              
ATOM      6  CA  GLN     6       6.218  33.241  54.442  1.00  0.00              
ATOM      7  C   GLN     6       6.876  32.734  53.169  1.00  0.00              
ATOM      8  O   GLN     6       7.511  31.682  53.162  1.00  0.00              
ATOM      9  N   ILE     7       6.721  33.495  52.093  1.00  0.00              
ATOM     10  CA  ILE     7       7.292  33.131  50.813  1.00  0.00              
ATOM     11  C   ILE     7       8.799  33.373  50.791  1.00  0.00              
ATOM     12  O   ILE     7       9.539  32.685  50.090  1.00  0.00              
ATOM     13  N   LYS     8       9.258  34.350  51.556  1.00  0.00              
ATOM     14  CA  LYS     8      10.685  34.626  51.615  1.00  0.00              
ATOM     15  C   LYS     8      11.384  33.489  52.360  1.00  0.00              
ATOM     16  O   LYS     8      12.527  33.141  52.052  1.00  0.00              
ATOM     17  N   PHE     9      10.690  32.902  53.330  1.00  0.00              
ATOM     18  CA  PHE     9      11.252  31.802  54.102  1.00  0.00              
ATOM     19  C   PHE     9      11.332  30.534  53.256  1.00  0.00              
ATOM     20  O   PHE     9      12.307  29.801  53.321  1.00  0.00              
ATOM     21  N   LEU    10      10.308  30.278  52.455  1.00  0.00              
ATOM     22  CA  LEU    10      10.317  29.093  51.610  1.00  0.00              
ATOM     23  C   LEU    10      11.337  29.201  50.465  1.00  0.00              
ATOM     24  O   LEU    10      11.971  28.212  50.096  1.00  0.00              
ATOM     25  N   ARG    11      11.510  30.404  49.921  1.00  0.00              
ATOM     26  CA  ARG    11      12.458  30.617  48.819  1.00  0.00              
ATOM     27  C   ARG    11      13.897  30.253  49.198  1.00  0.00              
ATOM     28  O   ARG    11      14.682  29.829  48.348  1.00  0.00              
ATOM     29  N   SER    12      14.243  30.423  50.468  1.00  0.00              
ATOM     30  CA  SER    12      15.582  30.099  50.936  1.00  0.00              
ATOM     31  C   SER    12      15.888  28.616  50.734  1.00  0.00              
ATOM     32  O   SER    12      17.045  28.217  50.624  1.00  0.00              
ATOM     33  N   LEU    13      14.842  27.800  50.685  1.00  0.00              
ATOM     34  CA  LEU    13      15.019  26.367  50.515  1.00  0.00              
ATOM     35  C   LEU    13      15.551  26.007  49.127  1.00  0.00              
ATOM     36  O   LEU    13      15.862  24.844  48.861  1.00  0.00              
ATOM     37  N   ARG    14      15.667  26.997  48.241  1.00  0.00              
ATOM     38  CA  ARG    14      16.204  26.720  46.910  1.00  0.00              
ATOM     39  C   ARG    14      17.710  26.501  46.995  1.00  0.00              
ATOM     40  O   ARG    14      18.313  25.921  46.095  1.00  0.00              
ATOM     41  N   GLU    15      18.307  26.945  48.097  1.00  0.00              
ATOM     42  CA  GLU    15      19.738  26.775  48.308  1.00  0.00              
ATOM     43  C   GLU    15      19.997  25.614  49.275  1.00  0.00              
ATOM     44  O   GLU    15      19.240  25.411  50.227  1.00  0.00              
ATOM     45  N   ARG    16      21.059  24.849  49.031  1.00  0.00              
ATOM     46  CA  ARG    16      21.349  23.686  49.865  1.00  0.00              
ATOM     47  C   ARG    16      21.605  23.906  51.348  1.00  0.00              
ATOM     48  O   ARG    16      21.042  23.194  52.170  1.00  0.00              
ATOM     49  N   LYS    17      22.459  24.858  51.700  1.00  0.00              
ATOM     50  CA  LYS    17      22.754  25.098  53.110  1.00  0.00              
ATOM     51  C   LYS    17      21.486  25.317  53.943  1.00  0.00              
ATOM     52  O   LYS    17      21.386  24.835  55.068  1.00  0.00              
ATOM     53  N   TYR    18      20.526  26.046  53.383  1.00  0.00              
ATOM     54  CA  TYR    18      19.276  26.333  54.066  1.00  0.00              
ATOM     55  C   TYR    18      18.396  25.106  54.235  1.00  0.00              
ATOM     56  O   TYR    18      17.696  24.979  55.234  1.00  0.00              
ATOM     57  N   ARG    19      18.429  24.200  53.267  1.00  0.00              
ATOM     58  CA  ARG    19      17.639  22.984  53.364  1.00  0.00              
ATOM     59  C   ARG    19      18.226  22.096  54.447  1.00  0.00              
ATOM     60  O   ARG    19      17.504  21.507  55.246  1.00  0.00              
ATOM     61  N   LEU    20      19.550  22.007  54.470  1.00  0.00              
ATOM     62  CA  LEU    20      20.228  21.159  55.437  1.00  0.00              
ATOM     63  C   LEU    20      20.091  21.616  56.880  1.00  0.00              
ATOM     64  O   LEU    20      19.846  20.803  57.768  1.00  0.00              
ATOM     65  N   ARG    21      20.230  22.913  57.120  1.00  0.00              
ATOM     66  CA  ARG    21      20.149  23.399  58.482  1.00  0.00              
ATOM     67  C   ARG    21      18.732  23.325  59.020  1.00  0.00              
ATOM     68  O   ARG    21      18.534  23.025  60.190  1.00  0.00              
ATOM     69  N   GLU    22      17.745  23.573  58.168  1.00  0.00              
ATOM     70  CA  GLU    22      16.349  23.531  58.606  1.00  0.00              
ATOM     71  C   GLU    22      15.683  22.179  58.396  1.00  0.00              
ATOM     72  O   GLU    22      14.546  21.979  58.807  1.00  0.00              
ATOM     73  N   GLN    23      16.392  21.257  57.758  1.00  0.00              
ATOM     74  CA  GLN    23      15.854  19.932  57.488  1.00  0.00              
ATOM     75  C   GLN    23      14.517  19.980  56.760  1.00  0.00              
ATOM     76  O   GLN    23      13.595  19.229  57.081  1.00  0.00              
ATOM     77  N   ALA    24      14.421  20.859  55.772  1.00  0.00              
ATOM     78  CA  ALA    24      13.204  20.981  54.985  1.00  0.00              
ATOM     79  C   ALA    24      13.528  21.252  53.518  1.00  0.00              
ATOM     80  O   ALA    24      14.606  21.759  53.194  1.00  0.00              
ATOM     81  N   PHE    25      12.607  20.885  52.634  1.00  0.00              
ATOM     82  CA  PHE    25      12.807  21.090  51.210  1.00  0.00              
ATOM     83  C   PHE    25      11.471  21.147  50.485  1.00  0.00              
ATOM     84  O   PHE    25      10.456  20.654  50.983  1.00  0.00              
ATOM     85  N   ALA    26      11.489  21.765  49.308  1.00  0.00              
ATOM     86  CA  ALA    26      10.297  21.933  48.508  1.00  0.00              
ATOM     87  C   ALA    26      10.148  20.816  47.500  1.00  0.00              
ATOM     88  O   ALA    26      11.135  20.284  46.982  1.00  0.00              
ATOM     89  N   VAL    27       8.902  20.453  47.234  1.00  0.00              
ATOM     90  CA  VAL    27       8.623  19.413  46.272  1.00  0.00              
ATOM     91  C   VAL    27       7.594  19.932  45.271  1.00  0.00              
ATOM     92  O   VAL    27       6.401  19.994  45.565  1.00  0.00              
ATOM     93  N   GLU    28       8.076  20.318  44.093  1.00  0.00              
ATOM     94  CA  GLU    28       7.231  20.837  43.013  1.00  0.00              
ATOM     95  C   GLU    28       6.690  19.728  42.094  1.00  0.00              
ATOM     96  O   GLU    28       7.451  18.899  41.590  1.00  0.00              
ATOM     97  N   GLY    29       5.375  19.716  41.891  1.00  0.00              
ATOM     98  CA  GLY    29       4.771  18.724  41.024  1.00  0.00              
ATOM     99  C   GLY    29       3.945  17.681  41.746  1.00  0.00              
ATOM    100  O   GLY    29       4.391  17.090  42.734  1.00  0.00              
END
