
#######################################################
#                                                     #
#                        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   63 (  524),  selected   63 , name one
# Molecule2: number of CA atoms  114 (  953),  selected   63 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    40      23_A - 62_A        4.93    20.01
  LCS_AVERAGE:     27.22

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      46_A - 60_A        1.88    18.91
  LCS_AVERAGE:      8.91

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      48_A - 60_A        0.44    19.56
  LCS_AVERAGE:      6.36

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     D    23_A     D    23_A     11   14   40      5    7   11   12   15   20   24   26   29   31   33   36   38   39   39   39   40   40   42   43 
LCS_GDT     Y    24_A     Y    24_A     11   14   40      5    7   11   12   15   20   24   26   29   31   33   35   38   39   39   39   40   40   42   43 
LCS_GDT     E    25_A     E    25_A     11   14   40      5    7   11   12   15   20   24   26   29   31   33   36   38   39   39   39   40   40   42   43 
LCS_GDT     T    26_A     T    26_A     11   14   40      5    7   11   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     L    27_A     L    27_A     11   14   40      5    7   11   12   14   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     L    28_A     L    28_A     11   14   40      5    7   11   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     E    29_A     E    29_A     11   14   40      4    7   11   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     I    30_A     I    30_A     11   14   40      4    7   12   14   16   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     L    31_A     L    31_A     11   14   40      4    7   11   14   16   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     R    32_A     R    32_A     11   14   40      4    7   11   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     E    33_A     E    33_A     11   14   40      4    7   11   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     F    34_A     F    34_A      8   14   40      4    7    8   12   13   18   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     G    35_A     G    35_A      4   14   40      3    4    5    9   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     V    36_A     V    36_A      4   14   40      3    4    4    8   10   16   18   23   27   30   31   34   36   39   39   39   40   40   42   43 
LCS_GDT     A    37_A     A    37_A      6   10   40      3    4    6    9   13   18   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     K    38_A     K    38_A      6   10   40      3    5    6    9   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     L    39_A     L    39_A      6   10   40      4    5    6    9   13   18   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     V    40_A     V    40_A      6   10   40      4    5    6    9   12   19   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     L    41_A     L    41_A      6   10   40      4    5    6    8   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     N    42_A     N    42_A      6   10   40      4    5    6    9   12   17   22   25   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     G    43_A     G    43_A      6   10   40      4    4    6    9   12   17   22   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     R    44_A     R    44_A      6   10   40      4    4    7   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     E    45_A     E    45_A      6   10   40      4    4    7   12   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     F    46_A     F    46_A      6   15   40      4    4    6    9   15   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     A    47_A     A    47_A      6   15   40      3    4    7   12   16   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     S    48_A     S    48_A     13   15   40      4   13   13   14   16   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     P    49_A     P    49_A     13   15   40     11   13   13   14   16   20   24   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     E    50_A     E    50_A     13   15   40     11   13   13   14   16   18   23   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     E    51_A     E    51_A     13   15   40     11   13   13   14   16   18   22   25   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     A    52_A     A    52_A     13   15   40     11   13   13   14   16   18   22   25   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     V    53_A     V    53_A     13   15   40     11   13   13   14   16   18   23   26   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     Q    54_A     Q    54_A     13   15   40     11   13   13   14   16   18   22   25   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     W    55_A     W    55_A     13   15   40     11   13   13   14   16   18   22   25   27   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     A    56_A     A    56_A     13   15   40     11   13   13   14   16   18   22   25   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     R    57_A     R    57_A     13   15   40     11   13   13   14   16   18   22   25   29   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     D    58_A     D    58_A     13   15   40     11   13   13   14   16   18   20   25   26   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     T    59_A     T    59_A     13   15   40     10   13   13   14   16   18   22   25   27   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     G    60_A     G    60_A     13   15   40     11   13   13   14   16   18   22   25   27   31   35   36   38   39   39   39   40   40   42   43 
LCS_GDT     L    61_A     L    61_A      3   14   40      3    4    4    4    7   10   14   16   21   23   26   30   32   35   36   38   40   40   42   43 
LCS_GDT     R    62_A     R    62_A      3    3   40      2    5    6    7    9   12   14   16   19   23   26   29   31   33   36   37   39   40   42   43 
LCS_GDT     F    63_A     F    63_A      3    4   38      3    5    6    7    9   11   13   16   19   20   24   27   30   32   35   37   39   40   42   43 
LCS_GDT     L    64_A     L    64_A      3    4   37      3    3    3    4    7   10   13   16   19   20   24   27   29   32   35   37   39   40   42   43 
LCS_GDT     R    65_A     R    65_A      3    4   23      3    3    4    5    5    7    9   11   12   16   18   21   23   25   28   30   32   35   37   40 
LCS_GDT     L    66_A     L    66_A      3    4   20      3    3    3    4    4    5    9   11   12   14   16   19   21   24   25   29   31   32   35   38 
LCS_GDT     I    67_A     I    67_A      3    4   16      3    3    4    5    5    6    9   11   12   14   16   19   21   24   25   29   31   33   35   38 
LCS_GDT     R    68_A     R    68_A      3    4   13      3    3    3    4    4    4    5    7    8   10   12   15   16   18   20   24   26   29   33   34 
LCS_GDT     E    69_A     E    69_A      3    4   13      0    3    3    4    4    4    5    7    8    9   11   12   16   18   20   23   25   26   29   30 
LCS_GDT     R    70_A     R    70_A      3    3   13      1    3    3    3    4    6    8   10   10   10   11   12   16   18   20   23   25   26   29   30 
LCS_GDT     Y    71_A     Y    71_A      3    5   13      0    3    4    4    6    8    9   10   10   10   11   12   14   18   20   21   24   26   29   30 
LCS_GDT     E    72_A     E    72_A      3    5   13      3    3    3    4    5    7    9   10   10   10   10   11   13   15   19   20   23   25   25   27 
LCS_GDT     D    73_A     D    73_A      3    7   13      3    3    4    6    6    8    9   10   10   10   11   11   12   15   17   17   19   21   25   26 
LCS_GDT     G    74_A     G    74_A      5    7   13      3    5    5    6    6    8    9   10   10   10   11   11   13   15   17   20   21   24   25   27 
LCS_GDT     V    75_A     V    75_A      5    7   13      4    5    5    6    6    8    9   10   10   10   11   12   14   18   20   21   23   25   29   30 
LCS_GDT     Y    76_A     Y    76_A      5    7   13      4    5    5    6    6    8    9   10   10   10   11   12   14   18   20   22   25   26   29   30 
LCS_GDT     T    77_A     T    77_A      5    7   13      4    5    5    6    6    8    9   10   10   10   12   17   19   22   25   25   25   27   29   30 
LCS_GDT     V    78_A     V    78_A      5    7   13      4    5    5    6    6    8    9   10   10   12   14   18   20   22   25   25   29   32   33   38 
LCS_GDT     E    79_A     E    79_A      3    7   13      1    3    4    4    6    8    9   10   10   12   13   17   19   22   25   25   28   31   33   38 
LCS_GDT     D    80_A     D    80_A      3    4   13      3    3    3    3    4    4    5    6    8    9   13   15   19   20   25   25   26   30   33   38 
LCS_GDT     I    81_A     I    81_A      3    4   13      3    3    3    3    4    4    6    7   10   15   17   22   24   27   29   30   33   34   37   42 
LCS_GDT     V    82_A     V    82_A      3    4   10      3    3    3    3    4    4    5    6    8    9   10   13   15   16   26   29   31   35   40   43 
LCS_GDT     S    83_A     S    83_A      3    4   10      0    3    3    3    4    4    5    6    6    7    9   11   13   16   16   19   21   24   33   42 
LCS_GDT     R    84_A     R    84_A      3    3   10      0    3    3    3    3    3    4    5    5    7    9   10   10   12   15   17   36   39   42   43 
LCS_GDT     D    85_A     D    85_A      3    3    9      0    3    3    3    3    3    4   22   25   30   35   35   38   39   39   39   40   40   42   43 
LCS_AVERAGE  LCS_A:  14.17  (   6.36    8.91   27.22 )

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     11     13     13     14     16     20     24     26     29     31     35     36     38     39     39     39     40     40     42     43 
GDT PERCENT_AT   9.65  11.40  11.40  12.28  14.04  17.54  21.05  22.81  25.44  27.19  30.70  31.58  33.33  34.21  34.21  34.21  35.09  35.09  36.84  37.72
GDT RMS_LOCAL    0.26   0.44   0.44   1.15   1.47   2.16   2.46   2.73   3.12   3.36   3.85   4.01   4.16   4.28   4.28   4.28   4.55   4.55   5.20   5.47
GDT RMS_ALL_AT  19.59  19.56  19.56  19.06  18.76  24.90  25.13  24.65  23.93  23.44  20.20  20.99  20.80  20.95  20.95  20.95  20.50  20.50  19.46  18.94

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  E    33_A      E    33_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  Y    71_A      Y    71_A
#   possible swapping detected:  D    73_A      D    73_A
#   possible swapping detected:  Y    76_A      Y    76_A
#   possible swapping detected:  E    79_A      E    79_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    23_A      D    23_A     2.744     0    0.559   1.482     7.288   52.143   40.774
LGA    Y    24_A      Y    24_A     2.890     0    0.096   1.356     5.843   57.143   58.571
LGA    E    25_A      E    25_A     2.352     0    0.023   1.222     7.808   64.762   45.661
LGA    T    26_A      T    26_A     2.410     0    0.063   0.165     2.745   62.857   61.497
LGA    L    27_A      L    27_A     2.997     0    0.063   0.197     4.502   57.143   49.583
LGA    L    28_A      L    28_A     2.685     0    0.167   1.360     5.915   60.952   46.845
LGA    E    29_A      E    29_A     1.857     0    0.023   0.372     2.461   70.833   72.011
LGA    I    30_A      I    30_A     1.741     0    0.033   0.083     2.310   72.857   70.833
LGA    L    31_A      L    31_A     1.444     0    0.151   0.205     2.370   75.119   76.131
LGA    R    32_A      R    32_A     1.670     0    0.130   1.204     8.899   75.119   48.745
LGA    E    33_A      E    33_A     1.789     0    0.172   0.545     2.557   69.048   71.217
LGA    F    34_A      F    34_A     3.685     0    0.658   1.345     5.026   43.810   38.052
LGA    G    35_A      G    35_A     2.971     0    0.527   0.527     3.151   51.786   51.786
LGA    V    36_A      V    36_A     5.583     0    0.640   0.889    10.187   28.929   17.415
LGA    A    37_A      A    37_A     3.355     0    0.204   0.197     4.246   46.905   47.524
LGA    K    38_A      K    38_A     2.405     0    0.097   0.565    11.367   64.881   37.143
LGA    L    39_A      L    39_A     3.434     0    0.056   0.131     9.278   52.024   30.893
LGA    V    40_A      V    40_A     3.336     0    0.059   0.084     7.706   53.810   37.279
LGA    L    41_A      L    41_A     1.945     0    0.069   1.296     7.431   51.548   37.202
LGA    N    42_A      N    42_A     5.762     0    0.256   0.905     9.114   24.048   16.012
LGA    G    43_A      G    43_A     5.237     0    0.013   0.013     5.460   31.667   31.667
LGA    R    44_A      R    44_A     2.221     0    0.025   0.958     5.437   65.119   56.970
LGA    E    45_A      E    45_A     2.042     0    0.018   0.612     8.339   68.810   40.952
LGA    F    46_A      F    46_A     2.463     0    0.167   1.104     3.600   68.810   62.381
LGA    A    47_A      A    47_A     2.098     0    0.751   0.707     3.930   65.119   60.762
LGA    S    48_A      S    48_A     2.101     0    0.607   0.818     4.458   68.810   60.397
LGA    P    49_A      P    49_A     1.979     0    0.120   0.345     2.925   66.786   62.653
LGA    E    50_A      E    50_A     4.205     0    0.026   0.836     5.610   37.976   33.968
LGA    E    51_A      E    51_A     6.203     0    0.061   1.240     7.554   18.214   25.979
LGA    A    52_A      A    52_A     5.750     0    0.046   0.056     6.638   20.595   21.714
LGA    V    53_A      V    53_A     4.875     0    0.064   0.058     6.657   23.333   30.272
LGA    Q    54_A      Q    54_A     8.360     0    0.075   1.451    13.976    4.881    2.487
LGA    W    55_A      W    55_A    10.291     0    0.040   1.285    20.503    0.357    0.102
LGA    A    56_A      A    56_A     8.898     0    0.020   0.025     9.975    1.905    3.524
LGA    R    57_A      R    57_A     9.543     0    0.027   1.692    15.200    0.833    0.563
LGA    D    58_A      D    58_A    13.138     0    0.046   0.075    14.918    0.000    0.000
LGA    T    59_A      T    59_A    13.900     0    0.192   1.147    15.514    0.000    0.000
LGA    G    60_A      G    60_A    12.883     0    0.403   0.403    16.396    0.000    0.000
LGA    L    61_A      L    61_A    18.681     0    0.603   1.337    21.868    0.000    0.000
LGA    R    62_A      R    62_A    22.323     0    0.596   1.166    26.300    0.000    0.000
LGA    F    63_A      F    63_A    23.418     0    0.596   1.110    26.497    0.000    0.000
LGA    L    64_A      L    64_A    26.859     0    0.030   0.390    30.398    0.000    0.000
LGA    R    65_A      R    65_A    33.560     0    0.613   1.032    41.639    0.000    0.000
LGA    L    66_A      L    66_A    35.917     0    0.619   1.416    38.824    0.000    0.000
LGA    I    67_A      I    67_A    37.988     0    0.011   0.081    41.629    0.000    0.000
LGA    R    68_A      R    68_A    41.725     0    0.527   1.264    43.421    0.000    0.000
LGA    E    69_A      E    69_A    44.647     0    0.600   1.255    48.698    0.000    0.000
LGA    R    70_A      R    70_A    48.029     0    0.578   1.453    52.826    0.000    0.000
LGA    Y    71_A      Y    71_A    48.583     0    0.659   0.421    52.599    0.000    0.000
LGA    E    72_A      E    72_A    53.187     0    0.620   0.627    54.241    0.000    0.000
LGA    D    73_A      D    73_A    56.788     0    0.604   1.138    59.775    0.000    0.000
LGA    G    74_A      G    74_A    54.062     0    0.699   0.699    54.408    0.000    0.000
LGA    V    75_A      V    75_A    51.054     0    0.042   0.081    54.148    0.000    0.000
LGA    Y    76_A      Y    76_A    45.688     0    0.058   1.371    47.080    0.000    0.000
LGA    T    77_A      T    77_A    42.935     0    0.178   1.091    45.841    0.000    0.000
LGA    V    78_A      V    78_A    36.473     0    0.617   0.628    38.501    0.000    0.000
LGA    E    79_A      E    79_A    37.302     0    0.614   1.086    40.580    0.000    0.000
LGA    D    80_A      D    80_A    36.426     0    0.617   1.273    37.300    0.000    0.000
LGA    I    81_A      I    81_A    31.432     0    0.650   0.726    35.235    0.000    0.000
LGA    V    82_A      V    82_A    25.839     0    0.612   1.509    28.001    0.000    0.000
LGA    S    83_A      S    83_A    25.714     0    0.696   0.616    26.826    0.000    0.000
LGA    R    84_A      R    84_A    22.986     0    0.640   1.240    29.447    0.000    0.000
LGA    D    85_A      D    85_A    16.473     0    0.607   1.098    18.444    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     524    524  100.00               114
SUMMARY(RMSD_GDC):    12.462         12.306                 12.874           14.727   12.715

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63  114    4.0     26    2.73    20.175    18.187     0.919

LGA_LOCAL      RMSD:   2.728  Number of atoms:   26  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  24.654  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:  12.462  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.926134 * X  +  -0.347115 * Y  +  -0.147602 * Z  +  15.866949
  Y_new =  -0.270717 * X  +  -0.339204 * Y  +  -0.900918 * Z  + -11.755877
  Z_new =   0.262654 * X  +   0.874329 * Y  +  -0.408119 * Z  +  23.828474 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.284385 -0.265772  2.007516   [DEG:  -16.2941  -15.2276  115.0222 ]
ZXZ: -0.162393  1.991189  0.291830   [DEG:   -9.3044  114.0867   16.7206 ]
 
# END of job
