
#######################################################
#                                                     #
#                        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   67 (  448),  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:    44      22_A - 65_A        4.44    21.00
  LCS_AVERAGE:     59.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23      26_A - 48_A        1.91    21.25
  LCS_AVERAGE:     30.83

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.79    26.35
  LCS_AVERAGE:     18.97

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   44      3    3    3    3   13   17   22   26   31   39   39   41   42   42   42   43   43   43   43   43 
LCS_GDT     D    23_A     D    23_A      3    4   44      3    3    3    4   11   24   30   34   37   39   39   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    24_A     G    24_A      3   20   44      3    4   11   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     D    25_A     D    25_A     16   21   44      3    3    4   12   17   19   28   33   35   38   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    26_A     G    26_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     Q    27_A     Q    27_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    28_A     G    28_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     L    29_A     L    29_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     Y    30_A     Y    30_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    31_A     A    31_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    32_A     A    32_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     N    33_A     N    33_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     C    34_A     C    34_A     16   23   44      8   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    35_A     A    35_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    36_A     A    36_A     16   23   44      8   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     C    37_A     C    37_A     16   23   44      8   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     H    38_A     H    38_A     16   23   44     10   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    39_A     G    39_A     16   23   44      8   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    40_A     A    40_A     16   23   44      9   15   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     L    41_A     L    41_A     16   23   44      4    5   10   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    42_A     A    42_A      3   23   44      3    3    4    5    6   20   29   33   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     T    43_A     T    43_A      3   23   44      3    4   12   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     S    44_A     S    44_A      3   23   44      3    3    5    6    6   17   27   33   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     E    45_A     E    45_A      3   23   44      6   14   17   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     K    46_A     K    46_A      3   23   44      3    3    4    9   18   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     K    47_A     K    47_A      3   23   44      3    3   10   20   22   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    48_A     G    48_A      3   23   44      3    3   17   20   21   22   29   33   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     T    49_A     T    49_A     12   15   44     10   11   12   12   13   20   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     T    50_A     T    50_A     12   15   44     10   11   12   12   17   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     L    51_A     L    51_A     12   15   44     10   11   12   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    52_A     A    52_A     12   15   44     10   11   15   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     R    53_A     R    53_A     12   15   44     10   11   12   17   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     L    54_A     L    54_A     12   15   44     10   11   12   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     Q    55_A     Q    55_A     12   15   44     10   11   15   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     S    56_A     S    56_A     12   15   44     10   11   15   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    57_A     A    57_A     12   15   44     10   11   15   20   26   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     V    58_A     V    58_A     12   15   44     10   11   12   14   21   25   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     S    59_A     S    59_A     12   15   44      7   11   12   12   13   25   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    60_A     A    60_A     12   15   44      4    9   12   12   13   16   30   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     N    61_A     N    61_A      4   15   44      3    4    4   11   14   18   30   33   36   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     A    62_A     A    62_A      4   15   44      3    4    5   14   25   28   31   34   37   39   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    63_A     G    63_A      4   15   44      3    4    5    9   17   21   22   33   36   38   40   41   42   42   42   43   43   43   43   43 
LCS_GDT     G    64_A     G    64_A      3   20   44      3    3   10   15   19   21   22   22   22   24   30   36   39   41   41   43   43   43   43   43 
LCS_GDT     M    65_A     M    65_A      3   21   44      3    3    8   15   19   21   22   22   22   23   23   23   24   24   25   30   34   38   39   41 
LCS_GDT     G    66_A     G    66_A      3   21   26      3    4    4   13   17   21   22   22   22   23   23   23   24   24   25   25   30   32   37   39 
LCS_GDT     F    67_A     F    67_A      5   21   26      3    4    5    6    7   13   16   20   21   23   23   23   24   24   25   25   26   26   28   31 
LCS_GDT     L    68_A     L    68_A     16   21   26      4    4   11   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     S    69_A     S    69_A     17   21   26      4    4   15   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     S    70_A     S    70_A     17   21   26      4   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     L    71_A     L    71_A     17   21   26      6   11   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     T    72_A     T    72_A     17   21   26      7   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     S    73_A     S    73_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     A    74_A     A    74_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     Q    75_A     Q    75_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     L    76_A     L    76_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     Q    77_A     Q    77_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     A    78_A     A    78_A     17   21   26      7   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     I    79_A     I    79_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     V    80_A     V    80_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     D    81_A     D    81_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     V    82_A     V    82_A     17   21   26      9   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     L    83_A     L    83_A     17   21   26      7   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     A    84_A     A    84_A     17   21   26      7   14   16   18   18   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_GDT     V    85_A     V    85_A     17   21   26      7   14   16   18   19   21   22   22   22   23   23   23   24   24   25   25   26   26   26   27 
LCS_AVERAGE  LCS_A:  36.59  (  18.97   30.83   59.96 )

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     10     15     17     20     26     28     31     34     37     39     40     41     42     42     42     43     43     43     43     43 
GDT PERCENT_AT  15.62  23.44  26.56  31.25  40.62  43.75  48.44  53.12  57.81  60.94  62.50  64.06  65.62  65.62  65.62  67.19  67.19  67.19  67.19  67.19
GDT RMS_LOCAL    0.27   0.53   0.72   1.23   1.73   1.97   2.16   2.36   2.72   2.86   3.03   3.14   3.28   3.28   3.28   3.72   3.72   3.72   3.72   3.72
GDT RMS_ALL_AT  21.38  21.38  21.53  21.60  21.89  21.83  21.70  21.71  21.70  21.54  21.49  21.45  21.38  21.38  21.38  21.23  21.23  21.23  21.23  21.23

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_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     7.381     0    0.606   0.557     8.228   10.357   11.714
LGA    D    23_A      D    23_A     5.856     0    0.126   0.181     8.870   29.762   17.857
LGA    G    24_A      G    24_A     1.676     0    0.497   0.497     4.184   56.190   56.190
LGA    D    25_A      D    25_A     5.905     0    0.316   1.133    10.068   24.048   12.857
LGA    G    26_A      G    26_A     3.204     0    0.117   0.117     3.806   53.810   53.810
LGA    Q    27_A      Q    27_A     2.290     0    0.012   0.833     4.951   69.048   58.783
LGA    G    28_A      G    28_A     1.613     0    0.000   0.000     1.963   75.000   75.000
LGA    L    29_A      L    29_A     2.035     0    0.014   0.165     3.543   70.833   62.262
LGA    Y    30_A      Y    30_A     1.309     0    0.053   0.173     1.668   81.548   87.540
LGA    A    31_A      A    31_A     0.882     0    0.021   0.023     1.375   85.952   86.857
LGA    A    32_A      A    32_A     1.116     0    0.047   0.054     1.957   77.143   79.810
LGA    N    33_A      N    33_A     2.331     0    0.194   0.274     3.321   63.095   59.226
LGA    C    34_A      C    34_A     0.897     0    0.031   0.087     1.380   88.214   87.460
LGA    A    35_A      A    35_A     1.036     0    0.073   0.083     1.826   81.548   81.524
LGA    A    36_A      A    36_A     1.059     0    0.054   0.063     1.547   81.548   83.333
LGA    C    37_A      C    37_A     1.476     0    0.057   0.157     1.974   77.143   78.571
LGA    H    38_A      H    38_A     1.275     0    0.034   0.149     1.591   79.286   80.571
LGA    G    39_A      G    39_A     1.673     0    0.015   0.015     1.673   81.548   81.548
LGA    A    40_A      A    40_A     1.581     0    0.051   0.051     2.811   72.976   69.810
LGA    L    41_A      L    41_A     1.397     0    0.260   1.386     7.090   83.690   57.798
LGA    A    42_A      A    42_A     5.382     0    0.287   0.268     7.245   33.452   28.762
LGA    T    43_A      T    43_A     2.557     0    0.430   0.912     3.541   55.357   61.156
LGA    S    44_A      S    44_A     5.290     0    0.608   0.726     8.670   30.476   21.984
LGA    E    45_A      E    45_A     1.548     0    0.672   0.958     7.844   77.143   52.116
LGA    K    46_A      K    46_A     3.677     0    0.465   1.074     6.731   43.452   29.365
LGA    K    47_A      K    47_A     3.774     0    0.014   0.067     4.265   41.786   41.958
LGA    G    48_A      G    48_A     5.131     0    0.648   0.648     5.131   49.048   49.048
LGA    T    49_A      T    49_A     4.107     0    0.577   1.393     7.787   38.690   27.483
LGA    T    50_A      T    50_A     3.279     0    0.094   1.053     4.778   51.905   46.599
LGA    L    51_A      L    51_A     1.960     0    0.050   1.195     4.296   70.833   61.548
LGA    A    52_A      A    52_A     2.025     0    0.030   0.032     2.537   66.786   64.857
LGA    R    53_A      R    53_A     2.304     0    0.043   0.583     6.902   68.810   43.074
LGA    L    54_A      L    54_A     2.163     0    0.000   1.415     6.967   68.810   49.762
LGA    Q    55_A      Q    55_A     1.991     0    0.015   0.899     3.625   70.833   67.831
LGA    S    56_A      S    56_A     1.718     0    0.043   0.605     2.059   70.833   72.937
LGA    A    57_A      A    57_A     1.630     0    0.063   0.077     2.810   69.048   69.810
LGA    V    58_A      V    58_A     3.428     0    0.161   0.150     4.818   45.476   42.857
LGA    S    59_A      S    59_A     3.511     0    0.000   0.729     4.938   43.452   42.540
LGA    A    60_A      A    60_A     3.650     0    0.626   0.574     4.654   42.024   43.619
LGA    N    61_A      N    61_A     4.918     0    0.396   0.573    10.793   40.357   21.667
LGA    A    62_A      A    62_A     3.395     0    0.056   0.063     6.947   34.881   34.190
LGA    G    63_A      G    63_A     7.269     0    0.634   0.634     9.128    9.762    9.762
LGA    G    64_A      G    64_A    12.888     0    0.527   0.527    17.313    0.000    0.000
LGA    M    65_A      M    65_A    18.310     0    0.571   0.987    22.397    0.000    0.000
LGA    G    66_A      G    66_A    22.724     0    0.634   0.634    27.019    0.000    0.000
LGA    F    67_A      F    67_A    27.439     0    0.605   1.214    31.137    0.000    0.000
LGA    L    68_A      L    68_A    32.371     0    0.275   0.257    35.951    0.000    0.000
LGA    S    69_A      S    69_A    36.001     0    0.148   0.163    40.590    0.000    0.000
LGA    S    70_A      S    70_A    41.713     0    0.098   0.622    45.498    0.000    0.000
LGA    L    71_A      L    71_A    42.709     0    0.644   0.610    44.562    0.000    0.000
LGA    T    72_A      T    72_A    46.577     0    0.063   1.164    51.140    0.000    0.000
LGA    S    73_A      S    73_A    46.325     0    0.047   0.620    49.225    0.000    0.000
LGA    A    74_A      A    74_A    50.313     0    0.065   0.070    53.154    0.000    0.000
LGA    Q    75_A      Q    75_A    46.088     0    0.016   0.388    50.850    0.000    0.000
LGA    L    76_A      L    76_A    39.456     0    0.041   0.129    42.043    0.000    0.000
LGA    Q    77_A      Q    77_A    42.050     0    0.096   0.122    45.348    0.000    0.000
LGA    A    78_A      A    78_A    43.691     0    0.024   0.027    45.893    0.000    0.000
LGA    I    79_A      I    79_A    37.003     0    0.023   0.052    39.556    0.000    0.000
LGA    V    80_A      V    80_A    33.443     0    0.033   0.029    34.932    0.000    0.000
LGA    D    81_A      D    81_A    37.528     0    0.084   1.114    42.724    0.000    0.000
LGA    V    82_A      V    82_A    35.885     0    0.105   0.910    38.997    0.000    0.000
LGA    L    83_A      L    83_A    28.374     0    0.129   0.155    31.260    0.000    0.000
LGA    A    84_A      A    84_A    28.767     0    0.100   0.109    30.912    0.000    0.000
LGA    V    85_A      V    85_A    31.607     0    0.291   1.329    35.735    0.000    0.000

# 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):    16.988         16.835                 17.576           38.531   35.398

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   64    4.0     34    2.36    43.750    42.954     1.383

LGA_LOCAL      RMSD:   2.358  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  21.712  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:  16.988  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.248097 * X  +  -0.034621 * Y  +  -0.968116 * Z  + 104.872581
  Y_new =   0.735800 * X  +  -0.643302 * Y  +   0.211567 * Z  + -63.179611
  Z_new =  -0.630116 * X  +  -0.764829 * Y  +  -0.134127 * Z  + 152.526932 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.245588  0.681703 -1.744400   [DEG:   71.3669   39.0587  -99.9467 ]
ZXZ: -1.785949  1.705329 -2.452468   [DEG: -102.3273   97.7082 -140.5161 ]
 
# END of job
