
#######################################################
#                                                     #
#                        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   74 (  578),  selected   71 , name one
# Molecule2: number of CA atoms  126 (  936),  selected   71 , 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:    31     125_A - 158_A       4.71    19.65
  LCS_AVERAGE:     23.17

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20     136_A - 158_A       2.00    23.01
  LCS_AVERAGE:     12.09

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      85_A - 100_A       0.95    24.66
  LONGEST_CONTINUOUS_SEGMENT:    16     128_A - 143_A       0.76    19.75
  LCS_AVERAGE:      9.05

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     P    85_A     P    85_A     16   17   29     12   14   15   16   16   16   16   17   18   20   24   27   29   29   29   30   31   32   34   35 
LCS_GDT     E    86_A     E    86_A     16   17   29     12   14   15   16   16   16   16   17   19   20   24   27   29   30   30   33   34   35   36   38 
LCS_GDT     A    87_A     A    87_A     16   17   29     12   14   15   16   16   16   16   17   20   23   27   29   29   30   30   33   34   35   36   38 
LCS_GDT     L    88_A     L    88_A     16   17   29     12   14   15   16   16   16   16   17   20   23   24   27   29   29   29   30   31   33   34   38 
LCS_GDT     E    89_A     E    89_A     16   17   29     12   14   15   16   16   16   16   17   19   22   24   27   29   29   29   30   31   33   34   37 
LCS_GDT     R    90_A     R    90_A     16   17   29     12   14   15   16   16   16   16   17   20   23   24   27   29   29   30   33   34   35   36   38 
LCS_GDT     S    91_A     S    91_A     16   17   29     12   14   15   16   16   16   16   18   20   23   24   27   29   29   29   33   34   35   36   38 
LCS_GDT     I    92_A     I    92_A     16   17   29     12   14   15   16   16   16   16   17   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     T    93_A     T    93_A     16   17   29     12   14   15   16   16   16   16   17   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     A    94_A     A    94_A     16   17   29     12   14   15   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     L    95_A     L    95_A     16   17   29     12   14   15   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     A    96_A     A    96_A     16   17   29      7   14   15   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     A    97_A     A    97_A     16   17   29      7   14   15   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     M    98_A     M    98_A     16   17   29     12   14   15   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     T    99_A     T    99_A     16   17   29      8   14   15   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     G   100_A     G   100_A     16   17   29      3    3    8   16   16   16   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     H   101_A     H   101_A      3   17   29      3    3    3    4    9   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     A   102_A     A   102_A     10   15   29      9   10   10   11   14   15   16   18   19   22   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     P   103_A     P   103_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     S   104_A     S   104_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     S   105_A     S   105_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     I   106_A     I   106_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     K   107_A     K   107_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     E   108_A     E   108_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     E   109_A     E   109_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     C   110_A     C   110_A     10   15   29      9   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     V   111_A     V   111_A     10   15   29      4   10   10   11   14   15   16   18   20   23   24   27   29   29   29   30   31   33   34   35 
LCS_GDT     E   112_A     E   112_A      3   11   29      3    3    3    4    4    7   10   17   19   22   24   26   29   29   29   30   31   33   34   35 
LCS_GDT     L   113_A     L   113_A      5    6   29      4    5    5    6    6    6    8   11   13   15   18   21   24   27   28   29   31   33   34   35 
LCS_GDT     I   114_A     I   114_A      5    6   25      4    5    5    6    6    7    8   10   12   15   17   19   21   24   25   26   30   33   34   35 
LCS_GDT     D   115_A     D   115_A      5    6   24      4    5    5    6    6    6    8   10   13   15   17   19   21   23   26   29   31   33   34   35 
LCS_GDT     K   116_A     K   116_A      5    6   22      4    5    5    6    6    7    8   11   12   14   16   19   21   22   24   25   30   33   33   35 
LCS_GDT     L   117_A     L   117_A      5    6   22      4    5    5    6    6    7    8   11   12   14   16   19   21   24   25   26   27   29   30   32 
LCS_GDT     D   118_A     D   118_A      3    6   22      1    3    3    6    6    7    8   11   12   15   17   20   22   24   25   26   28   29   29   32 
LCS_GDT     W   119_A     W   119_A      3    3   26      3    3    4    4    4    5    7   10   12   14   16   19   22   24   25   26   28   29   29   34 
LCS_GDT     L   120_A     L   120_A      3    3   26      3    3    4    6    6    6    9   13   15   18   21   22   24   25   26   30   33   35   36   38 
LCS_GDT     R   121_A     R   121_A      3    4   26      3    3    4    6    6   10   12   15   20   21   23   23   26   28   29   33   34   35   36   38 
LCS_GDT     V   122_A     V   122_A      4    5   26      3    4    4    6    7   10   15   18   20   21   23   23   26   27   29   32   34   35   36   38 
LCS_GDT     E   123_A     E   123_A      4    5   26      3    4    4    4    5    6    6    9   11   14   17   20   22   24   25   28   29   32   34   34 
LCS_GDT     N   124_A     N   124_A      4    5   26      3    4    4    4    5    5    5    8   10   12   15   17   20   24   25   28   29   35   36   37 
LCS_GDT     D   125_A     D   125_A      4    5   31      3    4    4    6    7   10   15   18   20   21   23   25   26   28   30   33   34   35   36   38 
LCS_GDT     V   126_A     V   126_A      4    5   31      3    3    4    7    8   12   17   18   20   21   23   25   26   28   30   33   34   35   36   38 
LCS_GDT     I   127_A     I   127_A      4   17   31      3    3    4    4    5   10   14   18   20   21   23   25   26   30   30   33   34   35   36   38 
LCS_GDT     Q   128_A     Q   128_A     16   18   31     10   15   16   16   16   17   19   22   25   26   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     Y   129_A     Y   129_A     16   18   31     10   15   16   16   16   19   20   24   25   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     P   130_A     P   130_A     16   18   31     10   15   16   16   16   19   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     T   131_A     T   131_A     16   18   31     10   15   16   16   16   19   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   132_A     L   132_A     16   18   31     10   15   16   16   16   19   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     S   133_A     S   133_A     16   18   31     10   15   16   16   16   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     K   134_A     K   134_A     16   18   31     10   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   135_A     L   135_A     16   18   31     10   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   136_A     L   136_A     16   20   31     10   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     E   137_A     E   137_A     16   20   31      9   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   138_A     L   138_A     16   20   31     10   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     Y   139_A     Y   139_A     16   20   31     10   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     N   140_A     N   140_A     16   20   31      5   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     S   141_A     S   141_A     16   20   31      7   15   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     Q   142_A     Q   142_A     16   20   31      3   15   16   16   16   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     N   143_A     N   143_A     16   20   31      3   12   16   16   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     H   147_A     H   147_A     10   20   31      3    4   10   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   148_A     L   148_A     11   20   31      3    9   11   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     S   149_A     S   149_A     11   20   31      7   10   11   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     I   150_A     I   150_A     11   20   31      7   10   11   12   17   21   22   23   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     E   151_A     E   151_A     11   20   31      7   10   11   12   17   21   22   23   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     K   152_A     K   152_A     11   20   31      7   10   11   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   153_A     L   153_A     11   20   31      7   10   11   13   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     I   154_A     I   154_A     11   20   31      7   10   11   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     A   155_A     A   155_A     11   20   31      7   10   11   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     G   156_A     G   156_A     11   20   31      7   10   11   12   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     L   157_A     L   157_A     11   20   31      6   10   11   13   19   21   22   24   26   27   28   29   29   30   30   33   34   35   36   38 
LCS_GDT     A   158_A     A   158_A     11   20   31      6   10   11   13   19   21   22   24   26   27   28   29   29   29   30   33   34   35   36   37 
LCS_AVERAGE  LCS_A:  14.77  (   9.05   12.09   23.17 )

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     12     15     16     16     19     21     22     24     26     27     28     29     29     30     30     33     34     35     36     38 
GDT PERCENT_AT   9.52  11.90  12.70  12.70  15.08  16.67  17.46  19.05  20.63  21.43  22.22  23.02  23.02  23.81  23.81  26.19  26.98  27.78  28.57  30.16
GDT RMS_LOCAL    0.34   0.65   0.76   0.76   2.00   2.07   2.16   2.53   2.73   2.88   3.04   3.37   3.37   4.19   3.77   4.99   5.30   5.52   5.83   6.50
GDT RMS_ALL_AT  23.61  19.81  19.75  19.75  22.00  22.75  22.42  21.00  21.26  20.99  20.68  20.86  20.86  20.73  21.06  19.95  19.64  19.41  18.99  18.14

# Checking swapping
#   possible swapping detected:  E    89_A      E    89_A
#   possible swapping detected:  E   109_A      E   109_A
#   possible swapping detected:  D   115_A      D   115_A
#   possible swapping detected:  D   125_A      D   125_A
#   possible swapping detected:  E   151_A      E   151_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P    85_A      P    85_A    17.721     0    0.207   0.200    21.222    0.000    0.000
LGA    E    86_A      E    86_A    11.659     0    0.183   0.916    13.859    0.357    0.159
LGA    A    87_A      A    87_A     8.944     0    0.088   0.097    10.136    1.548    1.524
LGA    L    88_A      L    88_A    13.439     0    0.059   1.450    18.844    0.000    0.000
LGA    E    89_A      E    89_A    14.065     0    0.035   1.402    18.229    0.000    0.000
LGA    R    90_A      R    90_A    10.101     0    0.018   0.139    12.379    0.000    8.398
LGA    S    91_A      S    91_A    12.012     0    0.036   0.047    15.797    0.000    0.238
LGA    I    92_A      I    92_A    18.264     0    0.078   0.147    21.599    0.000    0.000
LGA    T    93_A      T    93_A    18.547     0    0.037   0.067    21.109    0.000    0.000
LGA    A    94_A      A    94_A    18.198     0    0.042   0.056    21.934    0.000    0.000
LGA    L    95_A      L    95_A    21.953     0    0.053   0.176    26.257    0.000    0.000
LGA    A    96_A      A    96_A    26.808     0    0.124   0.124    30.299    0.000    0.000
LGA    A    97_A      A    97_A    28.107     0    0.254   0.243    30.095    0.000    0.000
LGA    M    98_A      M    98_A    29.072     0    0.054   1.222    32.226    0.000    0.000
LGA    T    99_A      T    99_A    32.148     0    0.218   1.095    35.747    0.000    0.000
LGA    G   100_A      G   100_A    37.398     0    0.646   0.646    38.965    0.000    0.000
LGA    H   101_A      H   101_A    38.474     5    0.609   0.639    39.379    0.000    0.000
LGA    A   102_A      A   102_A    38.404     0    0.370   0.369    38.863    0.000    0.000
LGA    P   103_A      P   103_A    34.086     0    0.057   0.440    37.540    0.000    0.000
LGA    S   104_A      S   104_A    38.050     0    0.055   0.692    41.679    0.000    0.000
LGA    S   105_A      S   105_A    37.317     0    0.086   0.277    39.396    0.000    0.000
LGA    I   106_A      I   106_A    31.159     0    0.034   0.667    33.413    0.000    0.000
LGA    K   107_A      K   107_A    31.966     0    0.036   0.826    33.382    0.000    0.000
LGA    E   108_A      E   108_A    35.923     3    0.018   0.713    39.158    0.000    0.000
LGA    E   109_A      E   109_A    31.627     0    0.068   1.198    33.931    0.000    0.000
LGA    C   110_A      C   110_A    27.709     0    0.276   0.263    29.215    0.000    0.000
LGA    V   111_A      V   111_A    32.230     0    0.389   0.556    35.935    0.000    0.000
LGA    E   112_A      E   112_A    33.664     0    0.630   1.399    36.940    0.000    0.000
LGA    L   113_A      L   113_A    34.260     0    0.578   0.535    37.807    0.000    0.000
LGA    I   114_A      I   114_A    31.802     0    0.059   1.313    34.942    0.000    0.000
LGA    D   115_A      D   115_A    36.114     0    0.094   1.444    41.029    0.000    0.000
LGA    K   116_A      K   116_A    33.550     2    0.218   0.231    36.237    0.000    0.000
LGA    L   117_A      L   117_A    26.998     0    0.606   1.460    29.297    0.000    0.000
LGA    D   118_A      D   118_A    26.866     0    0.525   0.577    28.828    0.000    0.000
LGA    W   119_A      W   119_A    24.293     0    0.630   1.364    28.193    0.000    0.000
LGA    L   120_A      L   120_A    18.591     0    0.669   0.573    20.150    0.000    0.000
LGA    R   121_A      R   121_A    17.545     0    0.572   1.005    22.045    0.000    0.000
LGA    V   122_A      V   122_A    19.701     0    0.589   0.586    21.036    0.000    0.000
LGA    E   123_A      E   123_A    24.312     4    0.339   0.340    25.403    0.000    0.000
LGA    N   124_A      N   124_A    21.778     0    0.366   0.359    25.907    0.000    0.000
LGA    D   125_A      D   125_A    16.677     0    0.644   0.782    18.782    0.000    0.000
LGA    V   126_A      V   126_A    15.834     0    0.530   0.573    19.281    0.000    0.000
LGA    I   127_A      I   127_A    11.555     0    0.052   0.667    16.798    0.119    0.060
LGA    Q   128_A      Q   128_A     6.108     0    0.620   1.110     8.031   21.190   22.857
LGA    Y   129_A      Y   129_A     4.904     0    0.024   1.286    13.214   34.524   15.913
LGA    P   130_A      P   130_A     3.303     0    0.114   0.132     4.301   52.024   46.531
LGA    T   131_A      T   131_A     4.118     0    0.055   0.149     5.280   41.905   36.667
LGA    L   132_A      L   132_A     3.912     0    0.060   1.442     4.483   46.905   45.238
LGA    S   133_A      S   133_A     2.454     0    0.026   0.628     3.000   67.262   66.508
LGA    K   134_A      K   134_A     1.333     4    0.051   0.082     1.710   81.548   44.339
LGA    L   135_A      L   135_A     1.726     0    0.060   1.317     3.200   72.857   67.976
LGA    L   136_A      L   136_A     2.036     0    0.097   1.307     4.860   68.810   55.714
LGA    E   137_A      E   137_A     1.272     4    0.047   0.059     1.458   81.429   46.243
LGA    L   138_A      L   138_A     0.632     3    0.012   0.028     1.691   83.810   54.405
LGA    Y   139_A      Y   139_A     2.053     0    0.049   0.299     4.960   67.024   52.262
LGA    N   140_A      N   140_A     2.153     0    0.060   1.137     5.480   66.786   54.821
LGA    S   141_A      S   141_A     1.708     0    0.155   0.172     2.903   66.905   71.746
LGA    Q   142_A      Q   142_A     2.824     4    0.071   0.068     3.357   59.048   31.799
LGA    N   143_A      N   143_A     1.956     3    0.392   0.380     2.266   72.976   44.583
LGA    H   147_A      H   147_A     2.600     0    0.631   1.174    10.868   73.214   35.333
LGA    L   148_A      L   148_A     2.133     0    0.213   0.340     6.604   59.167   44.524
LGA    S   149_A      S   149_A     3.470     0    0.047   0.603     4.252   53.571   49.127
LGA    I   150_A      I   150_A     4.603     0    0.015   1.286     8.357   34.286   26.488
LGA    E   151_A      E   151_A     5.240     0    0.068   0.799    11.432   34.524   18.519
LGA    K   152_A      K   152_A     2.842     0    0.046   0.753     4.892   61.548   48.942
LGA    L   153_A      L   153_A     1.750     0    0.031   1.413     6.568   70.833   53.571
LGA    I   154_A      I   154_A     3.414     0    0.030   0.082     6.593   55.357   39.821
LGA    A   155_A      A   155_A     3.273     0    0.032   0.032     4.363   55.476   51.810
LGA    G   156_A      G   156_A     1.833     0    0.096   0.096     2.488   70.833   70.833
LGA    L   157_A      L   157_A     2.353     0    0.038   0.087     5.955   70.952   50.179
LGA    A   158_A      A   158_A     1.910     0    0.675   0.639     3.286   67.143   65.143

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     522    522  100.00               126
SUMMARY(RMSD_GDC):    13.271         13.245                 13.461           13.444   10.494

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   74  126    4.0     24    2.53    17.460    16.474     0.914

LGA_LOCAL      RMSD:   2.526  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.996  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:  13.271  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.638927 * X  +  -0.631235 * Y  +  -0.439675 * Z  + -13.497466
  Y_new =   0.468152 * X  +  -0.134465 * Y  +   0.873357 * Z  + -41.375313
  Z_new =  -0.610415 * X  +  -0.763846 * Y  +   0.209600 * Z  +  17.578510 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.632347  0.656585 -1.302987   [DEG:   36.2308   37.6195  -74.6556 ]
ZXZ: -2.675204  1.359630 -2.467380   [DEG: -153.2779   77.9011 -141.3705 ]
 
# END of job
