
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        3.16     3.16
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      23_A - 43_A        1.91     5.41
  LONGEST_CONTINUOUS_SEGMENT:    21      47_A - 67_A        1.99     8.01
  LCS_AVERAGE:     31.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      71_A - 85_A        0.83     4.46
  LCS_AVERAGE:     16.72

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     A    22_A     A    22_A      3   18   64      0    3    3    8   23   32   45   52   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3   21   64      2    9   17   28   34   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   21   64      3   13   22   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A      9   21   64      3    3    5   14   27   37   48   52   57   61   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     13   21   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     13   21   64      8   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     13   21   64     10   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     13   21   64      8   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     13   21   64      8   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     13   21   64      8   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     13   21   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     13   21   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     13   21   64      4   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     13   21   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     13   21   64      4   15   22   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     13   21   64      4   14   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     13   21   64      3   14   22   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     11   21   64      3    7   22   29   34   41   47   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A      4   21   64      3    4    6   14   23   36   46   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A      3   21   64      3    3    6   14   23   30   45   53   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      3   21   64      3    7   22   27   34   40   47   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      3   21   64      3    3   11   17   18   34   40   47   57   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      5   19   64      3    7   11   14   19   28   43   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      5   19   64      4    5   15   27   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A      5   19   64      4    6   11   21   34   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A      5   21   64      4    4    5   11   18   21   31   48   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A      5   21   64      4    4    5    5    8   16   33   48   54   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A      3   21   64      0    3    3    4    7   17   24   31   47   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     14   21   64     10   11   13   16   19   38   47   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     14   21   64     10   11   13   16   19   34   47   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     14   21   64     10   11   13   24   32   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     14   21   64     10   11   17   28   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     14   21   64     10   11   13   16   31   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     14   21   64     10   11   13   16   27   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     14   21   64     10   11   16   28   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     14   21   64     10   11   16   28   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     14   21   64     10   11   13   16   27   38   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     14   21   64     10   11   13   16   19   30   43   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     14   21   64      6   11   13   16   19   29   45   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     14   21   64      5   11   13   21   32   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     14   21   64      3    8   23   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     14   21   64      3    9   15   28   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      3   21   64      3    4    7   19   28   38   46   52   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      3   21   64      3    4   13   22   30   38   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      3   21   64      3    4   13   16   27   38   48   53   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      4   21   64      3    4    4    6   15   21   28   50   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A      4   18   64      3    4    5   24   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A      4   18   64      8   22   25   30   34   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A      4   18   64      3    5   12   27   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     15   18   64      3   14   22   29   34   40   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     15   18   64      3   12   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     15   18   64      9   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     15   18   64      9   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     15   18   64     11   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     15   18   64     10   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     15   18   64     10   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     15   18   64      3   22   25   30   35   42   48   54   58   63   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  49.33  (  16.72   31.27  100.00 )

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     22     25     30     35     42     48     54     58     63     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  17.19  34.38  39.06  46.88  54.69  65.62  75.00  84.38  90.62  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.38   0.61   0.71   1.13   1.56   1.92   2.24   2.61   2.79   3.13   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16
GDT RMS_ALL_AT   3.82   3.91   3.87   3.66   3.38   3.29   3.33   3.21   3.19   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16   3.16

# Checking swapping
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     4.158     0    0.481   0.497     5.529   49.048   44.476
LGA    D    23_A      D    23_A     2.803     0    0.458   1.226     8.505   59.524   34.286
LGA    G    24_A      G    24_A     1.255     0    0.509   0.509     3.733   65.595   65.595
LGA    D    25_A      D    25_A     4.201     0    0.298   1.230     7.444   41.667   28.036
LGA    G    26_A      G    26_A     1.036     0    0.148   0.148     1.596   81.548   81.548
LGA    Q    27_A      Q    27_A     1.469     0    0.066   1.039     3.899   81.429   71.587
LGA    G    28_A      G    28_A     1.491     0    0.038   0.038     1.491   81.429   81.429
LGA    L    29_A      L    29_A     0.735     0    0.056   1.023     4.814   88.214   74.583
LGA    Y    30_A      Y    30_A     1.123     0    0.052   0.144     2.746   83.690   73.175
LGA    A    31_A      A    31_A     1.636     0    0.040   0.037     1.779   75.000   74.571
LGA    A    32_A      A    32_A     1.331     0    0.106   0.123     1.421   81.429   81.429
LGA    N    33_A      N    33_A     1.365     0    0.074   0.373     2.844   81.429   72.202
LGA    C    34_A      C    34_A     1.547     0    0.094   0.164     1.609   75.000   75.714
LGA    A    35_A      A    35_A     1.650     0    0.092   0.090     1.924   72.857   72.857
LGA    A    36_A      A    36_A     2.501     0    0.083   0.082     2.818   61.071   60.286
LGA    C    37_A      C    37_A     2.514     0    0.169   0.750     3.435   57.262   56.032
LGA    H    38_A      H    38_A     2.597     0    0.434   1.073     5.326   57.262   50.429
LGA    G    39_A      G    39_A     3.087     0    0.099   0.099     4.544   45.476   45.476
LGA    A    40_A      A    40_A     4.526     0    0.449   0.488     6.439   38.929   34.571
LGA    L    41_A      L    41_A     4.778     0    0.478   0.484     7.261   40.833   28.631
LGA    A    42_A      A    42_A     4.028     0    0.064   0.068     5.179   40.476   37.619
LGA    T    43_A      T    43_A     5.464     0    0.060   1.067     9.973   25.595   16.122
LGA    S    44_A      S    44_A     5.357     0    0.604   0.780     7.833   32.976   25.397
LGA    E    45_A      E    45_A     2.292     0    0.263   0.798     3.759   71.905   61.534
LGA    K    46_A      K    46_A     2.826     0    0.537   0.468     4.688   47.262   49.683
LGA    K    47_A      K    47_A     6.386     0    0.124   0.101    11.392   22.738   11.481
LGA    G    48_A      G    48_A     6.653     0    0.656   0.656     6.892   17.500   17.500
LGA    T    49_A      T    49_A     6.683     0    0.439   1.284    11.133   18.929   12.245
LGA    T    50_A      T    50_A     3.983     0    0.593   1.408     6.576   43.452   35.714
LGA    L    51_A      L    51_A     4.237     0    0.053   1.384     8.014   40.238   27.143
LGA    A    52_A      A    52_A     2.789     0    0.044   0.051     3.278   59.167   58.762
LGA    R    53_A      R    53_A     1.832     0    0.048   0.993     4.305   70.833   56.234
LGA    L    54_A      L    54_A     2.900     0    0.038   0.239     4.159   57.143   49.524
LGA    Q    55_A      Q    55_A     3.409     0    0.042   0.174     5.475   51.786   41.852
LGA    S    56_A      S    56_A     1.919     0    0.034   0.033     2.352   68.810   73.016
LGA    A    57_A      A    57_A     1.740     0    0.039   0.041     2.672   66.905   68.095
LGA    V    58_A      V    58_A     3.791     0    0.065   0.064     5.232   40.476   37.483
LGA    S    59_A      S    59_A     4.205     0    0.026   0.492     4.888   37.262   38.254
LGA    A    60_A      A    60_A     3.987     0    0.674   0.673     6.631   34.286   37.429
LGA    N    61_A      N    61_A     2.689     0    0.658   1.212     4.372   59.167   50.536
LGA    A    62_A      A    62_A     1.621     0    0.188   0.216     2.839   75.238   71.619
LGA    G    63_A      G    63_A     1.782     0    0.084   0.084     3.253   69.524   69.524
LGA    G    64_A      G    64_A     5.155     0    0.566   0.566     5.155   34.524   34.524
LGA    M    65_A      M    65_A     4.146     0    0.662   1.188     4.802   34.286   41.905
LGA    G    66_A      G    66_A     4.492     0    0.679   0.679     6.185   30.714   30.714
LGA    F    67_A      F    67_A     5.277     0    0.274   1.252     8.494   31.786   18.528
LGA    L    68_A      L    68_A     2.504     0    0.269   1.393     9.065   71.071   42.619
LGA    S    69_A      S    69_A     2.997     0    0.582   0.691     5.625   52.500   50.714
LGA    S    70_A      S    70_A     2.097     0    0.699   0.604     3.521   77.381   67.143
LGA    L    71_A      L    71_A     3.299     0    0.202   1.296     9.230   48.571   31.488
LGA    T    72_A      T    72_A     2.057     0    0.497   0.933     6.316   72.976   54.762
LGA    S    73_A      S    73_A     2.343     0    0.055   0.073     2.754   64.762   62.222
LGA    A    74_A      A    74_A     1.993     0    0.041   0.041     2.107   70.833   71.238
LGA    Q    75_A      Q    75_A     1.009     0    0.072   1.306     4.674   81.429   67.302
LGA    L    76_A      L    76_A     1.392     0    0.049   1.156     3.914   79.286   73.452
LGA    Q    77_A      Q    77_A     1.951     0    0.089   1.206     6.496   72.857   56.085
LGA    A    78_A      A    78_A     1.544     0    0.039   0.038     1.637   72.857   74.571
LGA    I    79_A      I    79_A     1.599     0    0.022   0.054     1.687   72.857   72.857
LGA    V    80_A      V    80_A     1.779     0    0.052   0.107     2.242   72.857   71.701
LGA    D    81_A      D    81_A     1.929     0    0.044   1.038     2.741   70.833   74.286
LGA    V    82_A      V    82_A     1.854     0    0.103   0.918     3.666   72.857   72.517
LGA    L    83_A      L    83_A     2.020     0    0.166   0.930     4.128   70.833   65.357
LGA    A    84_A      A    84_A     2.390     0    0.110   0.116     2.583   62.857   61.714
LGA    V    85_A      V    85_A     2.468     0    0.189   0.276     3.252   64.762   59.456

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     3.157          3.102                  3.870           58.657   53.263

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     54    2.61    66.406    61.506     1.993

LGA_LOCAL      RMSD:   2.609  Number of atoms:   54  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.210  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.157  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.719699 * X  +   0.518094 * Y  +   0.462182 * Z  +  12.255891
  Y_new =  -0.627282 * X  +  -0.199907 * Y  +  -0.752698 * Z  +  50.871750
  Z_new =  -0.297575 * X  +  -0.831634 * Y  +   0.468864 * Z  + -22.617575 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.424698  0.302151 -1.057430   [DEG: -138.9250   17.3120  -60.5863 ]
ZXZ:  0.550674  1.082792 -2.797969   [DEG:   31.5513   62.0394 -160.3118 ]
 
# END of job
