
#######################################################
#                                                     #
#                        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   66 (  547),  selected   66 , name one
# Molecule2: number of CA atoms  114 (  953),  selected   66 , 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:    29      49_A - 77_A        4.98    15.01
  LONGEST_CONTINUOUS_SEGMENT:    29      50_A - 78_A        4.85    15.17
  LCS_AVERAGE:     22.73

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      23_A - 42_A        1.77    19.59
  LCS_AVERAGE:     10.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      23_A - 38_A        0.89    20.15
  LCS_AVERAGE:      7.93

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   66
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     D    23_A     D    23_A     16   20   26      6   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     Y    24_A     Y    24_A     16   20   26      8   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   34   35 
LCS_GDT     E    25_A     E    25_A     16   20   26      8   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   32   34   35 
LCS_GDT     T    26_A     T    26_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     L    27_A     L    27_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     L    28_A     L    28_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   35 
LCS_GDT     E    29_A     E    29_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     I    30_A     I    30_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   32 
LCS_GDT     L    31_A     L    31_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     R    32_A     R    32_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     E    33_A     E    33_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   32 
LCS_GDT     F    34_A     F    34_A     16   20   26      9   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   32 
LCS_GDT     G    35_A     G    35_A     16   20   26      8   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   32 
LCS_GDT     V    36_A     V    36_A     16   20   26      8   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     A    37_A     A    37_A     16   20   26      8   15   15   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     K    38_A     K    38_A     16   20   26      5    9   11   16   18   20   20   21   21   25   26   28   28   29   29   30   30   31   32   33 
LCS_GDT     L    39_A     L    39_A     10   20   26      6    9   10   16   18   20   20   21   21   25   26   28   28   29   29   30   30   32   34   35 
LCS_GDT     V    40_A     V    40_A     10   20   26      6    9   10   13   18   20   20   21   21   25   26   28   28   29   29   30   30   34   35   39 
LCS_GDT     L    41_A     L    41_A     10   20   26      6    9   10   13   17   20   20   21   23   25   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     N    42_A     N    42_A     10   20   26      6    9   10   13   17   20   20   21   23   25   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     G    43_A     G    43_A      6   10   26      4    6    7    9   12   13   17   21   23   25   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     R    44_A     R    44_A      6    7   26      4    6    7    9   12   13   17   21   23   25   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     E    45_A     E    45_A      6    7   26      4    6    7    9   12   13   15   18   22   25   26   28   28   30   32   35   37   38   41   42 
LCS_GDT     F    46_A     F    46_A      6    7   26      4    6    7    9   12   13   13   18   19   25   26   28   28   29   32   35   37   38   41   42 
LCS_GDT     A    47_A     A    47_A      6    7   26      3    6    7    9   12   13   13   18   19   23   24   26   26   27   29   35   37   38   41   42 
LCS_GDT     S    48_A     S    48_A      3   15   27      3    3    4   11   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     P    49_A     P    49_A     13   15   29      4   11   12   13   13   14   15   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     E    50_A     E    50_A     13   15   29     10   11   12   13   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     E    51_A     E    51_A     13   15   29     10   11   12   13   13   14   17   21   23   25   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     A    52_A     A    52_A     13   15   29     10   11   12   13   13   14   15   21   23   25   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     V    53_A     V    53_A     13   15   29     10   11   12   13   13   14   17   21   23   24   25   28   29   30   32   35   37   38   41   42 
LCS_GDT     Q    54_A     Q    54_A     13   15   29     10   11   12   13   14   18   20   21   23   24   26   28   29   30   32   35   37   38   41   42 
LCS_GDT     W    55_A     W    55_A     13   15   29     10   11   12   13   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     A    56_A     A    56_A     13   15   29     10   11   12   13   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     R    57_A     R    57_A     13   15   29     10   11   12   13   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     D    58_A     D    58_A     13   15   29     10   11   12   13   13   14   15   18   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     T    59_A     T    59_A     13   15   29     10   11   12   13   13   14   15   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     G    60_A     G    60_A     13   15   29      4   11   12   13   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     L    61_A     L    61_A     13   15   29      3    7   11   13   13   14   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     R    62_A     R    62_A      6   15   29      4    5    6    8   13   14   16   20   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     F    63_A     F    63_A      6    8   29      4    5    6    6    7   10   13   15   18   20   22   27   29   30   32   35   37   38   41   42 
LCS_GDT     L    64_A     L    64_A      6    8   29      4    5    6    6    7   10   13   14   17   20   22   24   27   30   32   35   37   38   41   42 
LCS_GDT     R    65_A     R    65_A      6    8   29      4    5    6    6    7    9   11   14   15   19   21   22   25   28   28   30   34   38   38   42 
LCS_GDT     L    66_A     L    66_A      5    8   29      4    5    5    6    7   10   13   15   18   20   21   24   27   28   30   34   37   38   39   42 
LCS_GDT     I    67_A     I    67_A      5    7   29      4    5    5    6    6    9   13   14   17   20   22   24   27   29   32   34   37   38   41   42 
LCS_GDT     R    68_A     R    68_A      5    7   29      4    5    5    6    7    9   13   15   18   20   22   24   27   30   32   35   37   38   41   42 
LCS_GDT     E    69_A     E    69_A      3    7   29      3    3    4    6    7    8   12   16   18   20   23   26   29   30   32   35   37   38   41   42 
LCS_GDT     R    70_A     R    70_A      3    7   29      0    3    4    5    6    9   13   16   18   20   24   27   29   30   32   35   37   38   41   42 
LCS_GDT     Y    71_A     Y    71_A      3    4   29      0    3    3    4    6    8   13   16   18   23   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     E    72_A     E    72_A      3    5   29      3    3    4    4    4   12   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     D    73_A     D    73_A      3    5   29      3    3    4    5   10   12   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     G    74_A     G    74_A      3    5   29      3    3    4    5   10   12   17   21   23   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     V    75_A     V    75_A      3    5   29      3    3    4    4    6    8   13   21   23   24   25   26   28   30   32   35   37   38   41   42 
LCS_GDT     Y    76_A     Y    76_A      3    5   29      1    3    3    6    8   11   13   17   22   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     T    77_A     T    77_A      3    3   29      3    3    5    6    8   11   13   17   18   23   24   27   29   30   32   35   37   38   41   42 
LCS_GDT     V    78_A     V    78_A      3    3   29      3    3    5    6    8   11   13   17   20   24   25   27   29   30   32   35   37   38   41   42 
LCS_GDT     E    79_A     E    79_A      3    3   26      3    3    3    3    5    8    9   14   16   19   20   22   24   26   28   31   33   36   41   42 
LCS_GDT     D    80_A     D    80_A      3    3   23      3    3    3    4    7    8    8    9   10   13   20   21   23   25   28   31   33   34   38   42 
LCS_GDT     I    81_A     I    81_A      3    3   21      3    4    4    6    7    8   10   11   13   13   14   20   22   24   28   31   33   35   41   42 
LCS_GDT     V    82_A     V    82_A      3    3   21      3    4    4    6    7    8   10   14   16   19   20   22   24   26   29   32   37   38   41   42 
LCS_GDT     S    83_A     S    83_A      3    4   12      0    4    4    6    7    8    9   11   13   13   14   15   19   22   23   26   32   34   35   39 
LCS_GDT     R    84_A     R    84_A      3    4   12      0    3    3    3    4    5    7    8   13   13   14   16   19   22   23   26   32   34   35   41 
LCS_GDT     D    85_A     D    85_A      3    4   12      0    3    3    4    4    4    7    7    7   11   14   15   16   18   23   24   25   33   34   40 
LCS_GDT     D    86_A     D    86_A      3    4   12      3    3    3    4    4    5    7    8    8   11   14   15   19   22   24   28   33   34   36   40 
LCS_GDT     G    87_A     G    87_A      3    4   12      3    3    3    4    7    8    8    9   16   19   20   22   24   26   29   32   37   38   41   42 
LCS_GDT     R    88_A     R    88_A      3    4   12      3    3    3    4    7    8    8   14   16   19   20   22   24   26   28   31   33   38   41   42 
LCS_AVERAGE  LCS_A:  13.74  (   7.93   10.55   22.73 )

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     15     16     18     20     20     21     23     25     26     28     29     30     32     35     37     38     41     42 
GDT PERCENT_AT   8.77  13.16  13.16  14.04  15.79  17.54  17.54  18.42  20.18  21.93  22.81  24.56  25.44  26.32  28.07  30.70  32.46  33.33  35.96  36.84
GDT RMS_LOCAL    0.19   0.64   0.64   0.89   1.36   1.77   1.77   2.00   3.09   3.65   3.66   3.95   4.46   4.43   4.75   5.24   5.58   5.76   6.40   6.55
GDT RMS_ALL_AT  20.04  20.70  20.70  20.15  19.85  19.59  19.59  19.26  14.75  19.97  19.98  19.77  14.53  14.57  14.62  14.67  14.69  14.71  14.91  14.89

# Checking swapping
#   possible swapping detected:  Y    24_A      Y    24_A
#   possible swapping detected:  E    29_A      E    29_A
#   possible swapping detected:  E    33_A      E    33_A
#   possible swapping detected:  F    34_A      F    34_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  F    46_A      F    46_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  D    58_A      D    58_A
#   possible swapping detected:  E    69_A      E    69_A
#   possible swapping detected:  Y    76_A      Y    76_A
#   possible swapping detected:  E    79_A      E    79_A
#   possible swapping detected:  D    80_A      D    80_A
#   possible swapping detected:  D    85_A      D    85_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    23_A      D    23_A     2.560     0    0.267   0.604     3.906   60.952   57.560
LGA    Y    24_A      Y    24_A     1.893     0    0.097   0.579     4.363   70.833   58.492
LGA    E    25_A      E    25_A     1.576     0    0.142   1.280     4.940   75.000   64.127
LGA    T    26_A      T    26_A     1.190     0    0.037   0.087     1.538   83.690   81.497
LGA    L    27_A      L    27_A     1.358     0    0.019   1.392     4.206   77.143   64.821
LGA    L    28_A      L    28_A     2.234     0    0.022   1.396     6.603   70.833   52.083
LGA    E    29_A      E    29_A     1.737     0    0.103   0.784     2.311   77.143   74.868
LGA    I    30_A      I    30_A     0.221     0    0.021   0.053     1.170   97.619   94.107
LGA    L    31_A      L    31_A     1.187     0    0.022   0.069     3.762   88.214   71.012
LGA    R    32_A      R    32_A     1.363     0    0.032   0.944     4.758   81.429   64.545
LGA    E    33_A      E    33_A     1.339     0    0.042   0.588     4.493   81.429   61.481
LGA    F    34_A      F    34_A     0.945     0    0.013   0.035     2.254   88.214   78.615
LGA    G    35_A      G    35_A     0.998     0    0.119   0.119     1.224   85.952   85.952
LGA    V    36_A      V    36_A     1.062     0    0.052   0.153     1.238   81.429   82.721
LGA    A    37_A      A    37_A     0.758     0    0.070   0.078     0.905   90.476   90.476
LGA    K    38_A      K    38_A     1.512     0    0.068   0.627     1.881   79.405   76.720
LGA    L    39_A      L    39_A     1.883     0    0.091   1.458     5.159   72.857   56.726
LGA    V    40_A      V    40_A     2.531     0    0.062   0.057     3.513   55.595   55.238
LGA    L    41_A      L    41_A     3.166     0    0.161   1.072     6.081   50.119   42.738
LGA    N    42_A      N    42_A     3.366     0    0.351   0.881     5.287   38.095   40.000
LGA    G    43_A      G    43_A     9.837     0    0.034   0.034    12.877    2.619    2.619
LGA    R    44_A      R    44_A     9.855     0    0.086   1.170    10.922    2.619    1.212
LGA    E    45_A      E    45_A    11.220     0    0.109   1.069    17.388    0.476    0.212
LGA    F    46_A      F    46_A     8.984     0    0.598   0.769    12.474    0.833   19.870
LGA    A    47_A      A    47_A    15.158     0    0.044   0.072    18.804    0.000    0.000
LGA    S    48_A      S    48_A    18.167     0    0.652   0.948    19.652    0.000    0.000
LGA    P    49_A      P    49_A    14.750     0    0.535   0.832    16.752    0.000    0.000
LGA    E    50_A      E    50_A    10.837     0    0.028   1.152    16.923    4.048    1.799
LGA    E    51_A      E    51_A     8.464     0    0.060   0.896    15.348    8.333    3.704
LGA    A    52_A      A    52_A     6.723     0    0.058   0.060     8.116   23.810   20.000
LGA    V    53_A      V    53_A     5.577     0    0.072   0.109     9.729   25.119   15.170
LGA    Q    54_A      Q    54_A     4.183     0    0.053   0.121     7.355   27.619   27.513
LGA    W    55_A      W    55_A     7.543     0    0.041   1.187    13.801    8.333    2.823
LGA    A    56_A      A    56_A     8.240     0    0.010   0.011    12.474    4.524    5.619
LGA    R    57_A      R    57_A    11.946     0    0.022   1.618    15.673    0.119    0.043
LGA    D    58_A      D    58_A    13.848     0    0.041   1.100    18.198    0.000    0.060
LGA    T    59_A      T    59_A    17.342     0    0.051   1.073    20.978    0.000    0.000
LGA    G    60_A      G    60_A    20.155     0    0.144   0.144    22.149    0.000    0.000
LGA    L    61_A      L    61_A    17.512     0    0.033   1.380    18.501    0.000    0.000
LGA    R    62_A      R    62_A    21.454     0    0.081   1.052    31.513    0.000    0.000
LGA    F    63_A      F    63_A    20.200     0    0.135   0.855    23.694    0.000    0.000
LGA    L    64_A      L    64_A    23.391     0    0.589   1.156    25.508    0.000    0.000
LGA    R    65_A      R    65_A    22.864     0    0.183   1.222    26.844    0.000    0.000
LGA    L    66_A      L    66_A    22.922     0    0.035   0.957    25.555    0.000    0.000
LGA    I    67_A      I    67_A    26.046     0    0.621   0.637    27.880    0.000    0.000
LGA    R    68_A      R    68_A    26.429     0    0.029   1.145    27.510    0.000    0.000
LGA    E    69_A      E    69_A    29.979     0    0.628   1.159    33.407    0.000    0.000
LGA    R    70_A      R    70_A    31.877     0    0.668   1.031    32.691    0.000    0.000
LGA    Y    71_A      Y    71_A    33.787     0    0.648   1.222    36.297    0.000    0.000
LGA    E    72_A      E    72_A    35.012     0    0.562   1.109    36.889    0.000    0.000
LGA    D    73_A      D    73_A    39.600     0    0.600   0.804    42.345    0.000    0.000
LGA    G    74_A      G    74_A    37.411     0    0.215   0.215    38.034    0.000    0.000
LGA    V    75_A      V    75_A    34.286     0    0.543   0.579    35.340    0.000    0.000
LGA    Y    76_A      Y    76_A    34.300     0    0.596   1.371    38.066    0.000    0.000
LGA    T    77_A      T    77_A    28.959     0    0.617   0.546    31.335    0.000    0.000
LGA    V    78_A      V    78_A    28.172     0    0.596   0.601    29.640    0.000    0.000
LGA    E    79_A      E    79_A    29.838     0    0.617   1.097    35.953    0.000    0.000
LGA    D    80_A      D    80_A    27.375     0    0.567   1.195    27.933    0.000    0.000
LGA    I    81_A      I    81_A    23.685     0    0.580   0.799    25.134    0.000    0.000
LGA    V    82_A      V    82_A    24.284     0    0.678   0.606    25.281    0.000    0.000
LGA    S    83_A      S    83_A    24.259     0    0.684   0.882    26.684    0.000    0.000
LGA    R    84_A      R    84_A    18.955     0    0.660   1.634    21.115    0.000    0.000
LGA    D    85_A      D    85_A    21.706     0    0.561   0.776    25.317    0.000    0.000
LGA    D    86_A      D    86_A    25.140     0    0.586   1.108    26.517    0.000    0.000
LGA    G    87_A      G    87_A    29.519     0    0.282   0.282    30.998    0.000    0.000
LGA    R    88_A      R    88_A    26.142     0    0.145   0.934    28.781    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       66     264    264  100.00     547    547  100.00               114
SUMMARY(RMSD_GDC):    12.659         12.630                 13.381           14.166   12.758

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   66  114    4.0     21    2.00    19.079    16.931     1.002

LGA_LOCAL      RMSD:   1.996  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  19.255  Number of assigned atoms:   66 
Std_ASGN_ATOMS RMSD:  12.659  Standard rmsd on all 66 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.930003 * X  +   0.137819 * Y  +   0.340736 * Z  +  -5.840736
  Y_new =   0.150758 * X  +   0.988502 * Y  +   0.011653 * Z  +  -2.615160
  Z_new =  -0.335212 * X  +   0.062206 * Y  +  -0.940087 * Z  +  15.332937 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.980886  0.341831  3.075518   [DEG:  170.7922   19.5854  176.2142 ]
ZXZ:  1.604983  2.793681 -1.387311   [DEG:   91.9587  160.0661  -79.4871 ]
 
# END of job
