
#######################################################
#                                                     #
#                        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   68 (  537),  selected   68 , name one
# Molecule2: number of CA atoms  207 ( 1517),  selected   68 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    36      67_B - 102_B       4.75    30.64
  LCS_AVERAGE:     14.58

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      78_B - 96_B        1.81    31.94
  LCS_AVERAGE:      6.78

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      79_B - 95_B        0.93    32.22
  LCS_AVERAGE:      5.63

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   68
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     L    67_B     L    67_B     11   11   36      9   11   11   11   11   11   11   11   12   21   25   28   29   32   32   34   35   36   36   37 
LCS_GDT     Y    68_B     Y    68_B     11   11   36      9   11   11   11   11   14   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    69_B     A    69_B     11   11   36      9   11   11   11   11   11   11   14   23   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     E    70_B     E    70_B     11   11   36      9   11   11   11   11   11   11   12   17   19   24   28   31   33   35   35   35   36   37   38 
LCS_GDT     M    71_B     M    71_B     11   11   36      9   11   11   11   11   11   12   17   22   24   25   30   32   33   35   35   35   36   37   38 
LCS_GDT     K    72_B     K    72_B     11   11   36      9   11   11   11   11   14   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    73_B     A    73_B     11   11   36      9   11   11   11   11   12   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    74_B     A    74_B     11   11   36      9   11   11   11   11   11   11   14   20   23   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     L    75_B     L    75_B     11   11   36      9   11   11   11   11   11   12   14   18   23   25   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    76_B     A    76_B     11   11   36      9   11   11   11   11   14   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    77_B     A    77_B     11   11   36      9   11   11   11   11   14   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    78_B     A    78_B      4   19   36      3    4    4    4    8   11   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     K    79_B     K    79_B     17   19   36      5   13   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     T    80_B     T    80_B     17   19   36      6   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     P    81_B     P    81_B     17   19   36      6   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     E    82_B     E    82_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     E    83_B     E    83_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     K    84_B     K    84_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     I    85_B     I    85_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    86_B     A    86_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     V    87_B     V    87_B     17   19   36      8   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     F    88_B     F    88_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     R    89_B     R    89_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     E    90_B     E    90_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     Y    91_B     Y    91_B     17   19   36      9   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     N    92_B     N    92_B     17   19   36      3   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    93_B     A    93_B     17   19   36      3   14   16   17   17   17   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     R    94_B     R    94_B     17   19   36      3   13   16   17   17   17   19   19   23   26   27   29   32   33   35   35   35   36   37   38 
LCS_GDT     F    95_B     F    95_B     17   19   36      3    5   15   17   17   17   19   19   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     L    96_B     L    96_B     16   19   36      8   13   16   16   17   18   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     A    97_B     A    97_B     16   17   36      8   12   16   16   17   18   18   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     E    98_B     E    98_B     16   17   36      8   14   16   16   17   18   19   21   25   26   27   30   32   33   35   35   35   36   37   38 
LCS_GDT     F    99_B     F    99_B     16   17   36     10   14   16   16   17   18   18   18   21   24   26   30   32   33   35   35   35   36   37   38 
LCS_GDT     D   100_B     D   100_B     16   17   36      8   14   16   16   17   18   18   18   19   21   25   29   32   33   35   35   35   36   37   38 
LCS_GDT     A   101_B     A   101_B     16   17   36      8   14   16   16   17   18   18   18   20   23   26   30   32   33   35   35   35   36   37   38 
LCS_GDT     L   102_B     L   102_B     16   17   36     10   14   16   16   17   18   18   18   20   22   25   29   32   33   35   35   35   36   37   38 
LCS_GDT     I   103_B     I   103_B     16   17   32     10   14   16   16   17   18   18   18   19   21   24   26   27   28   29   31   34   36   37   38 
LCS_GDT     D   104_B     D   104_B     16   17   31     10   14   16   16   17   18   18   18   19   21   24   26   27   28   29   30   31   34   37   37 
LCS_GDT     Q   105_B     Q   105_B     16   17   31     10   14   16   16   17   18   18   18   19   21   24   26   27   28   30   33   35   36   37   38 
LCS_GDT     A   106_B     A   106_B     16   17   31     10   14   16   16   17   18   18   18   19   21   24   26   27   28   29   31   32   34   37   38 
LCS_GDT     F   107_B     F   107_B     16   17   31     10   14   16   16   17   18   18   18   19   20   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     A   108_B     A   108_B     16   17   31     10   14   16   16   17   18   18   18   19   20   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     R   109_B     R   109_B     16   17   31     10   14   16   16   17   18   18   18   19   20   24   26   27   28   29   30   31   32   36   36 
LCS_GDT     L   110_B     L   110_B     16   17   31     10   14   16   16   17   18   18   18   19   20   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     K   111_B     K   111_B     16   17   31      4   14   16   16   17   18   18   18   19   20   21   23   25   25   28   30   31   32   33   36 
LCS_GDT     A   112_B     A   112_B      3   17   31      3    5    5    9   13   16   17   18   19   21   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     D   113_B     D   113_B      3    5   31      3    3    3    5    6   10   12   15   19   21   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     S   114_B     S   114_B      4    9   31      3    3    4    6   10   10   10   15   18   21   23   26   27   28   29   30   31   32   33   36 
LCS_GDT     L   115_B     L   115_B      6   10   31      3    6    6    8   10   10   12   15   19   21   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     T   116_B     T   116_B      6   10   31      4    6    7    8   10   11   14   15   19   21   24   26   27   28   29   30   31   32   33   35 
LCS_GDT     L   117_B     L   117_B      6   10   31      4    6    7    8   10   11   14   15   19   21   24   26   27   28   29   30   31   32   33   36 
LCS_GDT     K   118_B     K   118_B      6   10   31      4    6    7    8   10   10   10   12   17   20   23   26   27   28   29   30   31   32   33   36 
LCS_GDT     I   119_B     I   119_B      6   10   31      4    6    7    8   10   10   10   11   11   12   14   17   24   28   28   30   31   32   33   36 
LCS_GDT     H   120_B     H   120_B      6   10   29      4    6    7    8   10   10   10   11   11   12   14   14   17   23   26   29   30   32   33   36 
LCS_GDT     L   121_B     L   121_B      6   10   16      4    5    7    8   10   10   10   11   11   12   14   14   17   18   19   22   26   32   33   36 
LCS_GDT     S   122_B     S   122_B      5   10   16      4    4    7    8   10   10   10   11   11   12   14   14   17   18   19   22   25   26   29   32 
LCS_GDT     Q   123_B     Q   123_B      5   10   16      4    4    6    8    9    9   10   11   11   11   11   14   15   18   19   20   22   23   27   28 
LCS_GDT     G   124_B     G   124_B      3   10   16      3    3    4    7   10   10   10   11   11   12   14   14   17   18   19   22   25   29   33   36 
LCS_GDT     K   125_B     K   125_B      3    5   16      3    3    4    4    5    7    9   13   14   15   16   17   17   18   19   22   25   29   32   36 
LCS_GDT     G   126_B     G   126_B      3    9   16      3    3    4    4    6    9   11   13   14   15   16   17   17   18   19   22   25   29   32   36 
LCS_GDT     S   127_B     S   127_B      7    9   16      4    7    7    8    9   10   10   13   14   15   16   17   17   18   19   22   25   26   29   31 
LCS_GDT     Y   128_B     Y   128_B      7    9   15      4    7    7    8    9   10   11   13   14   15   16   17   17   18   19   22   25   29   32   36 
LCS_GDT     E   129_B     E   129_B      7    9   12      4    7    7    8    9   10   11   13   14   15   16   17   17   18   19   22   25   29   32   36 
LCS_GDT     I   130_B     I   130_B      7    9   12      4    7    7    8    9   10   11   13   14   15   16   17   17   22   24   27   28   32   33   36 
LCS_GDT     I   131_B     I   131_B      7    9   12      4    7    7    8    9   10   11   13   14   15   20   20   20   22   24   27   28   32   33   36 
LCS_GDT     F   132_B     F   132_B      7    9   12      4    7    7    8    9   10   11   14   19   19   20   21   22   22   24   27   28   32   33   36 
LCS_GDT     P   133_B     P   133_B      7    9   12      4    7    7    8   17   18   18   18   19   19   20   21   22   22   24   27   28   32   33   36 
LCS_GDT     P   134_B     P   134_B      3    9   12      3    3    4    8    9   18   18   18   19   19   20   20   22   22   23   25   28   30   32   36 
LCS_AVERAGE  LCS_A:   9.00  (   5.63    6.78   14.58 )

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     10     14     16     17     17     18     19     21     25     26     27     30     32     33     35     35     35     36     37     38 
GDT PERCENT_AT   4.83   6.76   7.73   8.21   8.21   8.70   9.18  10.14  12.08  12.56  13.04  14.49  15.46  15.94  16.91  16.91  16.91  17.39  17.87  18.36
GDT RMS_LOCAL    0.33   0.52   0.68   0.93   0.93   1.23   1.81   2.76   3.10   3.20   3.31   3.95   4.12   4.23   4.58   4.58   4.54   4.75   5.37   5.87
GDT RMS_ALL_AT  23.12  32.77  33.00  32.22  32.22  23.61  31.30  33.54  32.28  32.25  32.34  31.08  31.35  31.39  30.47  30.47  31.27  30.64  29.20  28.37

# Checking swapping
#   possible swapping detected:  F    88_B      F    88_B
#   possible swapping detected:  F    95_B      F    95_B
#   possible swapping detected:  E    98_B      E    98_B
#   possible swapping detected:  D   100_B      D   100_B
#   possible swapping detected:  D   104_B      D   104_B
#   possible swapping detected:  F   107_B      F   107_B
#   possible swapping detected:  D   113_B      D   113_B
#   possible swapping detected:  Y   128_B      Y   128_B
#   possible swapping detected:  F   132_B      F   132_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L    67_B      L    67_B     8.441     0    0.058   0.130    11.535    8.571    4.464
LGA    Y    68_B      Y    68_B     3.481     0    0.060   1.389     7.025   44.048   42.738
LGA    A    69_B      A    69_B     5.193     0    0.028   0.042     7.073   26.310   23.048
LGA    E    70_B      E    70_B     7.764     0    0.069   1.214     9.443   10.119    6.243
LGA    M    71_B      M    71_B     6.883     0    0.041   1.286     9.346   16.310   13.393
LGA    K    72_B      K    72_B     3.283     0    0.033   0.706     6.375   46.786   39.524
LGA    A    73_B      A    73_B     4.538     0    0.083   0.094     5.894   33.095   30.762
LGA    A    74_B      A    74_B     7.446     0    0.033   0.035     8.891   11.071    9.429
LGA    L    75_B      L    75_B     6.831     0    0.023   0.356     8.793   15.357   11.845
LGA    A    76_B      A    76_B     3.690     0    0.204   0.218     4.410   41.786   46.381
LGA    A    77_B      A    77_B     4.848     0    0.231   0.255     7.518   43.929   36.571
LGA    A    78_B      A    78_B     3.696     0    0.631   0.601     5.492   48.452   44.000
LGA    K    79_B      K    79_B     3.267     0    0.614   1.594    12.744   51.905   26.032
LGA    T    80_B      T    80_B     2.498     0    0.073   0.905     3.555   66.786   61.769
LGA    P    81_B      P    81_B     2.561     0    0.053   0.145     3.539   60.952   56.327
LGA    E    82_B      E    82_B     1.832     4    0.048   0.049     2.143   75.119   40.582
LGA    E    83_B      E    83_B     0.506     4    0.033   0.048     1.029   88.214   49.259
LGA    K    84_B      K    84_B     1.773     0    0.031   1.195     5.309   75.000   55.873
LGA    I    85_B      I    85_B     1.488     0    0.028   0.627     5.312   83.810   68.512
LGA    A    86_B      A    86_B     1.239     0    0.020   0.026     2.116   77.381   76.476
LGA    V    87_B      V    87_B     2.437     0    0.018   0.114     3.834   64.881   58.571
LGA    F    88_B      F    88_B     1.921     0    0.038   1.125     3.681   75.000   70.000
LGA    R    89_B      R    89_B     1.177     0    0.026   1.361     4.549   75.357   67.013
LGA    E    90_B      E    90_B     3.142     0    0.031   0.140     6.166   52.024   40.370
LGA    Y    91_B      Y    91_B     3.135     0    0.150   0.670     5.535   51.905   44.286
LGA    N    92_B      N    92_B     1.559     0    0.046   0.979     2.309   70.833   74.107
LGA    A    93_B      A    93_B     3.101     0    0.138   0.144     5.056   44.524   44.286
LGA    R    94_B      R    94_B     5.912     0    0.255   1.094    17.006   23.333    9.394
LGA    F    95_B      F    95_B     6.133     0    0.578   1.096    10.974   25.238   11.645
LGA    L    96_B      L    96_B     5.534     0    0.604   0.577    10.728   23.929   13.750
LGA    A    97_B      A    97_B     3.604     0    0.065   0.074     5.045   40.714   38.857
LGA    E    98_B      E    98_B     5.291     0    0.039   1.199     8.486   19.524   12.751
LGA    F    99_B      F    99_B    10.541     0    0.045   1.022    17.909    1.190    0.433
LGA    D   100_B      D   100_B    10.965     0    0.036   1.058    13.910    0.119    0.119
LGA    A   101_B      A   101_B    10.101     0    0.043   0.044    13.862    0.119    1.524
LGA    L   102_B      L   102_B    14.548     0    0.040   0.726    18.922    0.000    0.000
LGA    I   103_B      I   103_B    19.691     0    0.011   0.801    22.894    0.000    0.000
LGA    D   104_B      D   104_B    20.458     0    0.023   1.138    23.006    0.000    0.000
LGA    Q   105_B      Q   105_B    19.643     0    0.050   0.337    23.851    0.000    0.000
LGA    A   106_B      A   106_B    25.429     0    0.021   0.028    29.447    0.000    0.000
LGA    F   107_B      F   107_B    29.322     0    0.114   1.541    33.491    0.000    0.000
LGA    A   108_B      A   108_B    28.781     0    0.041   0.052    31.825    0.000    0.000
LGA    R   109_B      R   109_B    30.467     0    0.054   1.496    34.902    0.000    0.000
LGA    L   110_B      L   110_B    36.597     3    0.089   0.108    40.381    0.000    0.000
LGA    K   111_B      K   111_B    38.931     2    0.285   0.669    42.365    0.000    0.000
LGA    A   112_B      A   112_B    40.635     0    0.590   0.542    41.249    0.000    0.000
LGA    D   113_B      D   113_B    43.091     0    0.640   0.913    44.670    0.000    0.000
LGA    S   114_B      S   114_B    48.184     0    0.660   0.624    51.482    0.000    0.000
LGA    L   115_B      L   115_B    51.530     0    0.068   0.618    51.979    0.000    0.000
LGA    T   116_B      T   116_B    54.656     0    0.334   0.930    58.353    0.000    0.000
LGA    L   117_B      L   117_B    51.859     0    0.045   0.165    52.525    0.000    0.000
LGA    K   118_B      K   118_B    55.047     0    0.066   0.348    63.710    0.000    0.000
LGA    I   119_B      I   119_B    54.021     0    0.031   0.523    55.269    0.000    0.000
LGA    H   120_B      H   120_B    58.301     0    0.165   0.206    60.820    0.000    0.000
LGA    L   121_B      L   121_B    58.383     0    0.017   1.428    58.973    0.000    0.000
LGA    S   122_B      S   122_B    61.257     0    0.184   0.556    62.668    0.000    0.000
LGA    Q   123_B      Q   123_B    63.991     4    0.601   0.596    64.508    0.000    0.000
LGA    G   124_B      G   124_B    66.483     0    0.505   0.505    66.483    0.000    0.000
LGA    K   125_B      K   125_B    62.100     4    0.638   0.612    63.805    0.000    0.000
LGA    G   126_B      G   126_B    56.662     0    0.590   0.590    58.495    0.000    0.000
LGA    S   127_B      S   127_B    53.158     0    0.679   0.619    55.269    0.000    0.000
LGA    Y   128_B      Y   128_B    49.319     0    0.131   1.172    52.781    0.000    0.000
LGA    E   129_B      E   129_B    50.843     0    0.123   1.159    56.048    0.000    0.000
LGA    I   130_B      I   130_B    48.075     0    0.116   1.357    51.780    0.000    0.000
LGA    I   131_B      I   131_B    51.265     0    0.045   0.155    54.023    0.000    0.000
LGA    F   132_B      F   132_B    50.995     0    0.186   1.337    55.044    0.000    0.000
LGA    P   133_B      P   133_B    54.376     0    0.048   0.152    55.177    0.000    0.000
LGA    P   134_B      P   134_B    58.405     0    0.626   0.631    60.765    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       68     272    272  100.00     516    516  100.00               207
SUMMARY(RMSD_GDC):    13.496         13.559                 13.889            7.216    5.944

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   68  207    4.0     21    2.76    10.507     9.684     0.733

LGA_LOCAL      RMSD:   2.764  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  33.537  Number of assigned atoms:   68 
Std_ASGN_ATOMS RMSD:  13.496  Standard rmsd on all 68 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.965618 * X  +   0.224745 * Y  +  -0.130659 * Z  + -20.165255
  Y_new =   0.250845 * X  +  -0.937469 * Y  +   0.241306 * Z  +   6.168563
  Z_new =  -0.068256 * X  +  -0.265785 * Y  +  -0.961613 * Z  +  20.098484 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.254159  0.068310 -2.871930   [DEG:   14.5622    3.9139 -164.5495 ]
ZXZ: -2.645325  2.863617 -2.890214   [DEG: -151.5660  164.0732 -165.5971 ]
 
# END of job
