
#######################################################
#                                                     #
#                        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        3.04     3.04
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      46_A - 67_A        1.97     6.88
  LCS_AVERAGE:     32.06

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      48_A - 63_A        0.95     7.83
  LCS_AVERAGE:     18.36

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      4   21   64      3   12   24   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      5   21   64      3    5   10   14   31   43   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     12   21   64      3    7   19   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     15   21   64      3    5   15   32   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     15   21   64      7   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     15   21   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     15   21   64      5   11   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     15   21   64      5   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     15   21   64      3   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     15   21   64      4   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A      3   21   64      3    3    4   15   23   33   42   55   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A      3   21   64      3    3   15   28   39   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      3   21   64      3    3    8   21   27   33   42   49   56   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      3    4   64      3    5   10   11   16   24   37   47   55   61   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      4   21   64      4    4    6   16   18   22   37   54   58   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      4   21   64      4    8   13   26   39   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A      4   22   64      4    8   13   19   37   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A      4   22   64      4    8   14   16   19   29   48   55   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     16   22   64      3    7   11   15   17   19   29   49   55   59   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     16   22   64      4   14   15   17   19   40   49   55   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     16   22   64      9   14   15   17   24   44   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     16   22   64      9   14   15   17   19   41   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     16   22   64      9   14   22   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     16   22   64      9   14   17   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     16   22   64      9   14   15   23   37   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     16   22   64      9   14   15   23   33   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     16   22   64      9   14   18   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     16   22   64      8   14   22   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     16   22   64      8   14   15   17   29   42   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     16   22   64      9   14   15   17   19   37   47   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     16   22   64      9   14   15   17   34   41   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     16   22   64      9   14   15   29   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     16   22   64      3   23   28   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     16   22   64      8   13   22   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      3   22   64      3    3    5    6   27   40   46   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      3   22   64      3    3   10   17   27   41   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      3   22   64      0    3   10   17   27   41   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      3   22   64      0    3    3    4    6   25   48   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A      3   19   64      3   24   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A      3   19   64      1    3   19   31   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A      4   19   64      0    3    7   19   39   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A      4   19   64      3    3    4   12   31   41   46   52   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     14   19   64     11   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     14   19   64     14   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     14   19   64     11   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     14   19   64     11   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     14   19   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     14   19   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     14   19   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     14   19   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     14   19   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     14   19   64     15   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     14   19   64     11   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     14   19   64      9   25   29   33   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     14   19   64      9   25   29   32   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     14   19   64      3   25   29   32   40   45   49   56   59   62   63   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  50.14  (  18.36   32.06  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     15     25     29     33     40     45     49     56     59     62     63     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  23.44  39.06  45.31  51.56  62.50  70.31  76.56  87.50  92.19  96.88  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.56   0.74   1.21   1.49   1.81   2.02   2.46   2.64   2.86   2.94   3.04   3.04   3.04   3.04   3.04   3.04   3.04   3.04   3.04
GDT RMS_ALL_AT   3.63   3.69   3.58   3.30   3.29   3.18   3.18   3.16   3.08   3.04   3.04   3.04   3.04   3.04   3.04   3.04   3.04   3.04   3.04   3.04

# Checking swapping
#   possible swapping detected:  D    23_A      D    23_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  D    81_A      D    81_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     1.550     0    0.252   0.255     2.658   69.048   68.190
LGA    D    23_A      D    23_A     3.328     0    0.107   0.186     4.216   48.571   45.179
LGA    G    24_A      G    24_A     1.721     0    0.130   0.130     2.589   65.000   65.000
LGA    D    25_A      D    25_A     2.453     0    0.706   0.588     4.742   54.524   61.667
LGA    G    26_A      G    26_A     1.416     0    0.051   0.051     1.416   81.429   81.429
LGA    Q    27_A      Q    27_A     1.265     0    0.038   0.259     2.217   81.429   77.672
LGA    G    28_A      G    28_A     1.531     0    0.030   0.030     1.531   79.286   79.286
LGA    L    29_A      L    29_A     0.951     0    0.011   0.142     1.101   88.214   87.083
LGA    Y    30_A      Y    30_A     0.951     0    0.052   0.124     1.004   90.476   89.722
LGA    A    31_A      A    31_A     1.348     0    0.055   0.054     1.536   79.286   78.000
LGA    A    32_A      A    32_A     1.359     0    0.068   0.084     1.359   81.429   81.429
LGA    N    33_A      N    33_A     0.961     0    0.064   0.096     1.277   85.952   83.690
LGA    C    34_A      C    34_A     0.913     0    0.123   0.170     1.176   83.690   84.444
LGA    A    35_A      A    35_A     1.839     0    0.110   0.104     2.228   70.952   69.714
LGA    A    36_A      A    36_A     2.676     0    0.106   0.104     2.834   60.952   60.190
LGA    C    37_A      C    37_A     1.899     0    0.109   0.141     2.172   68.810   70.159
LGA    H    38_A      H    38_A     1.788     0    0.383   0.326     3.243   65.119   68.952
LGA    G    39_A      G    39_A     1.402     0    0.655   0.655     4.156   64.286   64.286
LGA    A    40_A      A    40_A     5.793     0    0.160   0.212     8.330   27.619   23.048
LGA    L    41_A      L    41_A     3.658     0    0.158   1.089     4.572   38.810   41.964
LGA    A    42_A      A    42_A     6.421     0    0.642   0.589     8.242   13.690   11.905
LGA    T    43_A      T    43_A     7.108     0    0.350   1.142    10.843   11.310    6.939
LGA    S    44_A      S    44_A     6.770     0    0.616   0.808     7.655   20.595   16.587
LGA    E    45_A      E    45_A     2.933     0    0.241   0.721     4.065   48.571   58.519
LGA    K    46_A      K    46_A     3.171     0    0.128   0.817     5.536   43.571   48.836
LGA    K    47_A      K    47_A     5.676     0    0.692   0.598     7.152   25.357   19.683
LGA    G    48_A      G    48_A     7.413     0    0.230   0.230     7.413   13.452   13.452
LGA    T    49_A      T    49_A     4.754     0    0.133   1.074     6.121   28.929   32.449
LGA    T    50_A      T    50_A     4.100     0    0.073   0.164     4.691   38.810   41.701
LGA    L    51_A      L    51_A     3.931     0    0.055   1.391     8.121   46.667   30.000
LGA    A    52_A      A    52_A     1.884     0    0.025   0.028     2.546   71.071   73.143
LGA    R    53_A      R    53_A     1.582     0    0.021   1.386     5.208   75.000   55.584
LGA    L    54_A      L    54_A     2.608     0    0.033   0.160     4.489   59.048   50.476
LGA    Q    55_A      Q    55_A     3.000     0    0.017   0.812     5.966   55.357   47.037
LGA    S    56_A      S    56_A     1.884     0    0.030   0.036     2.426   70.833   74.365
LGA    A    57_A      A    57_A     1.338     0    0.065   0.062     2.273   73.095   74.762
LGA    V    58_A      V    58_A     3.491     0    0.041   0.082     4.999   46.905   41.905
LGA    S    59_A      S    59_A     4.300     0    0.044   0.548     4.949   37.262   36.270
LGA    A    60_A      A    60_A     3.718     0    0.215   0.230     4.400   41.786   43.429
LGA    N    61_A      N    61_A     2.372     0    0.352   0.659     4.397   64.881   60.655
LGA    A    62_A      A    62_A     0.829     0    0.071   0.071     1.628   83.810   85.143
LGA    G    63_A      G    63_A     2.443     0    0.271   0.271     2.443   70.952   70.952
LGA    G    64_A      G    64_A     4.601     0    0.283   0.283     5.401   36.548   36.548
LGA    M    65_A      M    65_A     3.960     0    0.579   0.745     6.430   40.238   34.107
LGA    G    66_A      G    66_A     4.138     0    0.691   0.691     5.420   35.952   35.952
LGA    F    67_A      F    67_A     4.318     0    0.731   1.232     6.461   42.143   29.481
LGA    L    68_A      L    68_A     1.228     0    0.672   0.570     6.300   81.548   56.488
LGA    S    69_A      S    69_A     2.804     0    0.546   0.802     4.617   55.595   50.635
LGA    S    70_A      S    70_A     3.239     0    0.743   0.878     4.125   53.571   49.127
LGA    L    71_A      L    71_A     4.446     0    0.372   0.529     7.579   37.262   25.714
LGA    T    72_A      T    72_A     1.349     0    0.479   1.378     5.384   77.262   59.524
LGA    S    73_A      S    73_A     1.509     0    0.049   0.643     3.110   75.000   70.476
LGA    A    74_A      A    74_A     1.190     0    0.037   0.046     1.306   81.429   81.429
LGA    Q    75_A      Q    75_A     1.020     0    0.055   0.928     4.730   83.690   68.042
LGA    L    76_A      L    76_A     1.211     0    0.028   0.087     1.524   81.429   80.357
LGA    Q    77_A      Q    77_A     1.246     0    0.048   0.095     1.433   81.429   81.429
LGA    A    78_A      A    78_A     1.265     0    0.030   0.039     1.471   81.429   81.429
LGA    I    79_A      I    79_A     1.470     0    0.017   0.054     1.659   77.143   77.143
LGA    V    80_A      V    80_A     1.669     0    0.036   0.040     2.034   75.000   72.925
LGA    D    81_A      D    81_A     1.633     0    0.040   0.146     1.871   72.857   76.071
LGA    V    82_A      V    82_A     1.882     0    0.090   0.890     3.326   72.857   70.952
LGA    L    83_A      L    83_A     2.097     0    0.155   0.159     2.433   68.810   66.786
LGA    A    84_A      A    84_A     2.768     0    0.093   0.099     3.278   57.143   55.714
LGA    V    85_A      V    85_A     2.735     0    0.571   1.136     4.963   55.595   54.830

# 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):     3.036          3.049                  3.391           60.153   57.657

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     56    2.46    69.531    63.866     2.192

LGA_LOCAL      RMSD:   2.455  Number of atoms:   56  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.158  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.036  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.029731 * X  +   0.079972 * Y  +  -0.996354 * Z  + 106.881027
  Y_new =  -0.641896 * X  +  -0.762569 * Y  +  -0.080362 * Z  +  23.839451
  Z_new =  -0.766215 * X  +   0.641944 * Y  +   0.028662 * Z  +  37.868626 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.524511  0.872930  1.526178   [DEG:  -87.3481   50.0152   87.4435 ]
ZXZ: -1.490314  1.542131 -0.873421   [DEG:  -85.3887   88.3576  -50.0433 ]
 
# END of job
