
#######################################################
#                                                     #
#                        LGA                          #
#                  ---------------                    #
#                                                     #
#               Local-Global Alignment                #
#        A Method for Finding 3-D Similarities        #
#               in Protein Structures                 #
#                                                     #
#                  ------------ 10/2009               #
#                                                     #
#      Adam Zemla (adamz@llnl.gov)                    #
#      Lawrence Livermore National Laboratory, CA     #
#                                                     #
#######################################################

!!!   License for LGA program has expired  !!!
#   For updated version of the LGA program   #
# please contact Adam Zemla:  adamz@llnl.gov #

# Molecule1: number of CA atoms   64 (  550),  selected   64 , name one
# Molecule2: number of CA atoms  124 ( 1059),  selected   64 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36      89_D - 124_D       4.97    14.36
  LCS_AVERAGE:     23.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      95_D - 124_D       1.60    15.27
  LCS_AVERAGE:     13.46

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      98_D - 124_D       0.76    15.69
  LCS_AVERAGE:     11.14

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
LCS_GDT     RESIDUE       RESIDUE       SEGMENT_SIZE    GLOBAL DISTANCE TEST COLUMNS: number of residues under the threshold assigned to each residue pair
LCS_GDT   NAME NUMBER   NAME NUMBER    1.0  2.0  5.0    0.5  1.0  1.5  2.0  2.5  3.0  3.5  4.0  4.5  5.0  5.5  6.0  6.5  7.0  7.5  8.0  8.5  9.0  9.5 10.0
LCS_GDT     K    61_D     K    61_D      4    4   13      3    4    4    4    4    4    5    6    7    7    7    8    9   11   12   13   13   16   16   16 
LCS_GDT     C    62_D     C    62_D      4    4   15      3    4    4    4    4    6    7    7    8   10   12   14   15   15   16   16   18   22   22   24 
LCS_GDT     E    63_D     E    63_D      4    5   15      3    4    4    4    4    6    7    7    8   10   12   14   15   16   17   30   32   34   36   41 
LCS_GDT     N    64_D     N    64_D      4    5   15      3    4    4    4    5    6    7    7    8   10   12   14   26   27   29   31   32   35   39   43 
LCS_GDT     P    65_D     P    65_D      4    5   15      3    4    4    4    5    6    9   13   17   17   19   22   26   27   29   31   35   39   41   43 
LCS_GDT     K    66_D     K    66_D      4    5   15      3    4    4    4    5    6    7    7    8   10   19   22   26   27   29   31   35   37   40   43 
LCS_GDT     E    67_D     E    67_D      3    5   15      3    3    3    4    5    6    7    7    8   10   12   14   15   15   16   17   21   25   28   41 
LCS_GDT     Q    68_D     Q    68_D      3    5   15      3    3    4    4    5    6    7    7    8   10   12   14   15   15   18   21   30   36   39   42 
LCS_GDT     W    69_D     W    69_D      3    3   15      3    3    4    4    6    7    7    7   11   13   14   17   19   20   21   29   32   37   39   43 
LCS_GDT     V    70_D     V    70_D      3    4   15      3    3    4    4    6    7    7    8   11   13   14   17   19   20   21   23   24   36   39   42 
LCS_GDT     A    71_D     A    71_D      3    4   15      3    3    3    4    6    7    7    8   11   13   14   17   19   20   21   23   24   25   29   33 
LCS_GDT     N    72_D     N    72_D      3    5   15      3    3    3    5    5    6    7   11   12   14   14   17   19   20   21   23   24   25   29   30 
LCS_GDT     Y    73_D     Y    73_D      4    5   15      3    4    4    5    5    6    7   11   12   14   14   17   19   20   21   25   30   37   40   44 
LCS_GDT     Q    74_D     Q    74_D      4    5   15      3    4    4    5    5    6    7   11   12   14   14   17   19   20   21   23   24   25   29   30 
LCS_GDT     N    75_D     N    75_D      4    5   15      3    4    4    5    5    6    7   11   12   14   14   16   19   19   21   23   23   24   26   27 
LCS_GDT     L    76_D     L    76_D      4    5   18      3    4    4    5    5    6    7   11   12   14   14   16   19   20   21   23   24   25   29   31 
LCS_GDT     N    77_D     N    77_D      3    5   18      3    3    4    4    5    6    7    8   12   14   15   17   19   20   22   27   40   44   46   48 
LCS_GDT     N    78_D     N    78_D      3    5   18      3    3    4    5    5    6    7   11   12   14   15   17   19   23   31   39   43   44   46   48 
LCS_GDT     V    79_D     V    79_D      3    5   18      3    3    4    5    6    7    7   11   12   14   15   17   19   20   21   27   38   42   46   48 
LCS_GDT     V    80_D     V    80_D      3    5   18      3    3    4    5    5    7    7   11   12   14   16   25   34   37   40   43   43   45   46   48 
LCS_GDT     F    81_D     F    81_D      4    5   33      3    4    4    5    5    5   12   15   23   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     T    82_D     T    82_D      4    5   34      3    4    4    5   10   16   20   25   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     N    83_D     N    83_D      4    4   34      3    4    4    5    7   12   19   24   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K    84_D     K    84_D      4    4   34      3    4    4    5   10   16   20   26   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     E    85_D     E    85_D      3    4   34      3    3    4    4    4    8   11   15   21   24   29   34   36   37   40   43   43   45   46   48 
LCS_GDT     L    86_D     L    86_D      3    6   34      1    3    4    4    7   10   12   17   20   24   26   29   33   37   40   43   43   45   46   48 
LCS_GDT     E    87_D     E    87_D      3    6   34      3    3    4    6    9   10   12   16   19   21   24   26   28   31   36   38   42   45   46   48 
LCS_GDT     D    88_D     D    88_D      3    6   34      3    3    4    6    7   10   12   17   19   22   24   26   29   33   40   43   43   45   46   48 
LCS_GDT     I    89_D     I    89_D      3    6   36      3    3    4    6    7   10   12   17   19   24   26   31   35   37   40   43   43   45   46   48 
LCS_GDT     Y    90_D     Y    90_D      3    6   36      3    3    3    4    5    8   12   14   18   19   22   26   28   33   40   43   43   45   46   48 
LCS_GDT     D    91_D     D    91_D      4    6   36      4    4    4    4    5    8   12   14   18   19   21   26   28   33   40   43   43   45   46   48 
LCS_GDT     L    92_D     L    92_D      4    4   36      4    4    4    4    4    5    7   10   13   15   19   21   26   33   38   41   43   45   46   48 
LCS_GDT     S    93_D     S    93_D      4    4   36      4    4    4    4    4    5    7   10   13   15   19   22   28   33   40   43   43   45   46   48 
LCS_GDT     N    94_D     N    94_D      4    8   36      4    4    4    4    5   10   12   18   25   33   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K    95_D     K    95_D      5   30   36      4    5   10   15   24   27   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     E    96_D     E    96_D      5   30   36      4    5    8   11   18   27   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     E    97_D     E    97_D     25   30   36      4    5   17   25   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     T    98_D     T    98_D     27   30   36      4   20   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K    99_D     K    99_D     27   30   36     12   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     E   100_D     E   100_D     27   30   36     11   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     V   101_D     V   101_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     L   102_D     L   102_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K   103_D     K   103_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K   104_D     K   104_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     F   105_D     F   105_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K   106_D     K   106_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     E   107_D     E   107_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K   108_D     K   108_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     V   109_D     V   109_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     N   110_D     N   110_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     Q   111_D     Q   111_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     F   112_D     F   112_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     Y   113_D     Y   113_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     R   114_D     R   114_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     H   115_D     H   115_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     A   116_D     A   116_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     F   117_D     F   117_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     D   118_D     D   118_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     I   119_D     I   119_D     27   30   36     19   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     I   120_D     I   120_D     27   30   36     15   23   26   27   28   28   30   30   31   34   34   35   36   37   39   43   43   45   46   48 
LCS_GDT     N   121_D     N   121_D     27   30   36      6   23   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     K   122_D     K   122_D     27   30   36      3   12   26   27   28   28   30   30   31   34   34   35   36   37   40   43   43   45   46   48 
LCS_GDT     Y   123_D     Y   123_D     27   30   36      3   14   26   27   28   28   30   30   30   34   34   35   36   37   39   43   43   45   46   48 
LCS_GDT     G   124_D     G   124_D     27   30   36     11   23   26   27   28   28   30   30   30   34   34   35   36   37   39   43   43   45   46   48 
LCS_AVERAGE  LCS_A:  16.10  (  11.14   13.46   23.69 )

GLOBAL_DISTANCE_TEST (summary information about detected largest sets of residues (represented by selected AToms) that can fit under specified thresholds)
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_AT     19     23     26     27     28     28     30     30     31     34     34     35     36     37     40     43     43     45     46     48 
GDT PERCENT_AT  15.32  18.55  20.97  21.77  22.58  22.58  24.19  24.19  25.00  27.42  27.42  28.23  29.03  29.84  32.26  34.68  34.68  36.29  37.10  38.71
GDT RMS_LOCAL    0.33   0.52   0.67   0.76   1.03   1.03   1.60   1.60   2.73   2.91   2.91   3.18   3.52   3.84   5.13   5.18   5.18   5.53   5.74   6.15
GDT RMS_ALL_AT  15.77  15.60  15.71  15.69  15.83  15.83  15.27  15.27  13.88  13.89  13.89  13.82  13.52  13.39  12.32  12.79  12.79  12.65  12.45  12.19

# Checking swapping
#   possible swapping detected:  E    63_D      E    63_D
#   possible swapping detected:  E    85_D      E    85_D
#   possible swapping detected:  E    96_D      E    96_D
#   possible swapping detected:  E    97_D      E    97_D
#   possible swapping detected:  E   100_D      E   100_D
#   possible swapping detected:  F   112_D      F   112_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    61_D      K    61_D    30.306     0    0.425   1.141    35.491    0.000    0.000
LGA    C    62_D      C    62_D    24.789     0    0.027   0.849    27.492    0.000    0.000
LGA    E    63_D      E    63_D    24.667     0    0.586   1.086    24.978    0.000    0.000
LGA    N    64_D      N    64_D    26.240     0    0.044   0.901    30.884    0.000    0.000
LGA    P    65_D      P    65_D    24.877     0    0.714   0.639    26.205    0.000    0.000
LGA    K    66_D      K    66_D    27.669     0    0.579   0.595    31.748    0.000    0.000
LGA    E    67_D      E    67_D    32.435     0    0.674   1.220    38.309    0.000    0.000
LGA    Q    68_D      Q    68_D    29.033     0    0.623   1.512    33.530    0.000    0.000
LGA    W    69_D      W    69_D    26.734     0    0.619   0.449    27.116    0.000    0.000
LGA    V    70_D      V    70_D    28.831     0    0.596   0.587    31.204    0.000    0.000
LGA    A    71_D      A    71_D    28.793     0    0.652   0.634    29.260    0.000    0.000
LGA    N    72_D      N    72_D    27.275     0    0.533   0.628    30.807    0.000    0.000
LGA    Y    73_D      Y    73_D    22.002     0    0.465   0.932    23.749    0.000    0.000
LGA    Q    74_D      Q    74_D    27.159     0    0.051   0.585    34.986    0.000    0.000
LGA    N    75_D      N    75_D    27.641     0    0.526   0.911    32.589    0.000    0.000
LGA    L    76_D      L    76_D    21.544     0    0.649   1.088    23.372    0.000    0.000
LGA    N    77_D      N    77_D    17.903     0    0.618   1.190    20.141    0.000    0.000
LGA    N    78_D      N    78_D    17.836     0    0.401   0.499    19.329    0.000    0.000
LGA    V    79_D      V    79_D    18.188     0    0.025   1.180    20.953    0.000    0.000
LGA    V    80_D      V    80_D    12.503     0    0.622   0.637    14.457    0.000    0.204
LGA    F    81_D      F    81_D     8.674     0    0.563   1.178     9.879    1.905    7.100
LGA    T    82_D      T    82_D     8.685     0    0.649   1.265     9.566    2.976    4.626
LGA    N    83_D      N    83_D     8.574     0    0.313   1.088    12.671    3.333    2.024
LGA    K    84_D      K    84_D     8.335     0    0.605   1.436    13.517    4.524    2.751
LGA    E    85_D      E    85_D    12.532     0    0.607   0.749    21.278    0.000    0.000
LGA    L    86_D      L    86_D    11.837     0    0.645   1.428    12.296    0.000    0.000
LGA    E    87_D      E    87_D    12.577     0    0.617   1.188    14.776    0.000    0.000
LGA    D    88_D      D    88_D    13.805     0    0.350   0.460    16.991    0.000    0.000
LGA    I    89_D      I    89_D    11.974     0    0.208   1.291    13.155    0.000    0.000
LGA    Y    90_D      Y    90_D    12.924     0    0.593   1.374    16.524    0.000    0.000
LGA    D    91_D      D    91_D    14.576     0    0.620   1.252    18.971    0.000    0.000
LGA    L    92_D      L    92_D    16.618     0    0.057   1.396    20.994    0.000    0.000
LGA    S    93_D      S    93_D    14.533     0    0.578   0.735    15.481    0.000    0.000
LGA    N    94_D      N    94_D     9.522     0    0.332   1.042    10.688    5.952    3.274
LGA    K    95_D      K    95_D     4.373     0    0.622   1.147    11.882   39.762   20.370
LGA    E    96_D      E    96_D     4.176     0    0.060   1.397    10.009   43.571   25.026
LGA    E    97_D      E    97_D     2.437     0    0.029   0.865     3.969   69.405   56.455
LGA    T    98_D      T    98_D     0.950     0    0.097   0.158     2.853   88.214   75.986
LGA    K    99_D      K    99_D     0.730     0    0.007   1.192     5.334   88.214   74.974
LGA    E   100_D      E   100_D     0.994     0    0.026   1.125     4.640   85.952   67.249
LGA    V   101_D      V   101_D     1.313     0    0.034   0.914     2.713   77.143   72.041
LGA    L   102_D      L   102_D     1.503     0    0.045   1.362     4.026   75.000   63.988
LGA    K   103_D      K   103_D     1.379     0    0.069   1.258     5.365   81.429   66.455
LGA    K   104_D      K   104_D     1.204     0    0.023   1.123     4.701   81.429   73.069
LGA    F   105_D      F   105_D     1.133     0    0.047   0.146     1.476   83.690   82.251
LGA    K   106_D      K   106_D     1.267     0    0.053   0.695     2.560   81.429   74.921
LGA    E   107_D      E   107_D     1.251     0    0.042   0.887     5.521   81.429   64.339
LGA    K   108_D      K   108_D     1.070     0    0.043   0.711     2.921   81.429   79.048
LGA    V   109_D      V   109_D     1.083     0    0.047   0.086     1.350   81.429   81.429
LGA    N   110_D      N   110_D     1.188     0    0.050   1.224     4.879   81.429   69.107
LGA    Q   111_D      Q   111_D     0.854     0    0.045   0.434     1.489   90.476   89.471
LGA    F   112_D      F   112_D     0.648     0    0.022   0.348     2.293   90.476   82.554
LGA    Y   113_D      Y   113_D     0.772     0    0.022   0.319     1.620   90.476   85.278
LGA    R   114_D      R   114_D     0.505     0    0.008   0.692     2.023   90.476   80.130
LGA    H   115_D      H   115_D     0.716     0    0.041   1.063     2.746   90.476   79.333
LGA    A   116_D      A   116_D     0.654     0    0.029   0.055     0.854   90.476   90.476
LGA    F   117_D      F   117_D     0.762     0    0.042   0.159     1.967   90.476   82.424
LGA    D   118_D      D   118_D     0.611     0    0.026   0.712     3.369   92.857   79.226
LGA    I   119_D      I   119_D     0.377     0    0.022   1.304     3.006   95.238   83.571
LGA    I   120_D      I   120_D     0.978     0    0.028   0.988     2.327   83.810   80.595
LGA    N   121_D      N   121_D     1.568     0    0.125   0.318     2.828   71.071   71.964
LGA    K   122_D      K   122_D     2.041     0    0.091   1.296     9.685   66.905   46.561
LGA    Y   123_D      Y   123_D     1.794     0    0.211   0.442     3.623   75.000   67.302
LGA    G   124_D      G   124_D     1.369     0    0.307   0.307     3.948   60.238   60.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     550    550  100.00               124
SUMMARY(RMSD_GDC):     9.936          9.885                 10.524           19.501   17.305

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64  124    4.0     30    1.60    24.798    21.856     1.761

LGA_LOCAL      RMSD:   1.604  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.269  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   9.936  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.210778 * X  +   0.535875 * Y  +  -0.817564 * Z  +  66.165390
  Y_new =   0.895900 * X  +   0.440487 * Y  +   0.057745 * Z  + -203.342422
  Z_new =   0.391071 * X  +  -0.720284 * Y  +  -0.572935 * Z  + 188.187515 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.801864 -0.401795 -2.242745   [DEG:  103.2392  -23.0211 -128.4998 ]
ZXZ: -1.641310  2.180879  2.644186   [DEG:  -94.0401  124.9552  151.5007 ]
 
# END of job
