
#######################################################
#                                                     #
#                        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 T0354AL381_4
# Molecule2: number of CA atoms  122 (  928),  selected   26 , name T0354.pdb
# PARAMETERS: T0354AL381_4.T0354.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        44 - 69          2.06     2.06
  LCS_AVERAGE:     21.31

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25        44 - 68          1.64     2.09
  LCS_AVERAGE:     19.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24        44 - 67          0.97     2.25
  LCS_AVERAGE:     18.25

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:  122
LCS_GDT     S      44     S      44     24   25   26     8   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     N      45     N      45     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     R      46     R      46     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     Q      47     Q      47     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      48     V      48     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      49     K      49     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     A      50     A      50     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      51     L      51     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     A      52     A      52     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     N      53     N      53     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     S      54     S      54     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      55     V      55     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     Q      56     Q      56     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      57     V      57     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      58     K      58     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     L      59     L      59     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     K      60     K      60     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     E      61     E      61     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     A      62     A      62     24   25   26    14   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G      63     G      63     24   25   26    16   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      64     V      64     24   25   26    14   21   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     D      65     D      65     24   25   26     3    5   10   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     I      66     I      66     24   25   26     3    5   10   15   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     V      67     V      67     24   25   26     3    9   21   23   24   24   24   24   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     G      68     G      68      3   25   26     3    3    4    4    4    5   19   19   24   26   26   26   26   26   26   26   26   26   26   26 
LCS_GDT     S      69     S      69      0    4   26     0    0    3    3    4    4    5   10   11   26   26   26   26   26   26   26   26   26   26   26 
LCS_AVERAGE  LCS_A:  19.80  (  18.25   19.83   21.31 )

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     16     21     21     23     24     24     24     24     24     26     26     26     26     26     26     26     26     26     26     26 
GDT PERCENT_CA  13.11  17.21  17.21  18.85  19.67  19.67  19.67  19.67  19.67  21.31  21.31  21.31  21.31  21.31  21.31  21.31  21.31  21.31  21.31  21.31
GDT RMS_LOCAL    0.30   0.45   0.45   0.79   0.97   0.97   0.97   0.97   0.97   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06
GDT RMS_ALL_CA   2.30   2.30   2.30   2.23   2.25   2.25   2.25   2.25   2.25   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06   2.06

#      Molecule1      Molecule2       DISTANCE
LGA    S      44      S      44          0.922
LGA    N      45      N      45          0.408
LGA    R      46      R      46          0.431
LGA    Q      47      Q      47          0.678
LGA    V      48      V      48          0.649
LGA    K      49      K      49          0.398
LGA    A      50      A      50          0.532
LGA    L      51      L      51          0.827
LGA    A      52      A      52          0.728
LGA    N      53      N      53          0.321
LGA    S      54      S      54          0.649
LGA    V      55      V      55          0.844
LGA    Q      56      Q      56          0.590
LGA    V      57      V      57          0.250
LGA    K      58      K      58          0.113
LGA    L      59      L      59          0.175
LGA    K      60      K      60          0.647
LGA    E      61      E      61          0.556
LGA    A      62      A      62          0.635
LGA    G      63      G      63          0.394
LGA    V      64      V      64          0.525
LGA    D      65      D      65          2.189
LGA    I      66      I      66          2.738
LGA    V      67      V      67          1.869
LGA    G      68      G      68          7.265
LGA    S      69      S      69          7.520

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   26  122    4.0     24    0.97    19.262    19.672     2.234

LGA_LOCAL      RMSD =  0.974  Number of atoms =   24  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  2.254  Number of atoms =   26 
Std_ALL_ATOMS  RMSD =  2.064  (standard rmsd on all 26 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.749431 * X  +  -0.316012 * Y  +   0.581798 * Z  +  59.857609
  Y_new =  -0.284044 * X  +   0.947224 * Y  +   0.148614 * Z  + -18.845852
  Z_new =  -0.598057 * X  +  -0.053880 * Y  +  -0.799641 * Z  +  57.589668 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =  -3.074314    0.067279  [ DEG:  -176.1452      3.8548 ]
  Theta =   0.641074    2.500518  [ DEG:    36.7309    143.2691 ]
  Phi   =  -2.779309    0.362283  [ DEG:  -159.2427     20.7573 ]
 
# 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: T0354AL381_4                                  
REMARK     2: T0354.pdb                                     
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0354AL381_4.T0354.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   26  122   4.0   24   0.97  19.672     2.06
REMARK  ---------------------------------------------------------- 
MOLECULE T0354AL381_4
REMARK Aligment from pdb entry: 1uvxA
ATOM      1  N   SER    44      33.282  33.241  38.274  1.00  0.00              
ATOM      2  CA  SER    44      32.763  34.385  37.536  1.00  0.00              
ATOM      3  C   SER    44      33.739  34.771  36.433  1.00  0.00              
ATOM      4  O   SER    44      34.686  34.036  36.149  1.00  0.00              
ATOM      5  N   ASN    45      33.510  35.928  35.820  1.00  0.00              
ATOM      6  CA  ASN    45      34.351  36.387  34.722  1.00  0.00              
ATOM      7  C   ASN    45      35.710  36.895  35.193  1.00  0.00              
ATOM      8  O   ASN    45      36.612  37.114  34.384  1.00  0.00              
ATOM      9  N   ARG    46      35.856  37.087  36.500  1.00  0.00              
ATOM     10  CA  ARG    46      37.144  37.477  37.061  1.00  0.00              
ATOM     11  C   ARG    46      38.122  36.306  36.991  1.00  0.00              
ATOM     12  O   ARG    46      39.295  36.484  36.667  1.00  0.00              
ATOM     13  N   GLN    47      37.628  35.109  37.291  1.00  0.00              
ATOM     14  CA  GLN    47      38.442  33.900  37.229  1.00  0.00              
ATOM     15  C   GLN    47      38.656  33.452  35.789  1.00  0.00              
ATOM     16  O   GLN    47      39.749  33.017  35.425  1.00  0.00              
ATOM     17  N   VAL    48      37.614  33.552  34.971  1.00  0.00              
ATOM     18  CA  VAL    48      37.726  33.150  33.575  1.00  0.00              
ATOM     19  C   VAL    48      38.705  34.036  32.813  1.00  0.00              
ATOM     20  O   VAL    48      39.462  33.554  31.969  1.00  0.00              
ATOM     21  N   LYS    49      38.686  35.330  33.114  1.00  0.00              
ATOM     22  CA  LYS    49      39.576  36.281  32.464  1.00  0.00              
ATOM     23  C   LYS    49      41.014  36.082  32.923  1.00  0.00              
ATOM     24  O   LYS    49      41.956  36.269  32.151  1.00  0.00              
ATOM     25  N   ALA    50      41.179  35.703  34.186  1.00  0.00              
ATOM     26  CA  ALA    50      42.503  35.410  34.715  1.00  0.00              
ATOM     27  C   ALA    50      43.095  34.212  33.978  1.00  0.00              
ATOM     28  O   ALA    50      44.231  34.258  33.503  1.00  0.00              
ATOM     29  N   LEU    51      42.312  33.142  33.879  1.00  0.00              
ATOM     30  CA  LEU    51      42.757  31.928  33.206  1.00  0.00              
ATOM     31  C   LEU    51      43.093  32.206  31.743  1.00  0.00              
ATOM     32  O   LEU    51      44.103  31.728  31.228  1.00  0.00              
ATOM     33  N   ALA    52      42.240  32.982  31.082  1.00  0.00              
ATOM     34  CA  ALA    52      42.472  33.355  29.692  1.00  0.00              
ATOM     35  C   ALA    52      43.776  34.129  29.554  1.00  0.00              
ATOM     36  O   ALA    52      44.606  33.822  28.699  1.00  0.00              
ATOM     37  N   ASN    53      43.951  35.135  30.403  1.00  0.00              
ATOM     38  CA  ASN    53      45.140  35.975  30.358  1.00  0.00              
ATOM     39  C   ASN    53      46.407  35.159  30.590  1.00  0.00              
ATOM     40  O   ASN    53      47.450  35.423  29.990  1.00  0.00              
ATOM     41  N   SER    54      46.307  34.163  31.464  1.00  0.00              
ATOM     42  CA  SER    54      47.450  33.327  31.800  1.00  0.00              
ATOM     43  C   SER    54      47.870  32.439  30.634  1.00  0.00              
ATOM     44  O   SER    54      49.059  32.192  30.429  1.00  0.00              
ATOM     45  N   VAL    55      46.892  31.960  29.873  1.00  0.00              
ATOM     46  CA  VAL    55      47.174  31.150  28.695  1.00  0.00              
ATOM     47  C   VAL    55      47.781  32.019  27.600  1.00  0.00              
ATOM     48  O   VAL    55      48.808  31.673  27.015  1.00  0.00              
ATOM     49  N   GLN    56      47.140  33.150  27.328  1.00  0.00              
ATOM     50  CA  GLN    56      47.667  34.109  26.366  1.00  0.00              
ATOM     51  C   GLN    56      49.128  34.418  26.680  1.00  0.00              
ATOM     52  O   GLN    56      50.003  34.266  25.827  1.00  0.00              
ATOM     53  N   VAL    57      49.382  34.853  27.911  1.00  0.00              
ATOM     54  CA  VAL    57      50.736  35.138  28.367  1.00  0.00              
ATOM     55  C   VAL    57      51.647  33.933  28.156  1.00  0.00              
ATOM     56  O   VAL    57      52.788  34.077  27.716  1.00  0.00              
ATOM     57  N   LYS    58      51.140  32.745  28.474  1.00  0.00              
ATOM     58  CA  LYS    58      51.895  31.512  28.282  1.00  0.00              
ATOM     59  C   LYS    58      52.366  31.371  26.838  1.00  0.00              
ATOM     60  O   LYS    58      53.561  31.234  26.574  1.00  0.00              
ATOM     61  N   LEU    59      51.415  31.399  25.911  1.00  0.00              
ATOM     62  CA  LEU    59      51.719  31.232  24.494  1.00  0.00              
ATOM     63  C   LEU    59      52.659  32.320  23.987  1.00  0.00              
ATOM     64  O   LEU    59      53.581  32.048  23.216  1.00  0.00              
ATOM     65  N   LYS    60      52.418  33.554  24.416  1.00  0.00              
ATOM     66  CA  LYS    60      53.255  34.674  24.004  1.00  0.00              
ATOM     67  C   LYS    60      54.710  34.417  24.378  1.00  0.00              
ATOM     68  O   LYS    60      55.623  34.743  23.623  1.00  0.00              
ATOM     69  N   GLU    61      54.915  33.823  25.549  1.00  0.00              
ATOM     70  CA  GLU    61      56.258  33.556  26.048  1.00  0.00              
ATOM     71  C   GLU    61      56.871  32.319  25.398  1.00  0.00              
ATOM     72  O   GLU    61      58.081  32.101  25.473  1.00  0.00              
ATOM     73  N   ALA    62      56.028  31.515  24.759  1.00  0.00              
ATOM     74  CA  ALA    62      56.484  30.302  24.092  1.00  0.00              
ATOM     75  C   ALA    62      56.741  30.548  22.609  1.00  0.00              
ATOM     76  O   ALA    62      57.086  29.627  21.867  1.00  0.00              
ATOM     77  N   GLY    63      56.572  31.797  22.184  1.00  0.00              
ATOM     78  CA  GLY    63      56.970  32.216  20.853  1.00  0.00              
ATOM     79  C   GLY    63      55.924  32.003  19.777  1.00  0.00              
ATOM     80  O   GLY    63      56.250  31.928  18.591  1.00  0.00              
ATOM     81  N   VAL    64      54.663  31.912  20.187  1.00  0.00              
ATOM     82  CA  VAL    64      53.570  31.656  19.256  1.00  0.00              
ATOM     83  C   VAL    64      53.171  32.918  18.500  1.00  0.00              
ATOM     84  O   VAL    64      52.967  33.971  19.103  1.00  0.00              
ATOM     85  N   ASP    65      53.063  32.809  17.180  1.00  0.00              
ATOM     86  CA  ASP    65      52.546  33.903  16.350  1.00  0.00              
ATOM     87  C   ASP    65      51.268  34.478  16.948  1.00  0.00              
ATOM     88  O   ASP    65      50.403  33.719  17.384  1.00  0.00              
ATOM     89  N   ILE    66      51.148  35.802  16.959  1.00  0.00              
ATOM     90  CA  ILE    66      49.994  36.471  17.568  1.00  0.00              
ATOM     91  C   ILE    66      48.678  36.000  16.957  1.00  0.00              
ATOM     92  O   ILE    66      47.679  35.886  17.668  1.00  0.00              
ATOM     93  N   VAL    67      48.682  35.733  15.655  1.00  0.00              
ATOM     94  CA  VAL    67      47.478  35.280  14.969  1.00  0.00              
ATOM     95  C   VAL    67      47.066  33.904  15.476  1.00  0.00              
ATOM     96  O   VAL    67      45.880  33.586  15.542  1.00  0.00              
ATOM     97  N   GLY    68      48.055  33.093  15.840  1.00  0.00              
ATOM     98  CA  GLY    68      47.795  31.776  16.406  1.00  0.00              
ATOM     99  C   GLY    68      47.252  31.899  17.825  1.00  0.00              
ATOM    100  O   GLY    68      46.409  31.108  18.249  1.00  0.00              
ATOM    101  N   SER    69      47.741  32.893  18.558  1.00  0.00              
ATOM    102  CA  SER    69      47.241  33.153  19.902  1.00  0.00              
ATOM    103  C   SER    69      45.782  33.595  19.824  1.00  0.00              
ATOM    104  O   SER    69      44.983  33.312  20.718  1.00  0.00              
END
