
#######################################################
#                                                     #
#                        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   72 (  538),  selected   72 , name one
# Molecule2: number of CA atoms  105 (  764),  selected   72 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62      33_B - 94_B        4.69     6.28
  LCS_AVERAGE:     53.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      56_B - 81_B        1.88     6.88
  LCS_AVERAGE:     17.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      58_B - 79_B        0.99     6.83
  LCS_AVERAGE:     13.31

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   72
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     F    33_B     F    33_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     T    34_B     T    34_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     K    35_B     K    35_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    36_B     V    36_B     20   21   62     21   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     D    37_B     D    37_B     20   21   62     10   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    38_B     A    38_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    39_B     A    39_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     T    40_B     T    40_B     20   21   62     18   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     K    41_B     K    41_B     20   21   62      5   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    42_B     A    42_B     20   21   62     20   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     P    43_B     P    43_B     20   21   62     22   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     L    44_B     L    44_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    45_B     A    45_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     G    46_B     G    46_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    47_B     A    47_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    48_B     V    48_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     F    49_B     F    49_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     Q    50_B     Q    50_B     20   21   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    51_B     V    51_B     20   21   62     11   32   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    52_B     V    52_B     20   21   62      4   15   34   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     E    53_B     E    53_B      5   21   62      3    5    7   19   29   42   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     K    54_B     K    54_B      5   11   62      3    5    7    9   11   14   23   35   46   54   56   61   61   62   62   64   65   66   67   68 
LCS_GDT     D    55_B     D    55_B      5   11   62      3    5    6    9   11   12   14   19   20   34   46   54   56   58   59   63   65   66   67   68 
LCS_GDT     G    56_B     G    56_B      5   26   62      3    4    7   10   24   34   47   50   52   54   56   57   61   62   62   64   65   66   67   68 
LCS_GDT     D    57_B     D    57_B      5   26   62      3   13   23   36   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     I    58_B     I    58_B     22   26   62      3   17   33   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     T    59_B     T    59_B     22   26   62     15   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     L    60_B     L    60_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     Y    61_B     Y    61_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     E    62_B     E    62_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     L    63_B     L    63_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     S    64_B     S    64_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     S    65_B     S    65_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     P    66_B     P    66_B     22   26   62     11   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    67_B     A    67_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     G    68_B     G    68_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     Y    69_B     Y    69_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    70_B     V    70_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     P    71_B     P    71_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    72_B     V    72_B     22   26   62     10   36   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     T    73_B     T    73_B     22   26   62      6   36   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     N    74_B     N    74_B     22   26   62     13   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     K    75_B     K    75_B     22   26   62     23   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     P    76_B     P    76_B     22   26   62     15   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     I    77_B     I    77_B     22   26   62      7   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     Y    78_B     Y    78_B     22   26   62      3   30   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     N    79_B     N    79_B     22   26   62      5   15   24   38   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     I    80_B     I    80_B      5   26   62      0    5    6   19   36   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     S    81_B     S    81_B      5   26   62      3    5    9   20   34   45   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     T    82_B     T    82_B      3    6   62      3    3    4    9   16   29   37   44   52   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     G    83_B     G    83_B      3    6   62      3    3    4    4    6   10   13   15   46   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     E    84_B     E    84_B      3    9   62      3    3    7    9   10   11   39   49   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    85_B     A    85_B      3    9   62      3    3    7    9   10   11   19   47   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     F    86_B     F    86_B      3    9   62      3    3    7    9   10   11   14   19   22   27   55   61   61   62   62   64   65   66   67   68 
LCS_GDT     D    87_B     D    87_B      4    9   62      4    4    5    5    6   11   14   19   22   35   54   61   61   62   62   64   65   66   67   68 
LCS_GDT     S    88_B     S    88_B      4    9   62      4    4    7    9   10   10   14   19   21   25   29   40   44   49   54   58   65   66   67   68 
LCS_GDT     A    89_B     A    89_B      4    9   62      4    4    5    5    9   10   14   19   21   25   31   40   44   49   57   63   65   66   67   68 
LCS_GDT     A    90_B     A    90_B      4    9   62      4    4    7    9   10   11   14   19   32   50   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     A    91_B     A    91_B      3    9   62      3    4    5    9   10   11   13   18   32   50   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     S    92_B     S    92_B      3    9   62      3    3    7    9   10   11   14   38   42   49   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     V    93_B     V    93_B      4    7   62      3    4    4    5    6    7    9   13   18   23   27   32   46   55   60   64   65   66   67   68 
LCS_GDT     V    94_B     V    94_B      4    6   62      3    4    4    5    6    7    9   11   16   18   22   27   29   45   45   53   54   60   64   68 
LCS_GDT     K    95_B     K    95_B      4    5   24      3    4    4    4    5    7    9   15   15   18   23   26   29   32   37   37   45   49   61   61 
LCS_GDT     E    96_B     E    96_B      4    5   24      3    4    4    4    5    7    9   13   16   18   22   26   29   31   36   37   43   49   61   61 
LCS_GDT     D    97_B     D    97_B      3    5   24      3    3    4    4    6    7    9   13   16   18   22   26   29   31   36   38   43   49   61   61 
LCS_GDT     G    98_B     G    98_B      3    5   24      3    3    4    4    6    7    8   13   16   18   22   26   29   31   36   38   54   56   61   61 
LCS_GDT     Q    99_B     Q    99_B      3    5   24      3    3    3    4    8   13   15   23   28   33   46   49   52   58   62   64   65   66   67   68 
LCS_GDT     Y   100_B     Y   100_B      5    5   24      3   24   36   44   46   47   48   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     Y   101_B     Y   101_B      5    5   24     18   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     I   102_B     I   102_B      5    5   19     20   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     T   103_B     T   103_B      5    5   11     18   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_GDT     N   104_B     N   104_B      5    5   11     11   37   43   45   47   47   50   51   53   54   57   61   61   62   62   64   65   66   67   68 
LCS_AVERAGE  LCS_A:  28.02  (  13.31   17.13   53.61 )

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     23     37     43     45     47     47     50     51     53     54     57     61     61     62     62     64     65     66     67     68 
GDT PERCENT_AT  21.90  35.24  40.95  42.86  44.76  44.76  47.62  48.57  50.48  51.43  54.29  58.10  58.10  59.05  59.05  60.95  61.90  62.86  63.81  64.76
GDT RMS_LOCAL    0.33   0.55   0.71   0.92   1.22   1.22   1.78   1.83   2.19   2.48   2.90   3.42   3.36   3.49   3.49   3.94   4.05   4.24   4.41   4.68
GDT RMS_ALL_AT   6.78   6.80   6.76   6.69   6.63   6.63   6.55   6.53   6.54   6.62   6.48   6.42   6.43   6.42   6.42   6.27   6.32   6.25   6.26   6.18

# Checking swapping
#   possible swapping detected:  D    37_B      D    37_B
#   possible swapping detected:  D    55_B      D    55_B
#   possible swapping detected:  D    97_B      D    97_B
#   possible swapping detected:  Y   100_B      Y   100_B
#   possible swapping detected:  Y   101_B      Y   101_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    F    33_B      F    33_B     1.490     0    0.033   0.256     2.660   79.286   70.909
LGA    T    34_B      T    34_B     1.317     0    0.071   0.082     1.686   79.286   80.204
LGA    K    35_B      K    35_B     1.108     0    0.078   0.592     1.316   81.429   83.439
LGA    V    36_B      V    36_B     1.136     0    0.019   0.129     1.370   83.690   84.014
LGA    D    37_B      D    37_B     1.013     0    0.052   0.974     4.176   85.952   73.988
LGA    A    38_B      A    38_B     0.815     0    0.095   0.094     1.408   85.952   88.762
LGA    A    39_B      A    39_B     1.166     0    0.029   0.050     1.833   79.405   79.810
LGA    T    40_B      T    40_B     2.300     0    0.094   0.082     2.989   64.881   62.653
LGA    K    41_B      K    41_B     2.107     0    0.020   1.052     7.410   64.881   49.841
LGA    A    42_B      A    42_B     2.025     0    0.077   0.091     2.234   70.833   69.619
LGA    P    43_B      P    43_B     1.593     0    0.034   0.403     1.771   77.143   75.306
LGA    L    44_B      L    44_B     0.824     0    0.031   0.106     1.156   88.214   88.214
LGA    A    45_B      A    45_B     0.407     0    0.043   0.059     0.579   97.619   98.095
LGA    G    46_B      G    46_B     0.508     0    0.062   0.062     0.925   92.857   92.857
LGA    A    47_B      A    47_B     0.749     0    0.160   0.187     1.377   88.214   88.667
LGA    V    48_B      V    48_B     0.384     0    0.084   1.061     2.353   95.238   87.211
LGA    F    49_B      F    49_B     1.080     0    0.044   0.126     1.198   85.952   85.541
LGA    Q    50_B      Q    50_B     1.497     0    0.055   0.245     1.568   83.690   77.672
LGA    V    51_B      V    51_B     1.010     0    0.028   0.233     2.074   90.714   83.129
LGA    V    52_B      V    52_B     1.256     0    0.146   1.068     4.707   73.452   67.347
LGA    E    53_B      E    53_B     5.340     0    0.023   0.699     7.060   24.048   18.571
LGA    K    54_B      K    54_B     9.144     0    0.167   0.812    12.416    2.262    1.164
LGA    D    55_B      D    55_B    11.911     0    0.494   1.143    17.802    0.833    0.417
LGA    G    56_B      G    56_B     6.782     0    0.635   0.635     8.904   15.952   15.952
LGA    D    57_B      D    57_B     2.854     0    0.133   1.182     4.189   54.048   56.607
LGA    I    58_B      I    58_B     1.801     0    0.122   0.601     4.574   68.810   58.869
LGA    T    59_B      T    59_B     1.549     0    0.125   1.073     3.355   75.000   72.041
LGA    L    60_B      L    60_B     1.578     0    0.096   0.158     2.041   72.857   71.845
LGA    Y    61_B      Y    61_B     1.447     0    0.085   0.187     1.867   77.143   81.548
LGA    E    62_B      E    62_B     0.812     0    0.046   0.169     0.943   90.476   90.476
LGA    L    63_B      L    63_B     0.809     0    0.165   0.357     1.954   88.214   83.750
LGA    S    64_B      S    64_B     0.861     0    0.032   0.651     2.277   90.476   84.683
LGA    S    65_B      S    65_B     0.655     0    0.046   0.718     1.668   90.476   87.540
LGA    P    66_B      P    66_B     0.814     0    0.064   0.286     1.238   92.857   90.544
LGA    A    67_B      A    67_B     0.866     0    0.326   0.432     2.652   84.524   82.190
LGA    G    68_B      G    68_B     1.003     0    0.042   0.042     1.458   90.714   90.714
LGA    Y    69_B      Y    69_B     0.440     0    0.063   0.163     0.700   92.857   93.651
LGA    V    70_B      V    70_B     0.827     0    0.095   0.094     1.051   90.476   89.184
LGA    P    71_B      P    71_B     0.682     0    0.063   0.111     0.915   90.476   90.476
LGA    V    72_B      V    72_B     1.038     0    0.091   0.328     1.409   83.690   84.014
LGA    T    73_B      T    73_B     1.535     0    0.061   0.984     3.384   75.000   73.333
LGA    N    74_B      N    74_B     1.609     0    0.062   0.156     2.313   75.000   70.893
LGA    K    75_B      K    75_B     0.991     0    0.155   0.964     6.139   85.952   65.979
LGA    P    76_B      P    76_B     0.903     0    0.111   0.217     0.916   90.476   90.476
LGA    I    77_B      I    77_B     0.655     0    0.373   1.450     3.790   79.881   72.857
LGA    Y    78_B      Y    78_B     0.968     0    0.149   1.341     4.278   81.786   67.579
LGA    N    79_B      N    79_B     2.656     0    0.210   0.701     5.952   63.214   48.393
LGA    I    80_B      I    80_B     4.159     0    0.665   1.035     7.547   47.143   33.036
LGA    S    81_B      S    81_B     5.507     0    0.585   0.931     7.615   18.333   16.984
LGA    T    82_B      T    82_B     8.950     0    0.202   1.098    13.279    5.476    3.129
LGA    G    83_B      G    83_B     6.944     0    0.476   0.476     7.053   12.500   12.500
LGA    E    84_B      E    84_B     6.999     0    0.198   0.740     8.982   12.500    8.624
LGA    A    85_B      A    85_B     6.726     0    0.074   0.119     7.932   10.238   11.619
LGA    F    86_B      F    86_B     9.210     0    0.080   1.224    11.483    2.024    0.736
LGA    D    87_B      D    87_B    10.347     0    0.674   1.269    12.985    0.119    0.833
LGA    S    88_B      S    88_B    13.392     0    0.103   0.634    14.788    0.000    0.000
LGA    A    89_B      A    89_B    11.453     0    0.501   0.471    11.453    0.000    0.000
LGA    A    90_B      A    90_B     8.815     0    0.662   0.601     9.815    1.905    2.095
LGA    A    91_B      A    91_B     8.889     0    0.737   0.687    11.213    1.786    1.524
LGA    S    92_B      S    92_B     8.124     0    0.675   0.901    11.032    3.333    6.667
LGA    V    93_B      V    93_B    11.082     0    0.562   0.598    13.328    0.357    0.272
LGA    V    94_B      V    94_B    13.900     0    0.057   1.057    14.972    0.000    0.000
LGA    K    95_B      K    95_B    18.187     0    0.124   1.053    24.254    0.000    0.000
LGA    E    96_B      E    96_B    18.595     0    0.281   0.861    19.869    0.000    0.000
LGA    D    97_B      D    97_B    18.694     0    0.345   0.466    21.445    0.000    0.000
LGA    G    98_B      G    98_B    15.650     0    0.702   0.702    16.414    0.000    0.000
LGA    Q    99_B      Q    99_B     9.892     0    0.130   0.210    13.747    3.690    1.693
LGA    Y   100_B      Y   100_B     3.261     0    0.591   1.415     5.594   44.643   57.857
LGA    Y   101_B      Y   101_B     1.711     0    0.078   0.211     3.489   72.857   64.405
LGA    I   102_B      I   102_B     1.678     0    0.061   1.232     3.310   75.000   67.202
LGA    T   103_B      T   103_B     1.480     0    0.063   1.219     3.300   79.286   73.333
LGA    N   104_B      N   104_B     1.095     1    0.060   0.516     2.124   83.690   70.357

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       72     288    288  100.00     537    537  100.00               105
SUMMARY(RMSD_GDC):     5.989          5.976                  6.340           38.582   36.704

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   72  105    4.0     51    1.83    46.905    40.310     2.645

LGA_LOCAL      RMSD:   1.828  Number of atoms:   51  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   6.535  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:   5.989  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.005475 * X  +   0.713926 * Y  +   0.700200 * Z  +  12.428707
  Y_new =   0.982484 * X  +   0.134267 * Y  +  -0.129216 * Z  + -83.612831
  Z_new =  -0.186265 * X  +   0.687228 * Y  +  -0.702156 * Z  + -56.541641 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.576369  0.187359  2.366938   [DEG:   90.3193   10.7349  135.6156 ]
ZXZ:  1.388307  2.349217 -0.264679   [DEG:   79.5442  134.6002  -15.1650 ]
 
# END of job
