
#######################################################
#                                                     #
#                        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   70 (  580),  selected   70 , name one
# Molecule2: number of CA atoms  114 (  953),  selected   70 , 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:    22      45_A - 66_A        4.97    18.90
  LCS_AVERAGE:     15.06

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      97_A - 104_A       1.74    21.03
  LCS_AVERAGE:      4.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      55_A - 60_A        0.15    19.84
  LCS_AVERAGE:      3.27

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   70
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     G    35_A     G    35_A      3    4   12      3    3    3    4    4    5    5    9   15   17   18   20   23   25   27   31   32   35   38   39 
LCS_GDT     V    36_A     V    36_A      4    7   12      3    3    4    7    7    7    7    9   15   17   18   20   23   25   28   31   32   35   38   39 
LCS_GDT     A    37_A     A    37_A      4    7   12      3    3    5    7    7    7    8    9   10   11   13   19   21   24   28   31   32   35   38   39 
LCS_GDT     K    38_A     K    38_A      5    7   12      4    5    5    7    7    7    8   10   10   11   12   14   20   24   26   28   30   32   36   38 
LCS_GDT     L    39_A     L    39_A      5    7   12      4    5    5    7    7    7    9   10   10   12   16   21   23   26   28   31   34   38   41   42 
LCS_GDT     V    40_A     V    40_A      5    7   14      4    5    5    7    7    7    9   11   12   13   14   16   20   24   27   30   34   38   41   42 
LCS_GDT     L    41_A     L    41_A      5    7   15      4    5    5    7    7    7    9   11   12   15   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     N    42_A     N    42_A      5    7   15      4    5    5    7    7    8    9   11   11   13   13   16   18   19   24   26   32   35   38   39 
LCS_GDT     G    43_A     G    43_A      3    7   19      3    3    4    5    6    8    9   11   11   13   15   18   22   25   27   31   32   35   38   39 
LCS_GDT     R    44_A     R    44_A      4    6   20      4    4    4    5    6    8   12   13   15   17   18   20   23   25   28   31   32   35   41   42 
LCS_GDT     E    45_A     E    45_A      4    6   22      4    4    4    5    7   10   12   13   15   17   18   20   23   25   28   31   32   35   41   42 
LCS_GDT     F    46_A     F    46_A      4    6   22      4    4    4    5    5   10   12   13   15   17   18   20   23   25   28   31   32   38   41   42 
LCS_GDT     A    47_A     A    47_A      4    6   22      4    4    4    6    7   10   12   13   15   17   18   20   23   25   27   30   32   37   41   42 
LCS_GDT     S    48_A     S    48_A      4    6   22      3    3    4    5    5    6    9   12   12   15   18   20   20   22   24   25   28   31   35   36 
LCS_GDT     P    49_A     P    49_A      4    4   22      3    3    4    5    5    6    7    8   11   12   15   20   20   22   23   24   28   29   35   36 
LCS_GDT     E    50_A     E    50_A      3    4   22      3    3    4    4    4    5    9   12   15   20   21   22   23   26   27   30   32   37   41   42 
LCS_GDT     E    51_A     E    51_A      3    4   22      3    4    4    6    7   10   12   13   16   20   21   22   23   26   28   34   34   38   41   42 
LCS_GDT     A    52_A     A    52_A      3    4   22      3    3    4    6    7   10   12   13   16   20   21   22   23   26   28   34   34   38   41   42 
LCS_GDT     V    53_A     V    53_A      3    4   22      3    4    4    6    7   10   12   13   15   20   21   22   23   26   28   34   34   38   41   42 
LCS_GDT     Q    54_A     Q    54_A      3    4   22      0    4    4    4    4    7    9   13   15   17   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     W    55_A     W    55_A      6    6   22      6    7    7    7    7    7    9   12   15   17   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     A    56_A     A    56_A      6    6   22      6    7    7    7    7    7    9   12   15   17   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     R    57_A     R    57_A      6    6   22      6    7    7    7    7    7   12   13   15   17   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     D    58_A     D    58_A      6    6   22      6    7    7    7    7   10   12   13   15   16   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     T    59_A     T    59_A      6    6   22      6    7    7    7    7   10   12   13   15   16   18   20   22   25   28   34   34   38   41   42 
LCS_GDT     G    60_A     G    60_A      6    6   22      6    7    7    7    7   10   12   13   15   17   18   20   23   25   28   34   34   38   41   42 
LCS_GDT     L    61_A     L    61_A      3    3   22      3    4    4    4    5    6    9   11   15   17   18   20   23   26   28   34   34   38   41   42 
LCS_GDT     R    62_A     R    62_A      3    3   22      0    4    4    5    7    8   10   13   16   20   21   22   23   26   28   34   34   38   41   42 
LCS_GDT     F    63_A     F    63_A      3    4   22      1    3    5    5    7    9   10   13   16   20   21   22   23   26   28   34   34   38   41   42 
LCS_GDT     L    64_A     L    64_A      3    4   22      1    3    5    5    7    7    9   13   16   20   21   22   23   26   28   34   34   38   41   42 
LCS_GDT     R    65_A     R    65_A      3    4   22      0    4    4    4    5    7    9   10   12   16   18   20   22   25   28   31   32   34   38   39 
LCS_GDT     L    66_A     L    66_A      3    4   22      3    4    4    4    5    5   10   11   15   17   18   20   23   25   28   31   32   35   38   39 
LCS_GDT     I    67_A     I    67_A      3    4   20      3    4    4    4    6    8    9   11   15   17   18   20   23   25   28   31   32   35   38   39 
LCS_GDT     R    68_A     R    68_A      3    4   18      3    3    3    4    6    8    9   11   11   15   18   20   22   25   28   31   32   35   38   39 
LCS_GDT     E    69_A     E    69_A      3    4   15      3    3    3    5    6    8    9   11   11   15   18   19   22   25   27   31   32   35   38   39 
LCS_GDT     R    70_A     R    70_A      3    3   15      3    3    3    5    5    6    9   10   11   13   18   20   22   25   27   31   32   35   38   39 
LCS_GDT     Y    71_A     Y    71_A      3    4   15      1    3    3    5    5    7    9   10   10   11   12   16   19   23   26   29   31   35   38   39 
LCS_GDT     E    72_A     E    72_A      3    4   15      3    3    3    4    5    7    9    9   10   11   11   15   16   17   20   22   24   25   33   38 
LCS_GDT     D    73_A     D    73_A      3    5   15      3    3    3    5    5    7    9    9   10   11   11   15   16   17   20   21   24   27   29   37 
LCS_GDT     G    74_A     G    74_A      3    5   15      3    3    3    5    5    7    9    9   10   11   11   15   16   18   23   26   29   32   35   38 
LCS_GDT     V    75_A     V    75_A      3    5   15      0    3    3    5    5    7    9    9   10   11   13   16   20   24   26   29   31   35   38   39 
LCS_GDT     Y    76_A     Y    76_A      3    5   15      1    3    3    5    5    7    9    9   10   11   13   17   21   24   28   30   32   35   38   39 
LCS_GDT     T    77_A     T    77_A      3    5   15      0    4    4    5    5    7    9    9   10   12   14   19   22   24   28   31   32   35   38   39 
LCS_GDT     V    78_A     V    78_A      3    4   15      1    3    3    5    5    6    9    9   10   12   18   20   23   25   28   31   32   35   38   39 
LCS_GDT     E    79_A     E    79_A      3    3   15      1    3    3    3    4    5    6    9   12   13   16   20   22   24   27   30   32   34   39   42 
LCS_GDT     D    80_A     D    80_A      3    3   15      3    4    4    4    4    5    8   10   15   16   18   20   23   24   27   30   32   38   41   42 
LCS_GDT     I    81_A     I    81_A      3    5   15      3    4    4    5    7   10   12   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     V    82_A     V    82_A      4    6   14      3    4    4    5    7    7   10   13   15   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     S    83_A     S    83_A      4    6   12      0    3    4    4    7    7   10   10   12   12   16   20   20   24   27   34   34   38   41   42 
LCS_GDT     R    84_A     R    84_A      4    6   12      2    3    4    4    7    7   10   10   12   12   13   17   20   22   25   27   28   31   38   38 
LCS_GDT     D    85_A     D    85_A      4    6   12      3    3    4    4    7    7   10   10   12   12   13   14   16   20   21   23   24   28   30   31 
LCS_GDT     D    86_A     D    86_A      3    6   12      3    3    3    4    7    7   10   10   12   12   13   14   16   19   21   23   24   27   30   31 
LCS_GDT     G    87_A     G    87_A      3    6   12      3    3    3    4    7    7   10   10   12   15   16   20   20   22   24   25   25   28   30   31 
LCS_GDT     R    88_A     R    88_A      3    6   12      3    3    3    4    5    7   10   12   12   15   17   20   20   22   23   28   31   34   38   40 
LCS_GDT     Y    89_A     Y    89_A      3    6   16      5    7    7    7    7    8   10   12   13   15   18   20   21   25   27   34   34   38   40   42 
LCS_GDT     Y    90_A     Y    90_A      3    5   16      3    4    4    5    6    7    9   11   13   15   18   21   23   26   27   34   34   38   41   42 
LCS_GDT     R    91_A     R    91_A      3    4   16      3    4    4    4    4    4    7   10   12   12   18   22   23   26   27   34   34   38   41   42 
LCS_GDT     H    92_A     H    92_A      3    4   16      3    3    3    3    4    7    7   10   14   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     T    93_A     T    93_A      3    4   16      3    3    4    4    7    9   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     S    94_A     S    94_A      3    4   16      3    3    5    5    7    9   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     T    95_A     T    95_A      3    4   16      1    3    5    5    7    9   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     L    96_A     L    96_A      3    4   16      1    3    5    5    7    9   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     R    97_A     R    97_A      4    8   16      3    4    6    6    7    8    9   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     R    98_A     R    98_A      5    8   16      3    4    6    6    7    9   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     Q    99_A     Q    99_A      5    8   16      4    4    6    6    7    8   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     P   100_A     P   100_A      5    8   16      4    4    6    6    7    8    9   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     D   101_A     D   101_A      5    8   16      4    4    5    6    7    8    9   11   13   17   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     G   102_A     G   102_A      5    8   16      4    4    5    6    7    8   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     S   103_A     S   103_A      3    8   16      3    4    6    6    7    9   10   13   16   20   21   22   23   26   27   34   34   38   41   42 
LCS_GDT     Y   104_A     Y   104_A      3    8   16      3    4    6    6    7    9   10   13   15   19   21   22   23   26   27   34   34   38   41   42 
LCS_AVERAGE  LCS_A:   7.68  (   3.27    4.71   15.06 )

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      6      7      7      7      7     10     12     13     16     20     21     22     23     26     28     34     34     38     41     42 
GDT PERCENT_AT   5.26   6.14   6.14   6.14   6.14   8.77  10.53  11.40  14.04  17.54  18.42  19.30  20.18  22.81  24.56  29.82  29.82  33.33  35.96  36.84
GDT RMS_LOCAL    0.15   0.43   0.43   0.43   0.43   2.27   2.57   2.72   3.49   3.88   3.99   4.09   4.25   4.79   5.53   5.97   6.06   6.46   6.94   7.00
GDT RMS_ALL_AT  19.84  19.68  19.68  19.68  19.68  18.06  17.77  17.38  14.53  14.75  14.69  14.67  14.77  14.81  15.64  15.56  15.18  15.24  15.02  15.13

# Checking swapping
#   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:  F    63_A      F    63_A
#   possible swapping detected:  E    72_A      E    72_A
#   possible swapping detected:  E    79_A      E    79_A
#   possible swapping detected:  D    85_A      D    85_A
#   possible swapping detected:  D    86_A      D    86_A
#   possible swapping detected:  Y    90_A      Y    90_A
#   possible swapping detected:  Y   104_A      Y   104_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G    35_A      G    35_A    13.555     0    0.066   0.066    14.358    0.000    0.000
LGA    V    36_A      V    36_A    11.368     0    0.121   0.139    13.466    0.000    1.633
LGA    A    37_A      A    37_A    17.673     0    0.671   0.610    20.303    0.000    0.000
LGA    K    38_A      K    38_A    16.950     0    0.662   1.236    19.877    0.000    0.000
LGA    L    39_A      L    39_A    10.617     0    0.016   0.147    12.723    0.000    7.262
LGA    V    40_A      V    40_A    10.928     0    0.051   0.081    15.527    0.357    0.204
LGA    L    41_A      L    41_A     6.664     0    0.157   1.003     7.824   10.119   22.560
LGA    N    42_A      N    42_A    11.246     0    0.400   1.269    13.590    0.119    0.060
LGA    G    43_A      G    43_A     9.387     0    0.715   0.715    10.000    4.167    4.167
LGA    R    44_A      R    44_A     3.039     0    0.618   1.192     5.783   50.833   44.762
LGA    E    45_A      E    45_A     2.466     0    0.083   0.707     5.454   62.976   46.931
LGA    F    46_A      F    46_A     3.060     0    0.607   1.378    12.090   55.476   24.156
LGA    A    47_A      A    47_A     2.811     0    0.693   0.648     5.576   40.000   40.667
LGA    S    48_A      S    48_A     8.525     0    0.285   0.711    10.700    6.429    4.365
LGA    P    49_A      P    49_A    10.291     0    0.702   0.730    13.750    0.833    0.476
LGA    E    50_A      E    50_A     6.012     0    0.583   1.472     8.321   26.190   22.169
LGA    E    51_A      E    51_A     2.080     0    0.099   0.990     7.198   65.595   46.508
LGA    A    52_A      A    52_A     2.509     0    0.579   0.564     5.098   49.524   49.619
LGA    V    53_A      V    53_A     2.391     0    0.679   0.696     4.356   57.500   54.490
LGA    Q    54_A      Q    54_A     4.743     0    0.621   0.930    11.924   36.190   17.037
LGA    W    55_A      W    55_A     4.764     0    0.604   1.313    10.694   38.810   16.361
LGA    A    56_A      A    56_A     5.103     0    0.039   0.050     6.544   36.429   31.810
LGA    R    57_A      R    57_A     3.479     0    0.039   1.043     5.635   55.714   45.628
LGA    D    58_A      D    58_A     2.003     0    0.084   0.806     5.603   61.190   47.738
LGA    T    59_A      T    59_A     3.327     0    0.154   0.143     5.811   57.262   46.395
LGA    G    60_A      G    60_A     1.714     0    0.427   0.427     3.217   63.214   63.214
LGA    L    61_A      L    61_A     6.745     0    0.600   1.416    12.418   14.762    7.738
LGA    R    62_A      R    62_A     8.729     0    0.590   1.245    12.637    4.643    1.991
LGA    F    63_A      F    63_A     9.161     0    0.636   0.801    10.708    1.071    1.255
LGA    L    64_A      L    64_A    12.676     0    0.059   0.678    15.663    0.000    0.060
LGA    R    65_A      R    65_A    17.210     0    0.599   1.178    24.343    0.000    0.000
LGA    L    66_A      L    66_A    16.324     0    0.599   0.482    17.330    0.000    0.000
LGA    I    67_A      I    67_A    17.833     0    0.036   1.443    21.144    0.000    0.000
LGA    R    68_A      R    68_A    24.394     0    0.535   1.477    27.213    0.000    0.000
LGA    E    69_A      E    69_A    25.859     0    0.554   0.925    27.037    0.000    0.000
LGA    R    70_A      R    70_A    25.111     0    0.609   1.078    26.412    0.000    0.000
LGA    Y    71_A      Y    71_A    29.562     0    0.581   1.420    37.531    0.000    0.000
LGA    E    72_A      E    72_A    35.278     0    0.602   0.807    37.385    0.000    0.000
LGA    D    73_A      D    73_A    36.870     0    0.583   0.777    39.767    0.000    0.000
LGA    G    74_A      G    74_A    34.845     0    0.713   0.713    35.239    0.000    0.000
LGA    V    75_A      V    75_A    28.695     0    0.586   0.500    31.175    0.000    0.000
LGA    Y    76_A      Y    76_A    25.196     0    0.530   1.037    29.284    0.000    0.000
LGA    T    77_A      T    77_A    17.997     0    0.617   1.324    20.762    0.000    0.000
LGA    V    78_A      V    78_A    15.910     0    0.620   0.544    19.497    0.000    0.000
LGA    E    79_A      E    79_A    12.990     0    0.615   1.027    16.972    0.000    0.000
LGA    D    80_A      D    80_A     6.440     0    0.528   1.330    10.084   18.214   11.131
LGA    I    81_A      I    81_A     1.668     0    0.591   0.730     3.897   65.119   59.643
LGA    V    82_A      V    82_A     3.814     0    0.543   1.416     8.210   39.167   28.571
LGA    S    83_A      S    83_A     7.049     0    0.172   0.514     8.387   10.238    9.286
LGA    R    84_A      R    84_A    10.508     0    0.592   1.062    17.581    0.357    0.130
LGA    D    85_A      D    85_A    14.715     0    0.624   1.061    17.687    0.000    0.000
LGA    D    86_A      D    86_A    18.422     0    0.691   1.238    22.539    0.000    0.000
LGA    G    87_A      G    87_A    15.805     0    0.701   0.701    16.427    0.000    0.000
LGA    R    88_A      R    88_A    15.074     0    0.622   1.187    24.209    0.000    0.000
LGA    Y    89_A      Y    89_A     9.857     0    0.406   0.645    15.725    0.119    0.317
LGA    Y    90_A      Y    90_A     9.307     0    0.582   1.586    13.689    1.548    0.992
LGA    R    91_A      R    91_A    13.471     0    0.622   1.059    16.099    0.000    0.000
LGA    H    92_A      H    92_A    12.758     0    0.589   0.848    13.785    0.000    0.000
LGA    T    93_A      T    93_A    14.961     0    0.388   0.361    16.906    0.000    0.000
LGA    S    94_A      S    94_A    17.146     0    0.604   0.511    20.193    0.000    0.000
LGA    T    95_A      T    95_A    21.212     0    0.570   0.992    22.691    0.000    0.000
LGA    L    96_A      L    96_A    19.720     0    0.621   1.465    23.248    0.000    0.000
LGA    R    97_A      R    97_A    26.725     0    0.599   1.050    35.083    0.000    0.000
LGA    R    98_A      R    98_A    28.467     0    0.093   1.440    38.622    0.000    0.000
LGA    Q    99_A      Q    99_A    28.125     0    0.069   1.057    29.749    0.000    0.000
LGA    P   100_A      P   100_A    30.618     0    0.097   0.102    31.653    0.000    0.000
LGA    D   101_A      D   101_A    26.285     0    0.308   1.239    27.555    0.000    0.000
LGA    G   102_A      G   102_A    27.351     0    0.743   0.743    27.351    0.000    0.000
LGA    S   103_A      S   103_A    27.927     0    0.076   0.597    31.274    0.000    0.000
LGA    Y   104_A      Y   104_A    27.226     0    0.367   1.385    29.214    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       70     280    280  100.00     580    580  100.00               114
SUMMARY(RMSD_GDC):    13.812         13.722                 14.199            8.194    6.661

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70  114    4.0     13    2.72    13.377    10.669     0.461

LGA_LOCAL      RMSD:   2.723  Number of atoms:   13  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.385  Number of assigned atoms:   70 
Std_ASGN_ATOMS RMSD:  13.812  Standard rmsd on all 70 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.807215 * X  +  -0.463972 * Y  +  -0.364874 * Z  +  22.555555
  Y_new =   0.044537 * X  +  -0.568523 * Y  +   0.821461 * Z  +   0.675517
  Z_new =  -0.588574 * X  +  -0.679347 * Y  +  -0.438256 * Z  +   3.860254 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.055118  0.629294 -2.143730   [DEG:    3.1580   36.0559 -122.8267 ]
ZXZ: -2.723592  2.024454 -2.427664   [DEG: -156.0503  115.9927 -139.0949 ]
 
# END of job
