
#######################################################
#                                                     #
#                        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   26 (  104),  selected   26 , name T0348AL381_2
# Molecule2: number of CA atoms   61 (  465),  selected   26 , name T0348.pdb
# PARAMETERS: T0348AL381_2.T0348.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:    26        10 - 35          2.57     2.57
  LCS_AVERAGE:     42.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12        10 - 21          1.99     2.73
  LONGEST_CONTINUOUS_SEGMENT:    12        24 - 35          1.52     3.06
  LCS_AVERAGE:     18.98

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10        26 - 35          0.83     3.13
  LCS_AVERAGE:     11.85

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:   61
LCS_GDT     V      10     V      10      7   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     C      11     C      11      7   12   26     5   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     P      12     P      12      7   12   26     5    9   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      13     L      13      7   12   26     5    9   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     C      14     C      14      7   12   26     3   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      15     K      15      7   12   26     5   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G      16     G      16      7   12   26     5    5    7   13   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     P      17     P      17      5   12   26     5    5    5    6   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      18     L      18      5   12   26     5    5    7   13   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      19     V      19      5   12   26     5    5    5    7    7   17   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     F      20     F      20      5   12   26     5    5    5    8   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      21     D      21      3   12   26     3   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      22     K      22      4    7   26     3    4    4    4    7    7   12   20   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     S      23     S      23      4    6   26     3    4    5    7   10   16   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      24     K      24      4   12   26     3    4    8   11   18   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      25     D      25      4   12   26     3    4    6   10   19   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     E      26     E      26     10   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      27     L      27     10   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     I      28     I      28     10   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     C      29     C      29     10   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      30     K      30     10   12   26     5   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G      31     G      31     10   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      32     D      32     10   12   26     6   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     R      33     R      33     10   12   26     3    4   11   17   19   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      34     L      34     10   12   26     3   11   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     A      35     A      35     10   12   26     3   13   16   17   20   22   24   25   25   26   26   26   26   26   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  24.49  (  11.85   18.98   42.62 )

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      6     13     16     17     20     22     24     25     25     26     26     26     26     26     26     26     26     26     26     26 
GDT PERCENT_CA   9.84  21.31  26.23  27.87  32.79  36.07  39.34  40.98  40.98  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62  42.62
GDT RMS_LOCAL    0.35   0.70   0.87   0.96   1.60   1.76   2.05   2.30   2.30   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57
GDT RMS_ALL_CA   2.99   3.01   3.08   3.13   2.89   2.80   2.68   2.60   2.60   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57   2.57

#      Molecule1      Molecule2       DISTANCE
LGA    V      10      V      10          0.316
LGA    C      11      C      11          0.859
LGA    P      12      P      12          1.766
LGA    L      13      L      13          2.596
LGA    C      14      C      14          2.367
LGA    K      15      K      15          0.956
LGA    G      16      G      16          2.151
LGA    P      17      P      17          2.824
LGA    L      18      L      18          2.634
LGA    V      19      V      19          3.639
LGA    F      20      F      20          2.245
LGA    D      21      D      21          2.632
LGA    K      22      K      22          5.593
LGA    S      23      S      23          3.993
LGA    K      24      K      24          2.765
LGA    D      25      D      25          2.196
LGA    E      26      E      26          1.763
LGA    L      27      L      27          1.361
LGA    I      28      I      28          1.827
LGA    C      29      C      29          1.896
LGA    K      30      K      30          2.325
LGA    G      31      G      31          2.494
LGA    D      32      D      32          2.587
LGA    R      33      R      33          3.694
LGA    L      34      L      34          2.608
LGA    A      35      A      35          2.639

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26   61    4.0     25    2.30    33.197    31.370     1.043

LGA_LOCAL      RMSD =  2.297  Number of atoms =   25  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.626  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  2.575  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =   0.505923 * X  +   0.058983 * Y  +   0.860560 * Z  +  10.156652
  Y_new =  -0.776108 * X  +   0.466504 * Y  +   0.424299 * Z  +  32.111137
  Z_new =  -0.376428 * X  +  -0.882550 * Y  +   0.281793 * Z  +  50.050896 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -1.261734    1.879858  [ DEG:   -72.2921    107.7079 ]
  Theta =   0.385938    2.755655  [ DEG:    22.1126    157.8874 ]
  Phi   =  -0.993106    2.148486  [ DEG:   -56.9008    123.0992 ]
 
# 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: T0348AL381_2                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_2.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26   61   4.0   25   2.30  31.370     2.57
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_2
REMARK Aligment from pdb entry: 1rlyA
ATOM      1  N   VAL    10       8.158  33.986  59.392  1.00  0.00              
ATOM      2  CA  VAL    10       8.926  32.903  60.009  1.00  0.00              
ATOM      3  C   VAL    10       8.152  31.592  59.934  1.00  0.00              
ATOM      4  O   VAL    10       7.190  31.475  59.176  1.00  0.00              
ATOM      5  N   CYS    11       8.594  30.602  60.698  1.00  0.00              
ATOM      6  CA  CYS    11       7.952  29.300  60.682  1.00  0.00              
ATOM      7  C   CYS    11       6.633  29.277  61.443  1.00  0.00              
ATOM      8  O   CYS    11       6.551  29.725  62.585  1.00  0.00              
ATOM      9  N   PRO    12       5.578  28.715  60.814  1.00  0.00              
ATOM     10  CA  PRO    12       4.263  28.597  61.437  1.00  0.00              
ATOM     11  C   PRO    12       4.349  27.753  62.694  1.00  0.00              
ATOM     12  O   PRO    12       3.658  28.010  63.680  1.00  0.00              
ATOM     13  N   LEU    13       5.238  26.760  62.666  1.00  0.00              
ATOM     14  CA  LEU    13       5.456  25.899  63.814  1.00  0.00              
ATOM     15  C   LEU    13       6.460  26.559  64.744  1.00  0.00              
ATOM     16  O   LEU    13       6.368  26.449  65.968  1.00  0.00              
ATOM     17  N   CYS    14       7.379  27.302  64.163  1.00  0.00              
ATOM     18  CA  CYS    14       8.353  28.022  64.950  1.00  0.00              
ATOM     19  C   CYS    14       8.582  29.419  64.400  1.00  0.00              
ATOM     20  O   CYS    14       9.495  29.655  63.594  1.00  0.00              
ATOM     21  N   LYS    15       7.770  30.380  64.859  1.00  0.00              
ATOM     22  CA  LYS    15       7.897  31.774  64.448  1.00  0.00              
ATOM     23  C   LYS    15       9.297  32.297  64.736  1.00  0.00              
ATOM     24  O   LYS    15       9.712  33.327  64.204  1.00  0.00              
ATOM     25  N   GLY    16      10.033  31.557  65.564  1.00  0.00              
ATOM     26  CA  GLY    16      11.395  31.914  65.901  1.00  0.00              
ATOM     27  C   GLY    16      12.336  31.438  64.800  1.00  0.00              
ATOM     28  O   GLY    16      13.078  32.230  64.220  1.00  0.00              
ATOM     29  N   PRO    17      12.302  30.133  64.515  1.00  0.00              
ATOM     30  CA  PRO    17      13.161  29.566  63.477  1.00  0.00              
ATOM     31  C   PRO    17      12.802  30.132  62.115  1.00  0.00              
ATOM     32  O   PRO    17      11.652  30.071  61.673  1.00  0.00              
ATOM     33  N   LEU    18      13.814  30.708  61.492  1.00  0.00              
ATOM     34  CA  LEU    18      13.661  31.340  60.192  1.00  0.00              
ATOM     35  C   LEU    18      13.810  30.350  59.038  1.00  0.00              
ATOM     36  O   LEU    18      14.875  29.764  58.842  1.00  0.00              
ATOM     37  N   VAL    19      12.739  30.197  58.256  1.00  0.00              
ATOM     38  CA  VAL    19      12.773  29.308  57.102  1.00  0.00              
ATOM     39  C   VAL    19      13.928  29.722  56.193  1.00  0.00              
ATOM     40  O   VAL    19      14.169  30.902  55.976  1.00  0.00              
ATOM     41  N   PHE    20      14.657  28.768  55.672  1.00  0.00              
ATOM     42  CA  PHE    20      15.774  29.097  54.819  1.00  0.00              
ATOM     43  C   PHE    20      15.372  29.102  53.361  1.00  0.00              
ATOM     44  O   PHE    20      14.441  28.415  52.952  1.00  0.00              
ATOM     45  N   ASP    21      15.350  28.420  49.559  1.00  0.00              
ATOM     46  CA  ASP    21      15.565  27.267  48.728  1.00  0.00              
ATOM     47  C   ASP    21      15.842  25.976  49.500  1.00  0.00              
ATOM     48  O   ASP    21      16.977  25.698  49.886  1.00  0.00              
ATOM     49  N   LYS    22      14.788  25.175  49.693  1.00  0.00              
ATOM     50  CA  LYS    22      14.901  23.893  50.387  1.00  0.00              
ATOM     51  C   LYS    22      15.709  22.912  49.555  1.00  0.00              
ATOM     52  O   LYS    22      15.154  22.217  48.704  1.00  0.00              
ATOM     53  N   SER    23      17.010  22.843  49.801  1.00  0.00              
ATOM     54  CA  SER    23      17.861  21.918  49.062  1.00  0.00              
ATOM     55  C   SER    23      17.543  21.980  47.570  1.00  0.00              
ATOM     56  O   SER    23      17.488  20.954  46.893  1.00  0.00              
ATOM     57  N   LYS    24      17.309  23.201  47.081  1.00  0.00              
ATOM     58  CA  LYS    24      16.964  23.448  45.680  1.00  0.00              
ATOM     59  C   LYS    24      15.453  23.588  45.526  1.00  0.00              
ATOM     60  O   LYS    24      14.878  23.170  44.521  1.00  0.00              
ATOM     61  N   ASP    25      14.816  24.178  46.536  1.00  0.00              
ATOM     62  CA  ASP    25      13.376  24.362  46.501  1.00  0.00              
ATOM     63  C   ASP    25      12.942  25.735  46.988  1.00  0.00              
ATOM     64  O   ASP    25      13.474  26.754  46.552  1.00  0.00              
ATOM     65  N   GLU    26      11.957  25.752  47.883  1.00  0.00              
ATOM     66  CA  GLU    26      11.425  27.001  48.429  1.00  0.00              
ATOM     67  C   GLU    26      12.044  27.318  49.796  1.00  0.00              
ATOM     68  O   GLU    26      13.239  27.125  49.996  1.00  0.00              
ATOM     69  N   LEU    27      11.241  27.825  50.729  1.00  0.00              
ATOM     70  CA  LEU    27      11.732  28.186  52.055  1.00  0.00              
ATOM     71  C   LEU    27      11.628  27.016  53.034  1.00  0.00              
ATOM     72  O   LEU    27      10.546  26.572  53.382  1.00  0.00              
ATOM     73  N   ILE    28      12.770  26.485  53.412  1.00  0.00              
ATOM     74  CA  ILE    28      12.836  25.317  54.277  1.00  0.00              
ATOM     75  C   ILE    28      13.045  25.673  55.743  1.00  0.00              
ATOM     76  O   ILE    28      14.049  26.263  56.123  1.00  0.00              
ATOM     77  N   CYS    29      12.085  25.298  56.570  1.00  0.00              
ATOM     78  CA  CYS    29      12.174  25.568  57.989  1.00  0.00              
ATOM     79  C   CYS    29      13.068  24.532  58.666  1.00  0.00              
ATOM     80  O   CYS    29      12.664  23.397  58.856  1.00  0.00              
ATOM     81  N   LYS    30      14.285  24.910  59.066  1.00  0.00              
ATOM     82  CA  LYS    30      15.233  23.985  59.689  1.00  0.00              
ATOM     83  C   LYS    30      14.651  23.111  60.789  1.00  0.00              
ATOM     84  O   LYS    30      15.259  22.108  61.159  1.00  0.00              
ATOM     85  N   GLY    31      13.498  23.469  61.327  1.00  0.00              
ATOM     86  CA  GLY    31      12.918  22.675  62.402  1.00  0.00              
ATOM     87  C   GLY    31      11.802  21.768  61.926  1.00  0.00              
ATOM     88  O   GLY    31      11.877  20.566  62.138  1.00  0.00              
ATOM     89  N   ASP    32      10.822  22.279  61.192  1.00  0.00              
ATOM     90  CA  ASP    32       9.815  21.372  60.659  1.00  0.00              
ATOM     91  C   ASP    32      10.237  21.044  59.251  1.00  0.00              
ATOM     92  O   ASP    32       9.731  20.122  58.639  1.00  0.00              
ATOM     93  N   ARG    33      11.193  21.832  58.766  1.00  0.00              
ATOM     94  CA  ARG    33      11.751  21.669  57.445  1.00  0.00              
ATOM     95  C   ARG    33      10.751  21.898  56.331  1.00  0.00              
ATOM     96  O   ARG    33      10.911  21.409  55.212  1.00  0.00              
ATOM     97  N   LEU    34       9.712  22.632  56.669  1.00  0.00              
ATOM     98  CA  LEU    34       8.630  22.945  55.749  1.00  0.00              
ATOM     99  C   LEU    34       9.110  23.822  54.598  1.00  0.00              
ATOM    100  O   LEU    34       9.977  24.673  54.783  1.00  0.00              
ATOM    101  N   ALA    35       8.554  23.599  53.413  1.00  0.00              
ATOM    102  CA  ALA    35       8.936  24.356  52.241  1.00  0.00              
ATOM    103  C   ALA    35       7.800  25.254  51.772  1.00  0.00              
ATOM    104  O   ALA    35       6.695  24.783  51.502  1.00  0.00              
END
