
#######################################################
#                                                     #
#                        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   73 (  570),  selected   71 , name one
# Molecule2: number of CA atoms   71 (  553),  selected   71 , 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:    71       1_B - 71_B        1.62     1.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71       1_B - 71_B        1.62     1.62
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    68       1_B - 68_B        0.96     1.68
  LONGEST_CONTINUOUS_SEGMENT:    68       2_B - 69_B        0.97     1.65
  LCS_AVERAGE:     93.20

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     1_B     G     1_B     68   71   71      5    9   49   68   69   69   69   69   69   69   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     2_B     S     2_B     68   71   71     15   47   63   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V     3_B     V     3_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     4_B     S     4_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K     5_B     K     5_B     68   71   71     25   52   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     W     6_B     W     6_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S     7_B     S     7_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T     8_B     T     8_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D     9_B     D     9_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    10_B     E    10_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    11_B     V    11_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    12_B     S    12_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    13_B     E    13_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    14_B     F    14_B     68   71   71     16   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    15_B     I    15_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    16_B     Q    16_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    17_B     S    17_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    18_B     L    18_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    19_B     P    19_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    20_B     G    20_B     68   71   71     15   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     C    21_B     C    21_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    22_B     E    22_B     68   71   71     16   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    23_B     E    23_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     H    24_B     H    24_B     68   71   71     15   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    25_B     G    25_B     68   71   71     14   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    26_B     K    26_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    27_B     V    27_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    28_B     F    28_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    29_B     K    29_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    30_B     D    30_B     68   71   71     25   47   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    31_B     E    31_B     68   71   71     25   50   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    32_B     Q    32_B     68   71   71     25   48   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    33_B     I    33_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    34_B     D    34_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    35_B     G    35_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    36_B     E    36_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    37_B     A    37_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    38_B     F    38_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    39_B     L    39_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    40_B     L    40_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    41_B     M    41_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    42_B     T    42_B     68   71   71      8   33   63   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     Q    43_B     Q    43_B     68   71   71      7   30   52   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     T    44_B     T    44_B     68   71   71     14   47   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     D    45_B     D    45_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    46_B     I    46_B     68   71   71     15   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     V    47_B     V    47_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    48_B     K    48_B     68   71   71     21   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    49_B     I    49_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    50_B     M    50_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    51_B     S    51_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    52_B     I    52_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    53_B     K    53_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    54_B     E    54_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     G    55_B     G    55_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     P    56_B     P    56_B     68   71   71     20   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    57_B     A    57_B     68   71   71     25   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    58_B     E    58_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    59_B     K    59_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    60_B     I    60_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    61_B     F    61_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     N    62_B     N    62_B     68   71   71     18   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     S    63_B     S    63_B     68   71   71     18   40   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     I    64_B     I    64_B     68   71   71     17   43   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     L    65_B     L    65_B     68   71   71     17   54   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     M    66_B     M    66_B     68   71   71     17   38   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     F    67_B     F    67_B     68   71   71     17   36   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     K    68_B     K    68_B     68   71   71     17   36   64   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     68   71   71      6   30   51   68   69   69   69   69   69   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     A    70_B     A    70_B      3   71   71      3    5   10   13   19   32   63   67   68   70   71   71   71   71   71   71   71   71   71   71 
LCS_GDT     E    71_B     E    71_B      3   71   71      3    4    4    4    5   38   41   48   68   70   71   71   71   71   71   71   71   71   71   71 
LCS_AVERAGE  LCS_A:  97.73  (  93.20  100.00  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     25     54     64     68     69     69     69     69     69     70     71     71     71     71     71     71     71     71     71     71 
GDT PERCENT_AT  35.21  76.06  90.14  95.77  97.18  97.18  97.18  97.18  97.18  98.59 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.71   0.87   0.96   1.01   1.01   1.01   1.01   1.01   1.59   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62
GDT RMS_ALL_AT   2.09   1.68   1.65   1.68   1.67   1.67   1.67   1.67   1.67   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62   1.62

# Checking swapping
#   possible swapping detected:  D     9_B      D     9_B
#   possible swapping detected:  E    10_B      E    10_B
#   possible swapping detected:  E    13_B      E    13_B
#   possible swapping detected:  E    36_B      E    36_B
#   possible swapping detected:  E    54_B      E    54_B
#   possible swapping detected:  E    58_B      E    58_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_B      G     1_B     2.269     0    0.251   0.251     3.355   71.667   71.667
LGA    S     2_B      S     2_B     1.225     0    0.022   0.646     2.045   85.952   81.667
LGA    V     3_B      V     3_B     0.640     0    0.063   1.117     3.246   90.476   78.912
LGA    S     4_B      S     4_B     0.680     0    0.011   0.091     1.117   90.476   88.968
LGA    K     5_B      K     5_B     0.985     0    0.063   0.805     5.547   90.476   65.661
LGA    W     6_B      W     6_B     0.702     0    0.052   0.086     0.937   90.476   90.476
LGA    S     7_B      S     7_B     0.644     0    0.029   0.102     0.926   90.476   90.476
LGA    T     8_B      T     8_B     0.513     0    0.021   0.108     1.061   95.238   91.905
LGA    D     9_B      D     9_B     0.345     0    0.029   0.751     3.163   95.238   85.655
LGA    E    10_B      E    10_B     0.769     0    0.030   0.838     2.478   90.476   85.661
LGA    V    11_B      V    11_B     0.415     0    0.031   0.059     0.490  100.000  100.000
LGA    S    12_B      S    12_B     0.897     0    0.048   0.725     1.982   90.476   86.032
LGA    E    13_B      E    13_B     1.196     0    0.020   0.739     4.545   83.690   66.772
LGA    F    14_B      F    14_B     0.972     0    0.026   0.098     2.467   88.214   77.792
LGA    I    15_B      I    15_B     0.499     0    0.018   0.620     1.717   92.857   91.845
LGA    Q    16_B      Q    16_B     0.935     0    0.065   0.670     2.860   88.214   82.751
LGA    S    17_B      S    17_B     1.075     0    0.064   0.075     1.241   88.214   85.952
LGA    L    18_B      L    18_B     0.858     0    0.052   0.070     0.982   90.476   90.476
LGA    P    19_B      P    19_B     0.960     0    0.093   0.375     1.308   92.857   87.959
LGA    G    20_B      G    20_B     0.957     0    0.038   0.038     0.957   90.476   90.476
LGA    C    21_B      C    21_B     0.444     0    0.036   0.058     0.604   95.238   96.825
LGA    E    22_B      E    22_B     0.949     0    0.075   0.786     3.791   88.214   75.661
LGA    E    23_B      E    23_B     0.863     0    0.201   0.738     3.099   88.214   74.550
LGA    H    24_B      H    24_B     0.581     0    0.089   0.210     0.895   90.476   90.476
LGA    G    25_B      G    25_B     1.040     0    0.050   0.050     1.130   83.690   83.690
LGA    K    26_B      K    26_B     1.074     0    0.016   1.144     6.571   81.429   60.212
LGA    V    27_B      V    27_B     1.015     0    0.024   1.050     3.425   88.214   80.816
LGA    F    28_B      F    28_B     0.554     0    0.011   0.051     0.682   90.476   92.208
LGA    K    29_B      K    29_B     0.620     0    0.020   0.820     2.984   90.476   81.058
LGA    D    30_B      D    30_B     1.286     0    0.089   0.119     2.064   83.690   77.262
LGA    E    31_B      E    31_B     1.111     0    0.020   0.129     1.651   81.429   81.481
LGA    Q    32_B      Q    32_B     1.153     0    0.018   0.779     4.605   85.952   69.206
LGA    I    33_B      I    33_B     0.583     0    0.024   0.575     1.243   95.238   91.786
LGA    D    34_B      D    34_B     0.451     0    0.025   0.105     1.355  100.000   94.107
LGA    G    35_B      G    35_B     0.468     0    0.055   0.055     0.468  100.000  100.000
LGA    E    36_B      E    36_B     0.823     0    0.052   0.886     1.976   90.476   82.593
LGA    A    37_B      A    37_B     0.745     0    0.015   0.018     0.758   90.476   90.476
LGA    F    38_B      F    38_B     0.183     0    0.023   0.185     0.447  100.000  100.000
LGA    L    39_B      L    39_B     0.356     0    0.058   0.075     0.407  100.000  100.000
LGA    L    40_B      L    40_B     0.553     0    0.104   0.134     0.922   95.238   92.857
LGA    M    41_B      M    41_B     0.417     0    0.113   0.218     1.646   92.857   90.714
LGA    T    42_B      T    42_B     1.508     0    0.033   0.125     1.747   77.143   75.306
LGA    Q    43_B      Q    43_B     2.034     0    0.014   0.381     4.647   70.833   58.042
LGA    T    44_B      T    44_B     1.262     0    0.016   1.125     3.295   83.810   75.918
LGA    D    45_B      D    45_B     0.697     0    0.025   0.048     0.859   90.476   90.476
LGA    I    46_B      I    46_B     0.786     0    0.108   0.093     1.804   90.476   84.881
LGA    V    47_B      V    47_B     0.538     0    0.012   0.030     1.051   92.857   90.544
LGA    K    48_B      K    48_B     0.564     0    0.019   1.285     8.077   92.857   64.233
LGA    I    49_B      I    49_B     0.829     0    0.070   0.635     1.809   88.214   86.012
LGA    M    50_B      M    50_B     0.808     0    0.080   0.207     1.138   90.476   88.214
LGA    S    51_B      S    51_B     0.925     0    0.140   0.125     1.556   90.476   86.032
LGA    I    52_B      I    52_B     0.931     0    0.045   0.047     1.813   90.476   84.881
LGA    K    53_B      K    53_B     1.140     0    0.052   0.941     6.167   85.952   68.571
LGA    E    54_B      E    54_B     0.997     0    0.022   0.776     4.230   88.214   70.159
LGA    G    55_B      G    55_B     1.020     0    0.033   0.033     1.020   88.214   88.214
LGA    P    56_B      P    56_B     0.495     0    0.020   0.300     1.179   97.619   93.265
LGA    A    57_B      A    57_B     0.305     0    0.046   0.045     0.535   97.619   98.095
LGA    E    58_B      E    58_B     0.710     0    0.047   0.814     4.407   90.476   74.392
LGA    K    59_B      K    59_B     0.740     0    0.023   0.539     1.665   90.476   87.513
LGA    I    60_B      I    60_B     0.576     0    0.022   0.091     0.716   90.476   94.048
LGA    F    61_B      F    61_B     0.647     0    0.039   0.055     0.711   90.476   90.476
LGA    N    62_B      N    62_B     0.914     0    0.046   0.084     1.111   85.952   83.690
LGA    S    63_B      S    63_B     1.396     0    0.029   0.634     1.708   81.429   81.508
LGA    I    64_B      I    64_B     1.154     0    0.027   0.071     1.167   81.429   82.560
LGA    L    65_B      L    65_B     0.868     0    0.012   0.081     1.209   85.952   91.786
LGA    M    66_B      M    66_B     1.550     0    0.046   1.269     5.058   75.000   61.548
LGA    F    67_B      F    67_B     1.762     0    0.023   0.936     3.763   72.857   69.048
LGA    K    68_B      K    68_B     1.754     0    0.189   0.988     2.985   68.810   71.217
LGA    A    69_B      A    69_B     2.590     0    0.071   0.079     4.794   49.167   52.286
LGA    A    70_B      A    70_B     7.269     0    0.221   0.215    10.469   11.548    9.524
LGA    E    71_B      E    71_B     8.659     0    0.122   0.724    11.286    4.762    2.487

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     553    553  100.00                71
SUMMARY(RMSD_GDC):     1.616          1.629                  2.078           85.954   81.014

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   71    4.0     69    1.01    92.254    96.213     6.233

LGA_LOCAL      RMSD:   1.007  Number of atoms:   69  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.669  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   1.616  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.556823 * X  +   0.683652 * Y  +   0.471772 * Z  + -20.848558
  Y_new =   0.826494 * X  +  -0.399397 * Y  +  -0.396723 * Z  +  27.555300
  Z_new =  -0.082796 * X  +   0.610821 * Y  +  -0.787427 * Z  +  34.698399 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.977929  0.082891  2.481834   [DEG:   56.0312    4.7493  142.1986 ]
ZXZ:  0.871597  2.477421 -0.134727   [DEG:   49.9388  141.9457   -7.7193 ]
 
# END of job
