
#######################################################
#                                                     #
#                        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        3.06     3.06
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.96     3.28
  LCS_AVERAGE:     35.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      25_A - 41_A        0.75     3.85
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.95     3.87
  LCS_AVERAGE:     22.27

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    3   64      0    3    5    7    7   10   13   14   17   21   45   53   62   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      0    3    5    7   20   22   30   42   57   61   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   20   64      3    3    9   22   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     17   20   64      3    7   18   32   37   45   48   55   59   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     17   20   64     10   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     17   20   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     17   20   64      5   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     17   20   64      4   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     17   20   64      4   23   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      4   20   64      3    3    5   26   31   39   48   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      3   20   64      3    3    3   12   24   34   44   51   58   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      7   24   64      3    5   16   17   20   33   51   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      7   24   64      3   10   26   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     16   24   64      4    7   16   23   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     16   24   64      4    8   16   18   27   46   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     16   24   64      6   13   16   18   20   28   50   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     16   24   64     11   13   16   18   20   46   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     16   24   64     11   13   16   18   38   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     16   24   64     11   13   16   18   26   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     16   24   64     11   13   18   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     16   24   64     11   13   22   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     16   24   64     11   13   16   32   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     16   24   64     11   13   16   22   41   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     16   24   64     11   13   18   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     16   24   64     11   13   31   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     16   24   64     11   13   16   18   24   46   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     16   24   64     11   13   16   18   23   38   52   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     16   24   64      7   13   16   18   24   46   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     16   25   64      7   13   19   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     16   25   64      7   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A      6   25   64      3    5   26   35   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      6   25   64     12   31   34   37   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      6   25   64     14   27   34   37   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      6   25   64      3    5   15   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      4   25   64      3    4    5    9   20   29   51   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A      4   25   64      3    4   11   13   25   45   52   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     17   25   64      4   16   25   35   42   45   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     17   25   64      3    6   16   33   42   47   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     17   25   64      8   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     17   25   64      9   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     17   25   64      9   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     17   25   64      9   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     17   25   64      9   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     17   25   64      8   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     17   25   64      9   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     17   25   64      9   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     17   25   64     11   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     17   25   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     17   25   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     17   25   64     14   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     17   25   64     12   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     17   25   64      4   31   34   38   43   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     17   25   64      4   23   34   37   42   48   53   57   60   62   62   63   63   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  52.47  (  22.27   35.16  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     14     31     34     38     43     48     53     57     60     62     62     63     63     64     64     64     64     64     64     64 
GDT PERCENT_AT  21.88  48.44  53.12  59.38  67.19  75.00  82.81  89.06  93.75  96.88  96.88  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.70   0.77   1.29   1.56   1.82   2.08   2.34   2.53   2.65   2.65   2.80   2.80   3.06   3.06   3.06   3.06   3.06   3.06   3.06
GDT RMS_ALL_AT   3.76   3.47   3.48   3.34   3.25   3.23   3.17   3.11   3.09   3.10   3.10   3.07   3.07   3.06   3.06   3.06   3.06   3.06   3.06   3.06

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A    10.747     0    0.098   0.095    12.970    1.071    0.857
LGA    D    23_A      D    23_A     7.867     0    0.698   1.337    12.047   15.714    8.214
LGA    G    24_A      G    24_A     3.098     0    0.406   0.406     5.306   46.548   46.548
LGA    D    25_A      D    25_A     3.825     0    0.284   1.092     8.292   45.238   27.500
LGA    G    26_A      G    26_A     1.466     0    0.093   0.093     1.700   79.286   79.286
LGA    Q    27_A      Q    27_A     1.397     0    0.035   1.106     3.382   81.429   70.688
LGA    G    28_A      G    28_A     1.568     0    0.053   0.053     1.568   77.143   77.143
LGA    L    29_A      L    29_A     1.160     0    0.024   0.872     2.218   81.429   77.202
LGA    Y    30_A      Y    30_A     0.935     0    0.042   0.161     1.164   90.476   88.214
LGA    A    31_A      A    31_A     1.162     0    0.046   0.050     1.445   83.690   83.238
LGA    A    32_A      A    32_A     0.936     0    0.106   0.105     1.144   88.214   86.857
LGA    N    33_A      N    33_A     0.911     0    0.212   1.064     3.111   81.786   77.679
LGA    C    34_A      C    34_A     0.659     0    0.023   0.130     0.983   92.857   92.063
LGA    A    35_A      A    35_A     1.399     0    0.036   0.043     1.661   81.429   79.714
LGA    A    36_A      A    36_A     1.115     0    0.097   0.090     1.449   81.429   81.429
LGA    C    37_A      C    37_A     1.474     0    0.132   0.658     2.568   73.214   74.524
LGA    H    38_A      H    38_A     1.582     0    0.233   1.007     3.321   72.976   69.905
LGA    G    39_A      G    39_A     1.986     0    0.084   0.084     1.986   79.405   79.405
LGA    A    40_A      A    40_A     1.485     0    0.067   0.092     2.320   81.548   78.190
LGA    L    41_A      L    41_A     0.601     0    0.569   1.431     2.844   83.810   77.500
LGA    A    42_A      A    42_A     4.310     0    0.628   0.568     6.529   33.333   29.333
LGA    T    43_A      T    43_A     6.203     0    0.340   0.297     8.821   20.000   12.925
LGA    S    44_A      S    44_A     5.508     0    0.585   0.528     7.831   34.881   27.302
LGA    E    45_A      E    45_A     2.071     0    0.632   1.206     7.286   55.714   42.063
LGA    K    46_A      K    46_A     2.936     0    0.028   0.511     3.772   51.905   55.820
LGA    K    47_A      K    47_A     4.115     0    0.058   0.913     7.882   40.238   28.201
LGA    G    48_A      G    48_A     5.076     0    0.198   0.198     5.076   31.548   31.548
LGA    T    49_A      T    49_A     4.256     0    0.087   0.168     4.563   38.810   38.095
LGA    T    50_A      T    50_A     3.579     0    0.034   1.069     3.996   45.000   49.320
LGA    L    51_A      L    51_A     3.913     0    0.044   0.260     6.275   45.000   36.488
LGA    A    52_A      A    52_A     2.508     0    0.026   0.044     2.758   60.952   61.714
LGA    R    53_A      R    53_A     1.929     0    0.042   1.409     4.991   70.833   56.537
LGA    L    54_A      L    54_A     2.899     0    0.044   1.382     6.997   55.357   39.940
LGA    Q    55_A      Q    55_A     3.335     0    0.048   0.708     3.431   50.000   63.016
LGA    S    56_A      S    56_A     2.267     0    0.071   0.062     2.694   62.857   66.190
LGA    A    57_A      A    57_A     1.680     0    0.036   0.049     2.433   68.810   71.333
LGA    V    58_A      V    58_A     3.809     0    0.043   0.056     5.163   43.690   39.320
LGA    S    59_A      S    59_A     4.557     0    0.086   0.566     5.191   34.286   32.460
LGA    A    60_A      A    60_A     3.861     0    0.320   0.323     4.591   42.024   42.286
LGA    N    61_A      N    61_A     2.066     0    0.598   0.678     3.944   57.500   64.226
LGA    A    62_A      A    62_A     0.794     0    0.067   0.066     1.641   81.548   81.524
LGA    G    63_A      G    63_A     2.264     0    0.663   0.663     3.969   61.429   61.429
LGA    G    64_A      G    64_A     1.852     0    0.271   0.271     2.722   66.905   66.905
LGA    M    65_A      M    65_A     2.080     0    0.656   0.859     4.446   66.905   61.488
LGA    G    66_A      G    66_A     2.369     0    0.624   0.624     3.312   59.167   59.167
LGA    F    67_A      F    67_A     4.978     0    0.086   1.105     7.353   40.357   23.983
LGA    L    68_A      L    68_A     3.671     0    0.277   1.215     9.380   52.024   31.369
LGA    S    69_A      S    69_A     3.139     0    0.222   0.208     4.235   54.048   48.413
LGA    S    70_A      S    70_A     3.008     0    0.086   0.083     3.573   59.167   56.190
LGA    L    71_A      L    71_A     1.051     0    0.032   0.062     1.702   79.286   87.262
LGA    T    72_A      T    72_A     1.538     0    0.063   0.073     1.556   77.143   77.755
LGA    S    73_A      S    73_A     1.846     0    0.042   0.623     3.433   72.857   67.698
LGA    A    74_A      A    74_A     1.314     0    0.052   0.051     1.469   81.429   81.429
LGA    Q    75_A      Q    75_A     0.855     0    0.055   0.470     1.543   90.476   88.519
LGA    L    76_A      L    76_A     1.332     0    0.033   1.435     3.630   81.429   74.524
LGA    Q    77_A      Q    77_A     1.347     0    0.046   0.703     3.784   81.429   64.497
LGA    A    78_A      A    78_A     1.153     0    0.029   0.035     1.214   81.429   81.429
LGA    I    79_A      I    79_A     1.258     0    0.031   0.108     1.368   81.429   81.429
LGA    V    80_A      V    80_A     1.508     0    0.048   0.121     1.851   77.143   76.531
LGA    D    81_A      D    81_A     1.370     0    0.021   1.112     3.298   79.286   73.274
LGA    V    82_A      V    82_A     1.689     0    0.055   1.255     4.277   72.857   64.490
LGA    L    83_A      L    83_A     1.658     0    0.136   0.300     2.745   70.833   72.024
LGA    A    84_A      A    84_A     1.459     0    0.070   0.068     2.184   75.119   76.381
LGA    V    85_A      V    85_A     2.306     0    0.599   1.137     3.556   59.524   57.619

# 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):     3.059          2.989                  3.512           63.510   60.306

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     57    2.34    74.219    67.458     2.335

LGA_LOCAL      RMSD:   2.341  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.109  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.059  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.324792 * X  +   0.826761 * Y  +   0.459322 * Z  +  24.699121
  Y_new =   0.354468 * X  +   0.343844 * Y  +  -0.869554 * Z  +  -7.603494
  Z_new =  -0.876848 * X  +   0.445239 * Y  +  -0.181383 * Z  + -42.414097 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.829060  1.069266  1.957651   [DEG:   47.5016   61.2644  112.1651 ]
ZXZ:  0.485974  1.753189 -1.100950   [DEG:   27.8443  100.4503  -63.0798 ]
 
# END of job
