
#######################################################
#                                                     #
#                        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 (  546),  selected   63 , name one
# Molecule2: number of CA atoms  124 ( 1059),  selected   63 , 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      88_D - 123_D       4.93    16.96
  LCS_AVERAGE:     23.37

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      95_D - 123_D       1.28    17.96
  LCS_AVERAGE:     12.88

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    27      97_D - 123_D       0.72    18.55
  LCS_AVERAGE:     11.11

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     K    61_D     K    61_D      4    4   13      2    4    4    4    5    6    8   11   11   11   12   12   12   14   16   16   19   22   24   25 
LCS_GDT     C    62_D     C    62_D      4    4   13      3    4    4    4    4    6    6    8    8   11   12   14   16   16   18   19   22   26   32   38 
LCS_GDT     E    63_D     E    63_D      4    4   13      3    4    4    4    4    6    6    8    8   10   11   14   16   16   18   19   22   24   26   28 
LCS_GDT     N    64_D     N    64_D      4    4   13      3    4    4    4    4    5    6    8    8   10   11   14   16   16   20   22   24   26   33   38 
LCS_GDT     P    65_D     P    65_D      4    4   13      3    4    4    4    4    6    6    8    8   10   11   14   16   18   21   25   27   32   39   42 
LCS_GDT     K    66_D     K    66_D      4    4   13      3    4    4    4    4    6    6    8    8   10   11   12   16   18   20   23   27   32   39   42 
LCS_GDT     E    67_D     E    67_D      3    4   14      3    3    3    4    4    6    6    8    8   10   11   14   16   18   21   25   27   31   34   38 
LCS_GDT     Q    68_D     Q    68_D      3    4   14      0    3    3    4    4    5    6    8    8   10   11   16   18   20   22   25   27   32   39   42 
LCS_GDT     W    69_D     W    69_D      3    3   14      3    3    3    3    3    4    6    9   11   15   15   16   18   20   22   25   33   37   41   43 
LCS_GDT     V    70_D     V    70_D      3    3   14      3    3    3    3    6    6    7   10   11   15   15   16   18   20   22   25   33   37   41   43 
LCS_GDT     A    71_D     A    71_D      3    4   14      3    3    3    3    4    6    7   10   11   15   15   16   18   20   22   25   27   32   39   42 
LCS_GDT     N    72_D     N    72_D      3    6   14      3    3    4    4    6    6    7   11   11   14   14   17   18   19   21   22   25   29   31   31 
LCS_GDT     Y    73_D     Y    73_D      4    6   14      4    4    4    4    6    6    7   10   11   14   14   17   18   23   25   32   37   44   46   48 
LCS_GDT     Q    74_D     Q    74_D      4    6   14      4    4    4    4    6    6    7   11   11   15   15   17   18   19   22   25   27   31   37   43 
LCS_GDT     N    75_D     N    75_D      4    6   14      4    4    4    4    6    6    8   11   11   14   14   15   17   19   21   21   23   24   25   28 
LCS_GDT     L    76_D     L    76_D      4    6   16      4    4    4    4    6    6    8   11   11   14   14   17   18   19   21   23   25   28   31   39 
LCS_GDT     N    77_D     N    77_D      4    6   18      3    3    4    4    5    6    8   11   11   14   14   17   18   23   26   32   39   44   46   48 
LCS_GDT     N    78_D     N    78_D      4    5   18      3    3    4    5    5    6    8   11   11   15   15   17   18   24   33   41   44   44   46   48 
LCS_GDT     V    79_D     V    79_D      4    5   18      3    3    4    5    5    6    8   11   11   15   15   17   18   20   26   32   39   44   46   48 
LCS_GDT     V    80_D     V    80_D      3    5   18      3    4    4    5    5    6    8   11   11   15   19   26   35   38   39   43   44   44   46   48 
LCS_GDT     F    81_D     F    81_D      4    5   34      3    4    4    5    5    5   12   24   27   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     T    82_D     T    82_D      4    5   34      3    4    6    8   10   16   22   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     N    83_D     N    83_D      4    4   34      3    4    6    8   10   13   17   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K    84_D     K    84_D      4    4   34      3    4    6    8   10   15   22   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     E    85_D     E    85_D      3    4   34      3    4    4    4    4    5   10   16   21   26   30   34   36   38   39   43   44   44   46   48 
LCS_GDT     L    86_D     L    86_D      4    6   34      3    4    4    5    7    9   12   15   19   23   26   30   35   38   39   43   44   44   46   48 
LCS_GDT     E    87_D     E    87_D      4    6   34      3    4    4    5    7   10   12   15   18   20   24   26   29   32   36   39   43   44   46   48 
LCS_GDT     D    88_D     D    88_D      4    6   36      3    3    4    5    7   10   12   15   18   21   24   26   29   34   39   43   44   44   46   48 
LCS_GDT     I    89_D     I    89_D      4    6   36      3    3    4    5    7    9   12   15   18   23   27   34   36   38   39   43   44   44   46   48 
LCS_GDT     Y    90_D     Y    90_D      3    6   36      3    3    3    4    5    7   11   14   17   18   22   25   29   34   39   43   44   44   46   48 
LCS_GDT     D    91_D     D    91_D      4    6   36      4    4    4    4    5    7   11   14   17   18   20   25   29   34   39   43   44   44   46   48 
LCS_GDT     L    92_D     L    92_D      4    4   36      4    4    4    4    5    5    8   11   12   15   19   23   27   35   39   43   44   44   46   48 
LCS_GDT     S    93_D     S    93_D      4    4   36      4    4    4    4    5    5    8   11   12   15   19   20   27   35   39   43   44   44   46   48 
LCS_GDT     N    94_D     N    94_D      4    6   36      4    4    4    4    4    8   13   16   23   32   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K    95_D     K    95_D      6   29   36      5    5    9   17   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     E    96_D     E    96_D      6   29   36      5    5    9   19   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     E    97_D     E    97_D     27   29   36      5    5    9   19   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     T    98_D     T    98_D     27   29   36      6   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K    99_D     K    99_D     27   29   36     22   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     E   100_D     E   100_D     27   29   36     22   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     V   101_D     V   101_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     L   102_D     L   102_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K   103_D     K   103_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K   104_D     K   104_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     F   105_D     F   105_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K   106_D     K   106_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     E   107_D     E   107_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K   108_D     K   108_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     V   109_D     V   109_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     N   110_D     N   110_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     Q   111_D     Q   111_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     F   112_D     F   112_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     Y   113_D     Y   113_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     R   114_D     R   114_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     H   115_D     H   115_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     A   116_D     A   116_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     F   117_D     F   117_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     D   118_D     D   118_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     I   119_D     I   119_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     I   120_D     I   120_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     N   121_D     N   121_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     K   122_D     K   122_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   39   43   44   44   46   48 
LCS_GDT     Y   123_D     Y   123_D     27   29   36     23   26   26   26   29   29   29   29   32   33   34   34   36   38   38   43   44   44   46   48 
LCS_AVERAGE  LCS_A:  15.79  (  11.11   12.88   23.37 )

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     23     26     26     26     29     29     29     29     32     33     34     34     36     38     39     43     44     44     46     48 
GDT PERCENT_AT  18.55  20.97  20.97  20.97  23.39  23.39  23.39  23.39  25.81  26.61  27.42  27.42  29.03  30.65  31.45  34.68  35.48  35.48  37.10  38.71
GDT RMS_LOCAL    0.21   0.33   0.33   0.33   1.28   1.28   1.28   1.28   2.51   2.69   3.00   3.00   3.65   4.13   4.82   5.21   5.45   5.33   5.77   6.20
GDT RMS_ALL_AT  18.54  18.41  18.41  18.41  17.96  17.96  17.96  17.96  16.42  16.10  16.08  16.08  15.66  15.38  14.94  14.99  14.74  15.04  14.63  14.19

# Checking swapping
#   possible swapping detected:  E    67_D      E    67_D
#   possible swapping detected:  Y    73_D      Y    73_D
#   possible swapping detected:  F    81_D      F    81_D
#   possible swapping detected:  E    85_D      E    85_D
#   possible swapping detected:  E    87_D      E    87_D
#   possible swapping detected:  E    97_D      E    97_D
#   possible swapping detected:  F   105_D      F   105_D
#   possible swapping detected:  Y   113_D      Y   113_D
#   possible swapping detected:  D   118_D      D   118_D
#   possible swapping detected:  Y   123_D      Y   123_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    61_D      K    61_D    45.277     0    0.462   1.168    46.274    0.000    0.000
LGA    C    62_D      C    62_D    41.135     0    0.085   0.668    42.986    0.000    0.000
LGA    E    63_D      E    63_D    43.967     0    0.593   1.083    47.150    0.000    0.000
LGA    N    64_D      N    64_D    41.476     0    0.146   0.805    45.915    0.000    0.000
LGA    P    65_D      P    65_D    35.239     0    0.642   0.558    37.343    0.000    0.000
LGA    K    66_D      K    66_D    34.539     0    0.584   1.293    39.495    0.000    0.000
LGA    E    67_D      E    67_D    36.110     0    0.616   1.284    40.014    0.000    0.000
LGA    Q    68_D      Q    68_D    30.990     0    0.642   0.723    32.917    0.000    0.000
LGA    W    69_D      W    69_D    26.839     0    0.622   0.920    27.877    0.000    0.000
LGA    V    70_D      V    70_D    27.899     0    0.595   0.575    29.938    0.000    0.000
LGA    A    71_D      A    71_D    27.238     0    0.191   0.188    27.238    0.000    0.000
LGA    N    72_D      N    72_D    25.949     0    0.390   0.355    30.101    0.000    0.000
LGA    Y    73_D      Y    73_D    20.470     0    0.306   1.198    22.266    0.000    0.000
LGA    Q    74_D      Q    74_D    25.171     0    0.190   0.894    32.864    0.000    0.000
LGA    N    75_D      N    75_D    26.950     0    0.161   1.107    29.587    0.000    0.000
LGA    L    76_D      L    76_D    20.760     0    0.593   1.011    22.620    0.000    0.000
LGA    N    77_D      N    77_D    17.909     0    0.649   1.214    20.664    0.000    0.000
LGA    N    78_D      N    78_D    17.852     0    0.368   0.410    19.667    0.000    0.000
LGA    V    79_D      V    79_D    17.855     0    0.165   1.227    20.474    0.000    0.000
LGA    V    80_D      V    80_D    12.436     0    0.623   0.654    14.253    0.000    0.204
LGA    F    81_D      F    81_D     9.038     0    0.530   1.227    10.071    0.833    4.372
LGA    T    82_D      T    82_D     8.770     0    0.648   0.559     9.603    2.262    2.517
LGA    N    83_D      N    83_D     8.460     0    0.262   0.869    11.587    4.286    2.500
LGA    K    84_D      K    84_D     8.346     0    0.579   0.484     9.107    4.524    6.349
LGA    E    85_D      E    85_D    12.622     0    0.590   0.963    21.635    0.000    0.000
LGA    L    86_D      L    86_D    11.519     0    0.625   0.987    11.796    0.000    0.000
LGA    E    87_D      E    87_D    12.258     0    0.576   1.184    15.003    0.000    0.000
LGA    D    88_D      D    88_D    13.310     0    0.381   0.407    16.163    0.000    0.000
LGA    I    89_D      I    89_D    11.298     0    0.196   1.398    12.673    0.119    0.060
LGA    Y    90_D      Y    90_D    12.644     0    0.596   1.361    16.627    0.000    0.000
LGA    D    91_D      D    91_D    14.099     0    0.674   1.238    18.848    0.000    0.000
LGA    L    92_D      L    92_D    15.671     0    0.007   0.126    22.368    0.000    0.000
LGA    S    93_D      S    93_D    13.860     0    0.457   0.709    15.034    0.000    0.000
LGA    N    94_D      N    94_D     9.391     0    0.067   0.303    10.252    7.024    5.536
LGA    K    95_D      K    95_D     3.740     0    0.602   1.044    12.977   44.881   24.127
LGA    E    96_D      E    96_D     3.413     0    0.017   0.578     4.418   53.810   52.646
LGA    E    97_D      E    97_D     2.486     0    0.143   0.912     7.510   64.881   44.233
LGA    T    98_D      T    98_D     0.702     0    0.204   1.062     2.718   90.595   79.592
LGA    K    99_D      K    99_D     0.795     0    0.042   0.782     2.715   90.476   85.767
LGA    E   100_D      E   100_D     1.008     0    0.020   1.153     4.867   83.690   68.042
LGA    V   101_D      V   101_D     1.382     0    0.022   0.156     1.575   79.286   78.980
LGA    L   102_D      L   102_D     1.310     0    0.019   1.359     3.412   81.429   72.381
LGA    K   103_D      K   103_D     1.162     0    0.016   0.904     3.465   83.690   73.545
LGA    K   104_D      K   104_D     0.984     0    0.017   0.524     2.605   90.476   83.757
LGA    F   105_D      F   105_D     0.875     0    0.015   0.167     1.032   88.214   88.009
LGA    K   106_D      K   106_D     0.858     0    0.031   0.901     4.930   90.476   73.862
LGA    E   107_D      E   107_D     0.838     0    0.025   0.131     1.369   90.476   87.460
LGA    K   108_D      K   108_D     0.680     0    0.034   0.603     2.153   90.476   85.661
LGA    V   109_D      V   109_D     0.573     0    0.043   0.056     0.685   90.476   90.476
LGA    N   110_D      N   110_D     0.728     0    0.017   0.058     0.885   90.476   90.476
LGA    Q   111_D      Q   111_D     0.567     0    0.034   0.220     1.175   95.238   90.582
LGA    F   112_D      F   112_D     0.224     0    0.014   0.131     0.928  100.000   96.537
LGA    Y   113_D      Y   113_D     0.345     0    0.006   0.076     0.828  100.000   94.444
LGA    R   114_D      R   114_D     0.150     0    0.019   0.302     0.878  100.000   99.134
LGA    H   115_D      H   115_D     0.445     0    0.057   1.157     2.922   97.619   86.619
LGA    A   116_D      A   116_D     0.619     0    0.014   0.015     0.864   92.857   92.381
LGA    F   117_D      F   117_D     0.361     0    0.035   0.096     1.144  100.000   93.160
LGA    D   118_D      D   118_D     0.321     0    0.037   0.889     4.262  100.000   79.345
LGA    I   119_D      I   119_D     0.591     0    0.037   0.110     0.831   92.857   91.667
LGA    I   120_D      I   120_D     0.628     0    0.021   0.725     3.359   90.476   85.417
LGA    N   121_D      N   121_D     0.579     0    0.050   0.756     2.318   90.476   82.917
LGA    K   122_D      K   122_D     0.968     0    0.155   0.685     4.203   90.476   74.497
LGA    Y   123_D      Y   123_D     0.949     0    0.694   0.503     2.358   81.786   86.825

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     546    546  100.00               124
SUMMARY(RMSD_GDC):    10.575         10.489                 11.338           20.602   18.984

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63  124    4.0     29    1.28    25.000    21.842     2.098

LGA_LOCAL      RMSD:   1.282  Number of atoms:   29  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.955  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:  10.575  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.533051 * X  +   0.485792 * Y  +  -0.692721 * Z  + -18.754276
  Y_new =  -0.755457 * X  +   0.095384 * Y  +   0.648217 * Z  + -19.344793
  Z_new =   0.380974 * X  +   0.868854 * Y  +   0.316151 * Z  +  48.941471 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.185271 -0.390849  1.221818   [DEG: -125.2068  -22.3940   70.0050 ]
ZXZ: -2.323018  1.249127  0.413231   [DEG: -133.0991   71.5697   23.6764 ]
 
# END of job
