
#######################################################
#                                                     #
#                        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   27 (  108),  selected   27 , name T0348AL381_5
# Molecule2: number of CA atoms   61 (  465),  selected   27 , name T0348.pdb
# PARAMETERS: T0348AL381_5.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:    27        10 - 36          2.16     2.16
  LCS_AVERAGE:     44.26

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14        23 - 36          1.58     2.37
  LCS_AVERAGE:     21.19

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11        25 - 35          0.96     2.70
  LONGEST_CONTINUOUS_SEGMENT:    11        26 - 36          0.66     3.00
  LCS_AVERAGE:     14.75

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      9   12   27     7   10   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     C      11     C      11      9   12   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     P      12     P      12      9   12   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L      13     L      13      9   12   27     7   10   13   16   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     C      14     C      14      9   12   27     7   10   13   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K      15     K      15      9   12   27     6   10   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     G      16     G      16      9   12   27     7   10   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     P      17     P      17      9   12   27     7   10   14   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L      18     L      18      9   12   27     3    8   10   13   18   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     V      19     V      19      5   12   27     3    5    6    9   21   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     F      20     F      20      5   12   27     4    5    8   15   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     D      21     D      21      5   12   27     4    5   12   18   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K      22     K      22      5    9   27     4    5    6    7    9   16   24   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     S      23     S      23      5   14   27     4    5   12   18   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K      24     K      24      5   14   27     4    4    6    8   11   23   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     D      25     D      25     11   14   27     4    5   13   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     E      26     E      26     11   14   27     4   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L      27     L      27     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     I      28     I      28     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     C      29     C      29     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     K      30     K      30     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     G      31     G      31     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     D      32     D      32     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     R      33     R      33     11   14   27     4   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     L      34     L      34     11   14   27     4   11   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     A      35     A      35     11   14   27     7   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_GDT     F      36     F      36     11   14   27     4   12   16   19   22   24   26   26   27   27   27   27   27   27   27   27   27   27   27   27 
LCS_AVERAGE  LCS_A:  26.74  (  14.75   21.19   44.26 )

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      7     12     16     19     22     24     26     26     27     27     27     27     27     27     27     27     27     27     27     27 
GDT PERCENT_CA  11.48  19.67  26.23  31.15  36.07  39.34  42.62  42.62  44.26  44.26  44.26  44.26  44.26  44.26  44.26  44.26  44.26  44.26  44.26  44.26
GDT RMS_LOCAL    0.29   0.62   1.04   1.30   1.50   1.71   1.94   1.94   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16
GDT RMS_ALL_CA   3.07   2.93   2.43   2.28   2.23   2.18   2.18   2.18   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16   2.16

#      Molecule1      Molecule2       DISTANCE
LGA    V      10      V      10          1.477
LGA    C      11      C      11          1.478
LGA    P      12      P      12          2.182
LGA    L      13      L      13          2.526
LGA    C      14      C      14          1.769
LGA    K      15      K      15          0.248
LGA    G      16      G      16          0.579
LGA    P      17      P      17          1.307
LGA    L      18      L      18          3.550
LGA    V      19      V      19          3.093
LGA    F      20      F      20          2.988
LGA    D      21      D      21          1.775
LGA    K      22      K      22          5.559
LGA    S      23      S      23          2.228
LGA    K      24      K      24          3.463
LGA    D      25      D      25          2.090
LGA    E      26      E      26          1.965
LGA    L      27      L      27          2.155
LGA    I      28      I      28          1.181
LGA    C      29      C      29          0.836
LGA    K      30      K      30          1.099
LGA    G      31      G      31          1.375
LGA    D      32      D      32          1.137
LGA    R      33      R      33          0.849
LGA    L      34      L      34          1.333
LGA    A      35      A      35          1.185
LGA    F      36      F      36          1.639

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   27   61    4.0     26    1.94    34.426    33.267     1.274

LGA_LOCAL      RMSD =  1.940  Number of atoms =   26  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.184  Number of atoms =   27 
Std_ALL_ATOMS  RMSD =  2.161  (standard rmsd on all 27 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.547420 * X  +   0.404666 * Y  +   0.732514 * Z  + -29.396152
  Y_new =   0.534602 * X  +  -0.504328 * Y  +   0.678126 * Z  + -11.997434
  Z_new =   0.643842 * X  +   0.762823 * Y  +   0.059744 * Z  + -152.988754 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.492636   -1.648957  [ DEG:    85.5217    -94.4783 ]
  Theta =  -0.699508   -2.442084  [ DEG:   -40.0789   -139.9211 ]
  Phi   =   2.368041   -0.773552  [ DEG:   135.6788    -44.3213 ]
 
# 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_5                                  
REMARK     2: T0348.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0348AL381_5.T0348.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   27   61   4.0   26   1.94  33.267     2.16
REMARK  ---------------------------------------------------------- 
MOLECULE T0348AL381_5
REMARK Aligment from pdb entry: 1s72Z
ATOM      1  N   VAL    10      11.061  33.674  59.018  1.00  0.00              
ATOM      2  CA  VAL    10      10.079  33.279  60.020  1.00  0.00              
ATOM      3  C   VAL    10       9.155  32.159  59.551  1.00  0.00              
ATOM      4  O   VAL    10       8.344  32.343  58.648  1.00  0.00              
ATOM      5  N   CYS    11       9.277  30.998  60.183  1.00  0.00              
ATOM      6  CA  CYS    11       8.454  29.853  59.835  1.00  0.00              
ATOM      7  C   CYS    11       6.962  30.166  59.904  1.00  0.00              
ATOM      8  O   CYS    11       6.505  30.796  60.850  1.00  0.00              
ATOM      9  N   PRO    12       6.186  29.745  58.887  1.00  0.00              
ATOM     10  CA  PRO    12       4.739  29.989  58.865  1.00  0.00              
ATOM     11  C   PRO    12       3.999  29.150  59.911  1.00  0.00              
ATOM     12  O   PRO    12       3.010  29.604  60.491  1.00  0.00              
ATOM     13  N   LEU    13       4.484  27.927  60.137  1.00  0.00              
ATOM     14  CA  LEU    13       3.887  26.994  61.099  1.00  0.00              
ATOM     15  C   LEU    13       4.037  27.576  62.510  1.00  0.00              
ATOM     16  O   LEU    13       3.073  28.079  63.085  1.00  0.00              
ATOM     17  N   CYS    14       5.238  27.497  63.075  1.00  0.00              
ATOM     18  CA  CYS    14       5.477  28.093  64.383  1.00  0.00              
ATOM     19  C   CYS    14       5.816  29.524  63.977  1.00  0.00              
ATOM     20  O   CYS    14       5.402  29.957  62.905  1.00  0.00              
ATOM     21  N   LYS    15       6.546  30.270  64.791  1.00  0.00              
ATOM     22  CA  LYS    15       6.875  31.629  64.382  1.00  0.00              
ATOM     23  C   LYS    15       8.368  31.861  64.468  1.00  0.00              
ATOM     24  O   LYS    15       8.864  32.978  64.302  1.00  0.00              
ATOM     25  N   GLY    16       9.079  30.773  64.730  1.00  0.00              
ATOM     26  CA  GLY    16      10.524  30.778  64.887  1.00  0.00              
ATOM     27  C   GLY    16      11.271  31.132  63.593  1.00  0.00              
ATOM     28  O   GLY    16      10.857  30.735  62.497  1.00  0.00              
ATOM     29  N   PRO    17      12.365  31.883  63.731  1.00  0.00              
ATOM     30  CA  PRO    17      13.198  32.291  62.596  1.00  0.00              
ATOM     31  C   PRO    17      14.180  31.184  62.213  1.00  0.00              
ATOM     32  O   PRO    17      15.398  31.383  62.258  1.00  0.00              
ATOM     33  N   LEU    18      13.649  30.025  61.830  1.00  0.00              
ATOM     34  CA  LEU    18      14.490  28.895  61.465  1.00  0.00              
ATOM     35  C   LEU    18      14.185  28.251  60.113  1.00  0.00              
ATOM     36  O   LEU    18      14.334  27.038  59.951  1.00  0.00              
ATOM     37  N   VAL    19      13.763  29.059  59.145  1.00  0.00              
ATOM     38  CA  VAL    19      13.452  28.550  57.818  1.00  0.00              
ATOM     39  C   VAL    19      14.631  28.716  56.856  1.00  0.00              
ATOM     40  O   VAL    19      15.136  29.823  56.656  1.00  0.00              
ATOM     41  N   PHE    20      15.073  27.600  56.278  1.00  0.00              
ATOM     42  CA  PHE    20      16.173  27.615  55.320  1.00  0.00              
ATOM     43  C   PHE    20      15.724  27.024  54.006  1.00  0.00              
ATOM     44  O   PHE    20      14.795  26.210  53.956  1.00  0.00              
ATOM     45  N   ASP    21      16.394  27.435  52.937  1.00  0.00              
ATOM     46  CA  ASP    21      16.069  26.941  51.611  1.00  0.00              
ATOM     47  C   ASP    21      16.646  25.534  51.501  1.00  0.00              
ATOM     48  O   ASP    21      17.758  25.283  51.960  1.00  0.00              
ATOM     49  N   LYS    22      15.885  24.611  50.920  1.00  0.00              
ATOM     50  CA  LYS    22      16.375  23.247  50.751  1.00  0.00              
ATOM     51  C   LYS    22      16.706  22.993  49.288  1.00  0.00              
ATOM     52  O   LYS    22      17.434  22.061  48.951  1.00  0.00              
ATOM     53  N   SER    23      16.167  23.843  48.423  1.00  0.00              
ATOM     54  CA  SER    23      16.395  23.720  46.998  1.00  0.00              
ATOM     55  C   SER    23      15.540  24.761  46.308  1.00  0.00              
ATOM     56  O   SER    23      14.986  25.636  46.968  1.00  0.00              
ATOM     57  N   LYS    24      15.417  24.668  44.990  1.00  0.00              
ATOM     58  CA  LYS    24      14.627  25.626  44.233  1.00  0.00              
ATOM     59  C   LYS    24      13.153  25.648  44.651  1.00  0.00              
ATOM     60  O   LYS    24      12.402  24.705  44.386  1.00  0.00              
ATOM     61  N   ASP    25      12.754  26.735  45.309  1.00  0.00              
ATOM     62  CA  ASP    25      11.379  26.888  45.757  1.00  0.00              
ATOM     63  C   ASP    25      10.971  26.044  46.957  1.00  0.00              
ATOM     64  O   ASP    25       9.806  26.051  47.356  1.00  0.00              
ATOM     65  N   GLU    26      11.917  25.321  47.544  1.00  0.00              
ATOM     66  CA  GLU    26      11.623  24.466  48.688  1.00  0.00              
ATOM     67  C   GLU    26      12.198  25.018  50.002  1.00  0.00              
ATOM     68  O   GLU    26      13.414  25.230  50.131  1.00  0.00              
ATOM     69  N   LEU    27      11.320  25.233  50.981  1.00  0.00              
ATOM     70  CA  LEU    27      11.744  25.767  52.273  1.00  0.00              
ATOM     71  C   LEU    27      11.428  24.850  53.450  1.00  0.00              
ATOM     72  O   LEU    27      10.430  24.119  53.441  1.00  0.00              
ATOM     73  N   ILE    28      12.289  24.882  54.463  1.00  0.00              
ATOM     74  CA  ILE    28      12.087  24.038  55.631  1.00  0.00              
ATOM     75  C   ILE    28      12.578  24.655  56.939  1.00  0.00              
ATOM     76  O   ILE    28      13.603  25.340  56.972  1.00  0.00              
ATOM     77  N   CYS    29      11.825  24.403  58.010  1.00  0.00              
ATOM     78  CA  CYS    29      12.150  24.903  59.344  1.00  0.00              
ATOM     79  C   CYS    29      12.986  23.863  60.093  1.00  0.00              
ATOM     80  O   CYS    29      12.544  22.730  60.301  1.00  0.00              
ATOM     81  N   LYS    30      14.193  24.253  60.491  1.00  0.00              
ATOM     82  CA  LYS    30      15.091  23.362  61.219  1.00  0.00              
ATOM     83  C   LYS    30      14.542  23.037  62.603  1.00  0.00              
ATOM     84  O   LYS    30      14.872  22.001  63.191  1.00  0.00              
ATOM     85  N   GLY    31      13.698  23.932  63.111  1.00  0.00              
ATOM     86  CA  GLY    31      13.093  23.786  64.426  1.00  0.00              
ATOM     87  C   GLY    31      11.989  22.732  64.473  1.00  0.00              
ATOM     88  O   GLY    31      12.126  21.721  65.164  1.00  0.00              
ATOM     89  N   ASP    32      10.900  22.958  63.741  1.00  0.00              
ATOM     90  CA  ASP    32       9.795  22.006  63.752  1.00  0.00              
ATOM     91  C   ASP    32       9.741  21.067  62.550  1.00  0.00              
ATOM     92  O   ASP    32       8.895  20.176  62.507  1.00  0.00              
ATOM     93  N   ARG    33      10.634  21.273  61.581  1.00  0.00              
ATOM     94  CA  ARG    33      10.702  20.440  60.376  1.00  0.00              
ATOM     95  C   ARG    33       9.732  20.800  59.245  1.00  0.00              
ATOM     96  O   ARG    33       9.785  20.198  58.174  1.00  0.00              
ATOM     97  N   LEU    34       8.852  21.770  59.474  1.00  0.00              
ATOM     98  CA  LEU    34       7.884  22.174  58.454  1.00  0.00              
ATOM     99  C   LEU    34       8.549  22.435  57.102  1.00  0.00              
ATOM    100  O   LEU    34       9.400  23.321  56.973  1.00  0.00              
ATOM    101  N   ALA    35       8.146  21.655  56.101  1.00  0.00              
ATOM    102  CA  ALA    35       8.683  21.775  54.749  1.00  0.00              
ATOM    103  C   ALA    35       7.574  22.309  53.841  1.00  0.00              
ATOM    104  O   ALA    35       6.502  21.711  53.747  1.00  0.00              
ATOM    105  N   PHE    36       7.829  23.429  53.172  1.00  0.00              
ATOM    106  CA  PHE    36       6.805  24.031  52.325  1.00  0.00              
ATOM    107  C   PHE    36       7.324  24.684  51.048  1.00  0.00              
ATOM    108  O   PHE    36       8.530  24.841  50.854  1.00  0.00              
END
