
#######################################################
#                                                     #
#                        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   34 (  136),  selected   34 , name T0361AL381_5-D1
# Molecule2: number of CA atoms  158 ( 1268),  selected   34 , name T0361_D1.pdb
# PARAMETERS: T0361AL381_5-D1.T0361_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:    15        39 - 53          4.49    11.08
  LCS_AVERAGE:      7.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8        40 - 47          1.86    15.06
  LCS_AVERAGE:      3.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6        53 - 58          0.45    21.07
  LCS_AVERAGE:      2.57

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:  158
LCS_GDT     P      39     P      39      4    5   15     4    4    4    4    7    9   10   10   11   12   15   15   16   19   21   23   24   25   26   27 
LCS_GDT     S      40     S      40      4    8   15     4    4    5    6    7    9   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     L      41     L      41      4    8   15     4    4    5    6    7    9   10   10   11   12   12   14   16   18   21   23   24   25   26   27 
LCS_GDT     F      42     F      42      4    8   15     4    4    4    4    7    9   10   10   11   12   12   14   15   16   18   21   24   25   26   27 
LCS_GDT     V      43     V      43      4    8   15     3    4    5    6    7    9   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     D      44     D      44      4    8   15     3    4    5    5    7    8   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     N      45     N      45      4    8   15     3    4    5    6    7    9   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     D      46     D      46      4    8   15     3    4    5    6    7    9   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     E      47     E      47      3    8   15     3    3    3    5    7    9   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     E      48     E      48      3    6   15     3    4    5    6    7    9   10   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     I      49     I      49      3    3   15     3    4    4    4    5    8    9   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     V      50     V      50      3    3   15     3    4    4    4    5    5    5    7    8   13   14   15   17   19   21   23   24   25   26   27 
LCS_GDT     E      51     E      51      3    3   15     3    3    4    4    4    4    5   10   11   13   14   15   17   19   21   23   24   25   26   27 
LCS_GDT     Y      52     Y      52      3    3   15     3    3    4    4    4    4    4    5    7    9   13   15   17   19   21   23   24   25   26   27 
LCS_GDT     A      53     A      53      6    6   15     5    6    6    6    6    6    7    7    7    8   10   14   17   19   21   23   24   25   26   27 
LCS_GDT     V      54     V      54      6    6   12     5    6    6    6    6    6    7    7    7    9   11   13   14   14   18   23   24   25   26   27 
LCS_GDT     K      55     K      55      6    6   11     5    6    6    6    6    6    7    7    7    7    9   13   14   14   15   16   18   21   22   24 
LCS_GDT     P      56     P      56      6    6   11     5    6    6    6    6    6    7    7    8   10   11   13   14   16   17   19   24   25   26   27 
LCS_GDT     L      57     L      57      6    6   11     5    6    6    6    6    6    7    7    8   10   11   13   15   15   17   21   24   25   26   27 
LCS_GDT     L      58     L      58      6    6   11     4    6    6    6    6    6    7    7    8   10   11   13   14   15   17   17   20   22   22   24 
LCS_GDT     A      59     A      59      3    3   11     3    3    3    3    3    4    5    7    7    7    7   11   14   15   17   18   20   22   22   24 
LCS_GDT     P      63     P      63      3    6   10     3    3    5    6    6    6    6    7    7    8    9    9   10   10   10   12   12   15   17   20 
LCS_GDT     L      64     L      64      5    6   10     3    3    4    6    6    6    6    7    7    7    7    9   10   10   10   10   10   11   11   13 
LCS_GDT     D      65     D      65      5    6   10     4    4    5    6    6    6    6    7    7    8    9    9   10   10   10   10   11   13   14   21 
LCS_GDT     D      66     D      66      5    6   10     4    4    5    6    6    6    6    7    7    8   14   15   17   18   21   23   24   25   26   27 
LCS_GDT     I      67     I      67      5    6   10     4    4    5    6    6    6    6    7    7   13   14   15   17   18   21   23   24   25   26   27 
LCS_GDT     D      68     D      68      5    6   10     4    4    5    6    7    8    9   10   10   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     V      69     V      69      3    5   10     3    4    4    4    7    8    9   10   10   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     A      70     A      70      3    3   10     3    3    4    5    7    8    9   10   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     L      71     L      71      3    3   10     3    3    3    3    3    5    6    8   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     R      72     R      72      3    3   10     3    3    3    3    3    4    6    8   11   11   15   15   16   19   21   23   24   25   26   27 
LCS_GDT     L      73     L      73      3    3    9     3    3    3    4    5    5    6    8   11   13   15   15   17   19   21   23   24   25   26   27 
LCS_GDT     I      74     I      74      3    3    9     3    3    3    4    4    5    7    8   11   11   12   14   15   19   21   23   24   25   26   27 
LCS_GDT     Y      75     Y      75      3    3    9     3    3    3    4    4    5    6    6    7    7    8   11   13   14   17   18   18   21   22   24 
LCS_AVERAGE  LCS_A:   4.60  (   2.57    3.44    7.80 )

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      5      6      6      6      7      9     10     10     11     13     15     15     17     19     21     23     24     25     26     27 
GDT PERCENT_CA   3.16   3.80   3.80   3.80   4.43   5.70   6.33   6.33   6.96   8.23   9.49   9.49  10.76  12.03  13.29  14.56  15.19  15.82  16.46  17.09
GDT RMS_LOCAL    0.24   0.45   0.45   0.45   1.51   2.02   2.25   2.25   2.65   3.52   3.91   3.91   4.44   4.95   5.20   5.58   5.74   6.05   6.32   6.65
GDT RMS_ALL_CA  21.28  21.07  21.07  21.07  11.94  12.58  12.56  12.56  12.35   9.89  10.07  10.07   9.67   9.58   9.53   9.40   9.39   9.27   9.21   9.18

#      Molecule1      Molecule2       DISTANCE
LGA    P      39      P      39          2.771
LGA    S      40      S      40          0.825
LGA    L      41      L      41          0.872
LGA    F      42      F      42          2.948
LGA    V      43      V      43          1.824
LGA    D      44      D      44          3.526
LGA    N      45      N      45          1.693
LGA    D      46      D      46          1.588
LGA    E      47      E      47          2.845
LGA    E      48      E      48          1.944
LGA    I      49      I      49          6.167
LGA    V      50      V      50          7.951
LGA    E      51      E      51          6.314
LGA    Y      52      Y      52          9.690
LGA    A      53      A      53         11.171
LGA    V      54      V      54         12.541
LGA    K      55      K      55         16.399
LGA    P      56      P      56         14.918
LGA    L      57      L      57         14.059
LGA    L      58      L      58         16.173
LGA    A      59      A      59         13.926
LGA    P      63      P      63         20.316
LGA    L      64      L      64         22.368
LGA    D      65      D      65         18.589
LGA    D      66      D      66         17.578
LGA    I      67      I      67         18.459
LGA    D      68      D      68         19.278
LGA    V      69      V      69         15.263
LGA    A      70      A      70         13.604
LGA    L      71      L      71         15.812
LGA    R      72      R      72         13.936
LGA    L      73      L      73         10.505
LGA    I      74      I      74         11.739
LGA    Y      75      Y      75         16.263

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   34  158    4.0     10    2.25     7.120     6.055     0.425

LGA_LOCAL      RMSD =  2.255  Number of atoms =   10  DIST =   4.00
LGA_ALL_ATOMS  RMSD = 12.564  Number of atoms =   34 
Std_ALL_ATOMS  RMSD =  9.118  (standard rmsd on all 34 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.883183 * X  +   0.412025 * Y  +  -0.224106 * Z  +   4.901921
  Y_new =  -0.441732 * X  +  -0.570065 * Y  +   0.692747 * Z  +   6.624600
  Z_new =   0.157674 * X  +   0.710817 * Y  +   0.685477 * Z  + -24.346970 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   0.803544   -2.338048  [ DEG:    46.0397   -133.9603 ]
  Theta =  -0.158335   -2.983258  [ DEG:    -9.0719   -170.9281 ]
  Phi   =  -2.677818    0.463775  [ DEG:  -153.4277     26.5723 ]
 
# 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: T0361AL381_5-D1                               
REMARK     2: T0361_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0361AL381_5-D1.T0361_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   34  158   4.0   10   2.25   6.055     9.12
REMARK  ---------------------------------------------------------- 
MOLECULE T0361AL381_5-D1
REMARK Aligment from pdb entry: 4dcg
ATOM      1  N   PRO    39      23.786   7.563   8.701  1.00  0.00              
ATOM      2  CA  PRO    39      24.970   8.082   9.396  1.00  0.00              
ATOM      3  C   PRO    39      25.579   6.906  10.159  1.00  0.00              
ATOM      4  O   PRO    39      26.787   6.663  10.108  1.00  0.00              
ATOM      5  N   SER    40      24.704   6.153  10.818  1.00  0.00              
ATOM      6  CA  SER    40      25.073   4.975  11.594  1.00  0.00              
ATOM      7  C   SER    40      25.801   3.951  10.720  1.00  0.00              
ATOM      8  O   SER    40      26.785   3.349  11.144  1.00  0.00              
ATOM      9  N   LEU    41      25.329   3.773   9.490  1.00  0.00              
ATOM     10  CA  LEU    41      25.940   2.824   8.564  1.00  0.00              
ATOM     11  C   LEU    41      27.104   3.426   7.793  1.00  0.00              
ATOM     12  O   LEU    41      27.669   2.782   6.906  1.00  0.00              
ATOM     13  N   PHE    42      27.423   4.681   8.097  1.00  0.00              
ATOM     14  CA  PHE    42      28.521   5.358   7.432  1.00  0.00              
ATOM     15  C   PHE    42      28.287   5.734   5.983  1.00  0.00              
ATOM     16  O   PHE    42      29.233   6.026   5.254  1.00  0.00              
ATOM     17  N   VAL    43      27.036   5.818   5.567  1.00  0.00              
ATOM     18  CA  VAL    43      26.776   6.152   4.179  1.00  0.00              
ATOM     19  C   VAL    43      26.309   7.574   3.900  1.00  0.00              
ATOM     20  O   VAL    43      26.093   7.951   2.750  1.00  0.00              
ATOM     21  N   ASP    44      26.223   8.385   4.947  1.00  0.00              
ATOM     22  CA  ASP    44      25.780   9.769   4.793  1.00  0.00              
ATOM     23  C   ASP    44      26.901  10.752   4.399  1.00  0.00              
ATOM     24  O   ASP    44      26.763  11.524   3.446  1.00  0.00              
ATOM     25  N   ASN    45      28.013  10.703   5.129  1.00  0.00              
ATOM     26  CA  ASN    45      29.134  11.612   4.884  1.00  0.00              
ATOM     27  C   ASN    45      29.631  11.548   3.452  1.00  0.00              
ATOM     28  O   ASN    45      29.908  10.471   2.928  1.00  0.00              
ATOM     29  N   ASP    46      29.714  12.712   2.822  1.00  0.00              
ATOM     30  CA  ASP    46      30.186  12.798   1.457  1.00  0.00              
ATOM     31  C   ASP    46      29.118  12.594   0.399  1.00  0.00              
ATOM     32  O   ASP    46      29.414  12.665  -0.787  1.00  0.00              
ATOM     33  N   GLU    47      27.882  12.342   0.804  1.00  0.00              
ATOM     34  CA  GLU    47      26.815  12.130  -0.171  1.00  0.00              
ATOM     35  C   GLU    47      26.139  13.412  -0.618  1.00  0.00              
ATOM     36  O   GLU    47      26.336  14.476  -0.014  1.00  0.00              
ATOM     37  N   GLU    48      25.404  13.322  -1.724  1.00  0.00              
ATOM     38  CA  GLU    48      24.605  14.437  -2.227  1.00  0.00              
ATOM     39  C   GLU    48      23.160  13.972  -2.060  1.00  0.00              
ATOM     40  O   GLU    48      22.795  12.893  -2.548  1.00  0.00              
ATOM     41  N   ILE    49      22.369  14.702  -1.278  1.00  0.00              
ATOM     42  CA  ILE    49      20.973  14.340  -1.091  1.00  0.00              
ATOM     43  C   ILE    49      20.154  15.031  -2.187  1.00  0.00              
ATOM     44  O   ILE    49      20.127  16.262  -2.274  1.00  0.00              
ATOM     45  N   VAL    50      19.554  14.239  -3.072  1.00  0.00              
ATOM     46  CA  VAL    50      18.705  14.779  -4.128  1.00  0.00              
ATOM     47  C   VAL    50      17.260  14.618  -3.614  1.00  0.00              
ATOM     48  O   VAL    50      16.785  13.492  -3.409  1.00  0.00              
ATOM     49  N   GLU    51      16.603  15.742  -3.320  1.00  0.00              
ATOM     50  CA  GLU    51      15.245  15.750  -2.788  1.00  0.00              
ATOM     51  C   GLU    51      14.353  16.299  -3.884  1.00  0.00              
ATOM     52  O   GLU    51      14.483  17.473  -4.275  1.00  0.00              
ATOM     53  N   TYR    52      13.480  15.437  -4.410  1.00  0.00              
ATOM     54  CA  TYR    52      12.537  15.798  -5.471  1.00  0.00              
ATOM     55  C   TYR    52      11.152  15.966  -4.846  1.00  0.00              
ATOM     56  O   TYR    52      10.641  15.065  -4.152  1.00  0.00              
ATOM     57  N   ALA    53      13.421   7.224 -10.853  1.00  0.00              
ATOM     58  CA  ALA    53      14.349   8.063 -10.091  1.00  0.00              
ATOM     59  C   ALA    53      15.479   7.163  -9.593  1.00  0.00              
ATOM     60  O   ALA    53      16.656   7.512  -9.677  1.00  0.00              
ATOM     61  N   VAL    54      15.105   6.002  -9.063  1.00  0.00              
ATOM     62  CA  VAL    54      16.071   5.033  -8.552  1.00  0.00              
ATOM     63  C   VAL    54      16.906   4.398  -9.674  1.00  0.00              
ATOM     64  O   VAL    54      18.139   4.341  -9.590  1.00  0.00              
ATOM     65  N   LYS    55      16.241   3.986 -10.753  1.00  0.00              
ATOM     66  CA  LYS    55      16.944   3.364 -11.873  1.00  0.00              
ATOM     67  C   LYS    55      17.934   4.282 -12.561  1.00  0.00              
ATOM     68  O   LYS    55      19.022   3.850 -12.927  1.00  0.00              
ATOM     69  N   PRO    56      17.555   5.543 -12.749  1.00  0.00              
ATOM     70  CA  PRO    56      18.447   6.506 -13.403  1.00  0.00              
ATOM     71  C   PRO    56      19.506   7.106 -12.462  1.00  0.00              
ATOM     72  O   PRO    56      20.677   7.190 -12.815  1.00  0.00              
ATOM     73  N   LEU    57      19.105   7.493 -11.258  1.00  0.00              
ATOM     74  CA  LEU    57      20.052   8.092 -10.322  1.00  0.00              
ATOM     75  C   LEU    57      20.959   7.067  -9.665  1.00  0.00              
ATOM     76  O   LEU    57      22.093   7.380  -9.302  1.00  0.00              
ATOM     77  N   LEU    58      20.467   5.842  -9.504  1.00  0.00              
ATOM     78  CA  LEU    58      21.246   4.781  -8.872  1.00  0.00              
ATOM     79  C   LEU    58      21.812   5.227  -7.500  1.00  0.00              
ATOM     80  O   LEU    58      23.028   5.228  -7.267  1.00  0.00              
ATOM     81  N   ALA    59      20.920   5.563  -6.560  1.00  0.00              
ATOM     82  CA  ALA    59      21.286   6.016  -5.219  1.00  0.00              
ATOM     83  C   ALA    59      21.767   4.928  -4.281  1.00  0.00              
ATOM     84  O   ALA    59      21.445   3.756  -4.475  1.00  0.00              
ATOM     85  N   PRO    63      -1.651  12.810   8.878  1.00  0.00              
ATOM     86  CA  PRO    63      -3.040  13.213   9.138  1.00  0.00              
ATOM     87  C   PRO    63      -3.745  12.073   9.888  1.00  0.00              
ATOM     88  O   PRO    63      -3.351  10.918   9.776  1.00  0.00              
ATOM     89  N   LEU    64      -4.766  12.418  10.664  1.00  0.00              
ATOM     90  CA  LEU    64      -5.511  11.468  11.483  1.00  0.00              
ATOM     91  C   LEU    64      -5.830  10.106  10.861  1.00  0.00              
ATOM     92  O   LEU    64      -5.649   9.068  11.505  1.00  0.00              
ATOM     93  N   ASP    65      -6.276  10.099   9.612  1.00  0.00              
ATOM     94  CA  ASP    65      -6.621   8.851   8.951  1.00  0.00              
ATOM     95  C   ASP    65      -5.810   8.510   7.719  1.00  0.00              
ATOM     96  O   ASP    65      -6.205   7.655   6.919  1.00  0.00              
ATOM     97  N   ASP    66      -4.634   9.112   7.598  1.00  0.00              
ATOM     98  CA  ASP    66      -3.762   8.847   6.471  1.00  0.00              
ATOM     99  C   ASP    66      -3.191   7.412   6.483  1.00  0.00              
ATOM    100  O   ASP    66      -2.801   6.874   7.533  1.00  0.00              
ATOM    101  N   ILE    67      -3.121   6.804   5.301  1.00  0.00              
ATOM    102  CA  ILE    67      -2.575   5.454   5.165  1.00  0.00              
ATOM    103  C   ILE    67      -1.172   5.543   4.572  1.00  0.00              
ATOM    104  O   ILE    67      -0.585   4.541   4.173  1.00  0.00              
ATOM    105  N   ASP    68      -0.617   6.756   4.540  1.00  0.00              
ATOM    106  CA  ASP    68       0.723   7.010   3.983  1.00  0.00              
ATOM    107  C   ASP    68       1.870   6.618   4.914  1.00  0.00              
ATOM    108  O   ASP    68       1.788   6.806   6.129  1.00  0.00              
ATOM    109  N   VAL    69       2.947   6.092   4.341  1.00  0.00              
ATOM    110  CA  VAL    69       4.140   5.722   5.103  1.00  0.00              
ATOM    111  C   VAL    69       5.352   6.071   4.237  1.00  0.00              
ATOM    112  O   VAL    69       5.191   6.655   3.157  1.00  0.00              
ATOM    113  N   ALA    70       6.562   5.798   4.719  1.00  0.00              
ATOM    114  CA  ALA    70       7.754   6.090   3.924  1.00  0.00              
ATOM    115  C   ALA    70       8.556   4.811   3.703  1.00  0.00              
ATOM    116  O   ALA    70       8.908   4.107   4.649  1.00  0.00              
ATOM    117  N   LEU    71       8.869   4.537   2.444  1.00  0.00              
ATOM    118  CA  LEU    71       9.623   3.345   2.052  1.00  0.00              
ATOM    119  C   LEU    71      11.113   3.702   2.113  1.00  0.00              
ATOM    120  O   LEU    71      11.577   4.552   1.357  1.00  0.00              
ATOM    121  N   ARG    72      11.835   3.066   3.038  1.00  0.00              
ATOM    122  CA  ARG    72      13.262   3.302   3.253  1.00  0.00              
ATOM    123  C   ARG    72      14.089   2.134   2.726  1.00  0.00              
ATOM    124  O   ARG    72      13.988   1.034   3.254  1.00  0.00              
ATOM    125  N   LEU    73      14.959   2.391   1.751  1.00  0.00              
ATOM    126  CA  LEU    73      15.793   1.343   1.150  1.00  0.00              
ATOM    127  C   LEU    73      17.280   1.709   1.087  1.00  0.00              
ATOM    128  O   LEU    73      17.641   2.871   0.887  1.00  0.00              
ATOM    129  N   ILE    74      18.134   0.705   1.248  1.00  0.00              
ATOM    130  CA  ILE    74      19.584   0.875   1.169  1.00  0.00              
ATOM    131  C   ILE    74      20.032  -0.092   0.081  1.00  0.00              
ATOM    132  O   ILE    74      19.733  -1.288   0.135  1.00  0.00              
ATOM    133  N   TYR    75      20.738   0.426  -0.910  1.00  0.00              
ATOM    134  CA  TYR    75      21.162  -0.389  -2.026  1.00  0.00              
ATOM    135  C   TYR    75      22.557  -0.966  -1.942  1.00  0.00              
ATOM    136  O   TYR    75      23.525  -0.250  -1.712  1.00  0.00              
END
