
#######################################################
#                                                     #
#                        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   31 (  124),  selected   31 , name T0363AL044_1-D1
# Molecule2: number of CA atoms   46 (  372),  selected   31 , name T0363_D1.pdb
# PARAMETERS: T0363AL044_1-D1.T0363_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:    19        32 - 56          4.40     8.69
  LCS_AVERAGE:     33.80

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     9        38 - 46          1.54    14.41
  LCS_AVERAGE:     13.39

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     7        13 - 19          0.71    14.35
  LONGEST_CONTINUOUS_SEGMENT:     7        39 - 45          0.86    14.54
  LCS_AVERAGE:      9.89

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:   46
LCS_GDT     I      13     I      13      7    8   11     3    7    7    7    8    8   11   12   15   16   18   23   26   27   28   28   30   30   30   30 
LCS_GDT     N      14     N      14      7    8   11     4    7    7    7    8    8   11   12   15   17   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     I      15     I      15      7    8   11     3    7    7    7    8    8   11   12   15   17   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     E      16     E      16      7    8   11     4    7    7    7    8    8   11   12   15   17   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     I      17     I      17      7    8   11     4    7    7    7    8    8    8   12   15   16   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     A      18     A      18      7    8   11     4    7    7    7    8    8    8   12   14   16   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     Y      19     Y      19      7    8   11     3    7    7    7    8    8    8    9   10   16   16   20   21   25   28   28   30   30   30   30 
LCS_GDT     A      20     A      20      3    8   11     3    3    3    4    8    8   11   13   16   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     F      21     F      21      3    4   11     3    3    6    6    8    9   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     P      22     P      22      3    4   11     3    3    3    3    4    8   10   15   17   18   19   21   26   27   28   28   30   30   30   30 
LCS_GDT     E      23     E      23      3    3   11     3    3    3    4    4    6    9   13   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     R      24     R      24      0    0    0     0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
LCS_GDT     V      32     V      32      0    0   19     1    2    3    4    5    9   10   12   14   17   19   21   21   22   23   26   30   30   30   30 
LCS_GDT     D      33     D      33      0    0   19     1    2    6    6    6    9   12   15   17   18   20   23   26   27   28   28   30   30   30   30 
LCS_GDT     V      38     V      38      0    9   19     0    0    0    6    9   10   10   11   11   15   16   18   21   22   25   28   30   30   30   30 
LCS_GDT     Q      39     Q      39      7    9   19     5    5    7    8    9   10   11   13   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     T      40     T      40      7    9   19     5    5    7    8    9   10   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     A      41     A      41      7    9   19     5    5    7    8    9   10   12   15   17   18   20   23   26   27   28   28   30   30   30   30 
LCS_GDT     I      42     I      42      7    9   19     5    5    7    8    9   10   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     T      43     T      43      7    9   19     5    5    7    8    9   10   11   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     Q      44     Q      44      7    9   19     4    5    7    8    9   10   11   13   17   18   20   23   26   27   28   28   30   30   30   30 
LCS_GDT     S      45     S      45      7    9   19     4    5    7    8    9   10   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     G      46     G      46      6    9   19     3    5    7    8    9   10   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     I      47     I      47      5    7   19     3    4    6    6    8    9   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     L      48     L      48      5    7   19     4    4    5    6    7    9   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     S      49     S      49      5    7   19     4    4    5    6    7    9   11   15   16   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     Q      50     Q      50      5    7   19     4    4    5    6    9   10   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     F      51     F      51      5    7   19     4    4    5    6    7    9   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     P      52     P      52      0    0   19     0    1    1    6    8    8    9   11   14   16   19   22   26   27   28   28   30   30   30   30 
LCS_GDT     E      53     E      53      0    0   19     0    0    0    0    1    2    8   11   14   16   21   23   26   27   28   28   30   30   30   30 
LCS_GDT     L      56     L      56      0    0   19     1    1    6    6    7    9   12   15   17   18   21   23   26   27   28   28   30   30   30   30 
LCS_AVERAGE  LCS_A:  19.03  (   9.89   13.39   33.80 )

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      7      7      8      9     10     12     15     17     18     21     23     26     27     28     28     30     30     30     30 
GDT PERCENT_CA  10.87  15.22  15.22  17.39  19.57  21.74  26.09  32.61  36.96  39.13  45.65  50.00  56.52  58.70  60.87  60.87  65.22  65.22  65.22  65.22
GDT RMS_LOCAL    0.43   0.71   0.71   1.10   1.33   1.67   2.69   2.98   3.42   3.41   4.23   4.39   4.75   4.87   4.98   4.98   5.45   5.45   5.45   5.45
GDT RMS_ALL_CA  14.96  14.35  14.35  14.60  14.41  14.75   8.71   8.66   8.28   8.56   8.59   8.36   8.32   8.24   8.28   8.28   8.17   8.17   8.17   8.17

#      Molecule1      Molecule2       DISTANCE
LGA    I      13      I      13         12.137
LGA    N      14      N      14         11.470
LGA    I      15      I      15         10.539
LGA    E      16      E      16          9.505
LGA    I      17      I      17          9.191
LGA    A      18      A      18          8.418
LGA    Y      19      Y      19          9.339
LGA    A      20      A      20          5.943
LGA    F      21      F      21          2.084
LGA    P      22      P      22          3.848
LGA    E      23      E      23          5.570
LGA    R      24      R      24         31.780
LGA    V      32      V      32          6.330
LGA    D      33      D      33          2.228
LGA    V      38      V      38          9.589
LGA    Q      39      Q      39          6.151
LGA    T      40      T      40          3.197
LGA    A      41      A      41          2.491
LGA    I      42      I      42          2.804
LGA    T      43      T      43          3.974
LGA    Q      44      Q      44          4.576
LGA    S      45      S      45          2.951
LGA    G      46      G      46          3.785
LGA    I      47      I      47          3.324
LGA    L      48      L      48          2.893
LGA    S      49      S      49          3.660
LGA    Q      50      Q      50          2.870
LGA    F      51      F      51          1.935
LGA    P      52      P      52          8.476
LGA    E      53      E      53          8.292
LGA    L      56      L      56          1.975

#              N1   N2   DIST      N    RMSD    GDT_TS     LGA_S     LGA_Q 
SUMMARY(GDT)   31   46    4.0     15    2.98    31.522    27.185     0.487

LGA_LOCAL      RMSD =  2.983  Number of atoms =   15  DIST =   4.00
LGA_ALL_ATOMS  RMSD =  8.551  Number of atoms =   31 
Std_ALL_ATOMS  RMSD =  8.075  (standard rmsd on all 31 assigned CA atoms) 

Unitary ROTATION matrix and the shift VECTOR superimpose MOLECULES  (1=>2)
  X_new =  -0.839851 * X  +  -0.337827 * Y  +  -0.424879 * Z  +  28.978148
  Y_new =  -0.223820 * X  +  -0.497574 * Y  +   0.838048 * Z  +  17.530899
  Z_new =  -0.494524 * X  +   0.798933 * Y  +   0.342276 * Z  +   5.333171 

Euler angles from the ROTATION matrix (XYZ convention, two solutions)
  Psi   =   1.166036   -1.975557  [ DEG:    66.8089   -113.1911 ]
  Theta =   0.517287    2.624305  [ DEG:    29.6384    150.3616 ]
  Phi   =  -2.881146    0.260446  [ DEG:  -165.0775     14.9225 ]
 
# 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: T0363AL044_1-D1                               
REMARK     2: T0363_D1.pdb                                  
REMARK   GDT and LCS analysis
REMARK   FIXED Atom-Atom correspondence
REMARK   LGA parameters: T0363AL044_1-D1.T0363_D1.pdb -3 -ie -o1 -sda -d:4 
REMARK   #CA        N1   N2  DIST    N   RMSD   LGA_S  RMSD_global
REMARK   SUMMARY:   31   46   4.0   15   2.98  27.185     8.07
REMARK  ---------------------------------------------------------- 
MOLECULE T0363AL044_1-D1
REMARK Aligment from pdb entry: 1wgk_A
ATOM      1  N   ILE    13      22.270   9.513  -2.145  1.00  0.00              
ATOM      2  CA  ILE    13      21.822  10.772  -1.564  1.00  0.00              
ATOM      3  C   ILE    13      22.301  11.961  -2.391  1.00  0.00              
ATOM      4  O   ILE    13      23.429  11.973  -2.886  1.00  0.00              
ATOM      5  N   ASN    14      21.437  12.959  -2.538  1.00  0.00              
ATOM      6  CA  ASN    14      21.772  14.155  -3.304  1.00  0.00              
ATOM      7  C   ASN    14      22.343  15.239  -2.397  1.00  0.00              
ATOM      8  O   ASN    14      21.623  15.838  -1.598  1.00  0.00              
ATOM      9  N   ILE    15      23.642  15.489  -2.527  1.00  0.00              
ATOM     10  CA  ILE    15      24.310  16.504  -1.720  1.00  0.00              
ATOM     11  C   ILE    15      24.462  17.808  -2.495  1.00  0.00              
ATOM     12  O   ILE    15      24.884  17.809  -3.651  1.00  0.00              
ATOM     13  N   GLU    16      24.116  18.918  -1.849  1.00  0.00              
ATOM     14  CA  GLU    16      24.214  20.229  -2.478  1.00  0.00              
ATOM     15  C   GLU    16      24.911  21.225  -1.555  1.00  0.00              
ATOM     16  O   GLU    16      24.639  21.271  -0.355  1.00  0.00              
ATOM     17  N   ILE    17      25.813  22.018  -2.124  1.00  0.00              
ATOM     18  CA  ILE    17      26.551  23.012  -1.354  1.00  0.00              
ATOM     19  C   ILE    17      26.257  24.422  -1.860  1.00  0.00              
ATOM     20  O   ILE    17      26.186  24.658  -3.066  1.00  0.00              
ATOM     21  N   ALA    18      26.087  25.355  -0.929  1.00  0.00              
ATOM     22  CA  ALA    18      25.801  26.729  -1.299  1.00  0.00              
ATOM     23  C   ALA    18      26.900  27.341  -2.144  1.00  0.00              
ATOM     24  O   ALA    18      27.569  26.643  -2.905  1.00  0.00              
ATOM     25  N   TYR    19      27.086  28.651  -2.013  1.00  0.00              
ATOM     26  CA  TYR    19      28.111  29.336  -2.779  1.00  0.00              
ATOM     27  C   TYR    19      29.449  29.360  -2.066  1.00  0.00              
ATOM     28  O   TYR    19      29.524  29.700  -0.885  1.00  0.00              
ATOM     29  N   ALA    20      30.507  28.997  -2.783  1.00  0.00              
ATOM     30  CA  ALA    20      31.833  28.984  -2.194  1.00  0.00              
ATOM     31  C   ALA    20      32.303  27.584  -1.855  1.00  0.00              
ATOM     32  O   ALA    20      33.430  27.206  -2.172  1.00  0.00              
ATOM     33  N   PHE    21      31.437  26.812  -1.206  1.00  0.00              
ATOM     34  CA  PHE    21      31.770  25.446  -0.822  1.00  0.00              
ATOM     35  C   PHE    21      31.800  24.526  -2.039  1.00  0.00              
ATOM     36  O   PHE    21      32.685  23.681  -2.168  1.00  0.00              
ATOM     37  N   PRO    22      30.827  24.698  -2.928  1.00  0.00              
ATOM     38  CA  PRO    22      30.743  23.882  -4.134  1.00  0.00              
ATOM     39  C   PRO    22      32.113  23.740  -4.792  1.00  0.00              
ATOM     40  O   PRO    22      32.464  22.673  -5.297  1.00  0.00              
ATOM     41  N   GLU    23      32.880  24.824  -4.785  1.00  0.00              
ATOM     42  CA  GLU    23      34.212  24.823  -5.381  1.00  0.00              
ATOM     43  C   GLU    23      35.069  23.705  -4.797  1.00  0.00              
ATOM     44  O   GLU    23      35.813  23.037  -5.517  1.00  0.00              
ATOM     45  N   ARG    24      25.910  -3.581   7.464  1.00  0.00              
ATOM     46  CA  ARG    24      24.989  -3.972   8.525  1.00  0.00              
ATOM     47  C   ARG    24      24.387  -2.745   9.204  1.00  0.00              
ATOM     48  O   ARG    24      23.229  -2.758   9.618  1.00  0.00              
ATOM     49  N   VAL    32      25.183  -1.687   9.312  1.00  0.00              
ATOM     50  CA  VAL    32      24.730  -0.451   9.941  1.00  0.00              
ATOM     51  C   VAL    32      24.444   0.620   8.893  1.00  0.00              
ATOM     52  O   VAL    32      25.156   0.757   7.897  1.00  0.00              
ATOM     53  N   ASP    33      23.375   1.399   9.119  1.00  0.00              
ATOM     54  CA  ASP    33      22.970   2.472   8.206  1.00  0.00              
ATOM     55  C   ASP    33      23.948   3.642   8.215  1.00  0.00              
ATOM     56  O   ASP    33      24.494   3.999   9.261  1.00  0.00              
ATOM     57  N   VAL    38      24.165   4.235   7.049  1.00  0.00              
ATOM     58  CA  VAL    38      25.077   5.366   6.923  1.00  0.00              
ATOM     59  C   VAL    38      24.572   6.564   7.720  1.00  0.00              
ATOM     60  O   VAL    38      23.565   7.177   7.365  1.00  0.00              
ATOM     61  N   GLN    39      25.220  10.421   9.574  1.00  0.00              
ATOM     62  CA  GLN    39      25.948  11.660   9.334  1.00  0.00              
ATOM     63  C   GLN    39      27.398  11.544   9.792  1.00  0.00              
ATOM     64  O   GLN    39      28.324  11.865   9.047  1.00  0.00              
ATOM     65  N   THR    40      27.589  11.080  11.023  1.00  0.00              
ATOM     66  CA  THR    40      28.926  10.919  11.581  1.00  0.00              
ATOM     67  C   THR    40      29.889  10.368  10.534  1.00  0.00              
ATOM     68  O   THR    40      30.914  10.979  10.236  1.00  0.00              
ATOM     69  N   ALA    41      29.552   9.208   9.980  1.00  0.00              
ATOM     70  CA  ALA    41      30.387   8.573   8.967  1.00  0.00              
ATOM     71  C   ALA    41      30.323   9.341   7.650  1.00  0.00              
ATOM     72  O   ALA    41      31.352   9.633   7.040  1.00  0.00              
ATOM     73  N   ILE    42      29.110   9.664   7.218  1.00  0.00              
ATOM     74  CA  ILE    42      28.911  10.399   5.974  1.00  0.00              
ATOM     75  C   ILE    42      30.029  11.412   5.756  1.00  0.00              
ATOM     76  O   ILE    42      30.541  11.557   4.644  1.00  0.00              
ATOM     77  N   THR    43      30.405  12.110   6.821  1.00  0.00              
ATOM     78  CA  THR    43      31.465  13.108   6.747  1.00  0.00              
ATOM     79  C   THR    43      32.741  12.506   6.168  1.00  0.00              
ATOM     80  O   THR    43      33.316  13.037   5.217  1.00  0.00              
ATOM     81  N   GLN    44      33.179  11.393   6.748  1.00  0.00              
ATOM     82  CA  GLN    44      34.387  10.715   6.288  1.00  0.00              
ATOM     83  C   GLN    44      34.374  10.539   4.773  1.00  0.00              
ATOM     84  O   GLN    44      35.400  10.697   4.112  1.00  0.00              
ATOM     85  N   SER    45      33.207  10.211   4.231  1.00  0.00              
ATOM     86  CA  SER    45      33.061  10.014   2.794  1.00  0.00              
ATOM     87  C   SER    45      33.079  11.347   2.056  1.00  0.00              
ATOM     88  O   SER    45      33.936  11.584   1.203  1.00  0.00              
ATOM     89  N   GLY    46      32.130  12.216   2.390  1.00  0.00              
ATOM     90  CA  GLY    46      32.039  13.526   1.759  1.00  0.00              
ATOM     91  C   GLY    46      33.322  14.325   1.963  1.00  0.00              
ATOM     92  O   GLY    46      33.593  15.282   1.238  1.00  0.00              
ATOM     93  N   ILE    47      34.109  13.924   2.955  1.00  0.00              
ATOM     94  CA  ILE    47      35.367  14.599   3.254  1.00  0.00              
ATOM     95  C   ILE    47      36.508  14.019   2.424  1.00  0.00              
ATOM     96  O   ILE    47      37.563  14.635   2.284  1.00  0.00              
ATOM     97  N   LEU    48      36.288  12.829   1.876  1.00  0.00              
ATOM     98  CA  LEU    48      37.296  12.165   1.058  1.00  0.00              
ATOM     99  C   LEU    48      36.797  11.974  -0.371  1.00  0.00              
ATOM    100  O   LEU    48      37.331  12.565  -1.309  1.00  0.00              
ATOM    101  N   SER    49      35.769  11.147  -0.529  1.00  0.00              
ATOM    102  CA  SER    49      35.198  10.879  -1.845  1.00  0.00              
ATOM    103  C   SER    49      34.849  12.181  -2.561  1.00  0.00              
ATOM    104  O   SER    49      35.488  12.549  -3.547  1.00  0.00              
ATOM    105  N   GLN    50      33.832  12.871  -2.057  1.00  0.00              
ATOM    106  CA  GLN    50      33.398  14.132  -2.649  1.00  0.00              
ATOM    107  C   GLN    50      34.481  15.199  -2.513  1.00  0.00              
ATOM    108  O   GLN    50      35.098  15.601  -3.500  1.00  0.00              
ATOM    109  N   PHE    51      34.705  15.652  -1.284  1.00  0.00              
ATOM    110  CA  PHE    51      35.716  16.671  -1.019  1.00  0.00              
ATOM    111  C   PHE    51      37.024  16.339  -1.729  1.00  0.00              
ATOM    112  O   PHE    51      37.671  15.335  -1.426  1.00  0.00              
ATOM    113  N   PRO    52      35.650  21.110   6.331  1.00  0.00              
ATOM    114  CA  PRO    52      35.270  20.534   7.616  1.00  0.00              
ATOM    115  C   PRO    52      36.496  20.068   8.394  1.00  0.00              
ATOM    116  O   PRO    52      37.520  19.724   7.806  1.00  0.00              
ATOM    117  N   GLU    53      36.381  20.060   9.718  1.00  0.00              
ATOM    118  CA  GLU    53      37.481  19.635  10.577  1.00  0.00              
ATOM    119  C   GLU    53      37.043  18.506  11.504  1.00  0.00              
ATOM    120  O   GLU    53      36.332  18.733  12.482  1.00  0.00              
ATOM    121  N   LEU    56      37.472  17.288  11.188  1.00  0.00              
ATOM    122  CA  LEU    56      37.113  16.141  12.003  1.00  0.00              
ATOM    123  C   LEU    56      35.889  15.419  11.480  1.00  0.00              
ATOM    124  O   LEU    56      35.426  15.691  10.372  1.00  0.00              
END
