
#######################################################
#                                                     #
#                        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 (  525),  selected   67 , name one
# Molecule2: number of CA atoms   78 (  613),  selected   67 , 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:    67      24_A - 90_A        2.10     2.10
  LCS_AVERAGE:     85.90

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    66      24_A - 89_A        1.97     2.11
  LONGEST_CONTINUOUS_SEGMENT:    66      25_A - 90_A        1.93     2.12
  LCS_AVERAGE:     84.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      61_A - 86_A        0.99     2.16
  LCS_AVERAGE:     26.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     Q    24_A     Q    24_A      3   66   67      0    3    3   13   16   26   41   56   63   65   65   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    25_A     Q    25_A      9   66   67      3   16   40   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    26_A     D    26_A     13   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    27_A     K    27_A     13   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    28_A     L    28_A     13   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    29_A     V    29_A     13   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    30_A     L    30_A     13   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    31_A     R    31_A     13   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    32_A     V    32_A     13   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    33_A     D    33_A     13   66   67      6   22   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    34_A     G    34_A     13   66   67      5   22   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    35_A     I    35_A     21   66   67      6   22   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     21   66   67      3   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    37_A     N    37_A     21   66   67      5   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    38_A     E    38_A     21   66   67      3   20   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    39_A     L    39_A     21   66   67      9   17   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    40_A     D    40_A     21   66   67      6   17   34   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    41_A     A    41_A     21   66   67      6   17   41   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    42_A     Q    42_A     21   66   67      9   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    43_A     V    43_A     21   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     21   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    45_A     E    45_A     21   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    46_A     G    46_A     21   66   67      9   22   43   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    47_A     I    47_A     21   66   67      9   22   43   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    48_A     L    48_A     21   66   67      6   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    49_A     T    49_A     21   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    50_A     R    50_A     21   66   67      9   17   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     21   66   67      9   17   33   54   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    52_A     N    52_A     21   66   67      6   17   34   52   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    53_A     G    53_A     21   66   67      7   17   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    54_A     V    54_A     21   66   67      7   17   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    55_A     R    55_A     21   66   67      3   19   37   54   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    56_A     Q    56_A     21   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    57_A     F    57_A     15   66   67      6   21   37   50   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    58_A     R    58_A     19   66   67      6   21   37   52   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     20   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    60_A     D    60_A     24   66   67      7   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    61_A     R    61_A     26   66   67      6   21   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    62_A     I    62_A     26   66   67      6   18   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    63_A     S    63_A     26   66   67      6   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    64_A     G    64_A     26   66   67      6   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    65_A     E    65_A     26   66   67      7   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    66_A     L    66_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    67_A     E    67_A     26   66   67     10   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    68_A     V    68_A     26   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    69_A     V    69_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    70_A     F    70_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    71_A     D    71_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    72_A     P    72_A     26   66   67      4   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    73_A     E    73_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    74_A     V    74_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    75_A     V    75_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    76_A     S    76_A     26   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    77_A     S    77_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     R    78_A     R    78_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    79_A     S    79_A     26   66   67      9   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    80_A     L    80_A     26   66   67      9   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    81_A     V    81_A     26   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    82_A     D    82_A     26   66   67     11   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    83_A     G    83_A     26   66   67      9   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    84_A     I    84_A     26   66   67      9   21   42   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    85_A     E    85_A     26   66   67      9   22   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    86_A     E    86_A     26   66   67      9   21   44   56   61   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    87_A     D    87_A     15   66   67      8   12   20   45   60   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    88_A     G    88_A     14   66   67      5   12   34   46   58   64   64   64   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     F    89_A     F    89_A      3   66   67      3    3    3    4    8   23   30   41   58   66   66   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    90_A     G    90_A      3   66   67      0    3    3    7   13   23   30   62   64   66   66   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A:  65.64  (  26.41   84.62   85.90 )

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     11     22     44     56     61     64     64     64     64     66     66     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  14.10  28.21  56.41  71.79  78.21  82.05  82.05  82.05  82.05  84.62  84.62  85.90  85.90  85.90  85.90  85.90  85.90  85.90  85.90  85.90
GDT RMS_LOCAL    0.36   0.70   1.11   1.29   1.43   1.56   1.56   1.56   1.56   1.93   1.93   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10
GDT RMS_ALL_AT   2.63   2.43   2.15   2.15   2.16   2.13   2.13   2.13   2.13   2.12   2.12   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10   2.10

# Checking swapping
#   possible swapping detected:  F    57_A      F    57_A
#   possible swapping detected:  D    60_A      D    60_A
#   possible swapping detected:  E    67_A      E    67_A
#   possible swapping detected:  F    70_A      F    70_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    24_A      Q    24_A     7.232     0    0.663   1.259     9.994   12.262    7.884
LGA    Q    25_A      Q    25_A     2.213     0    0.432   1.298     5.426   61.667   53.704
LGA    D    26_A      D    26_A     1.157     0    0.563   0.766     3.497   79.405   71.369
LGA    K    27_A      K    27_A     1.046     0    0.189   0.601     2.593   79.524   74.127
LGA    L    28_A      L    28_A     0.999     0    0.085   0.109     1.588   90.476   84.881
LGA    V    29_A      V    29_A     0.973     0    0.000   0.035     1.836   90.476   82.925
LGA    L    30_A      L    30_A     0.627     0    0.023   0.149     0.924   90.476   90.476
LGA    R    31_A      R    31_A     0.467     0    0.048   1.080     3.836   97.619   81.688
LGA    V    32_A      V    32_A     0.908     0    0.045   0.054     1.403   85.952   85.306
LGA    D    33_A      D    33_A     1.693     0    0.103   0.284     2.277   72.976   69.881
LGA    G    34_A      G    34_A     2.016     0    0.054   0.054     2.024   68.810   68.810
LGA    I    35_A      I    35_A     1.683     0    0.044   0.065     2.424   77.143   72.976
LGA    L    36_A      L    36_A     1.029     0    0.149   0.169     1.976   79.286   77.143
LGA    N    37_A      N    37_A     1.115     0    0.010   0.120     2.958   85.952   75.417
LGA    E    38_A      E    38_A     1.025     0    0.202   0.781     2.998   85.952   76.984
LGA    L    39_A      L    39_A     1.539     0    0.127   0.964     4.018   75.000   68.452
LGA    D    40_A      D    40_A     1.924     0    0.027   0.085     2.509   72.857   67.857
LGA    A    41_A      A    41_A     1.810     0    0.023   0.025     1.825   72.857   72.857
LGA    Q    42_A      Q    42_A     1.507     0    0.030   0.265     1.815   72.857   77.672
LGA    V    43_A      V    43_A     1.503     0    0.000   0.008     1.559   72.857   74.082
LGA    L    44_A      L    44_A     1.587     0    0.012   1.410     4.032   72.857   68.393
LGA    E    45_A      E    45_A     1.449     0    0.073   0.727     3.794   79.286   68.201
LGA    G    46_A      G    46_A     1.925     0    0.000   0.000     1.925   72.857   72.857
LGA    I    47_A      I    47_A     1.818     0    0.010   0.051     2.524   72.857   67.857
LGA    L    48_A      L    48_A     1.567     0    0.064   1.024     5.357   79.286   66.310
LGA    T    49_A      T    49_A     1.288     0    0.085   0.083     1.885   81.429   77.755
LGA    R    50_A      R    50_A     2.112     0    0.088   0.982     4.527   64.881   58.398
LGA    L    51_A      L    51_A     2.565     0    0.032   0.265     3.849   64.881   56.667
LGA    N    52_A      N    52_A     2.779     0    0.061   0.816     4.778   60.952   50.714
LGA    G    53_A      G    53_A     1.945     0    0.028   0.028     2.232   72.976   72.976
LGA    V    54_A      V    54_A     1.489     0    0.029   0.069     1.799   79.286   80.272
LGA    R    55_A      R    55_A     2.361     0    0.069   1.124     4.320   66.786   54.372
LGA    Q    56_A      Q    56_A     1.298     0    0.093   0.881     2.453   75.000   75.873
LGA    F    57_A      F    57_A     2.566     0    0.200   1.166     4.920   59.286   52.035
LGA    R    58_A      R    58_A     2.367     0    0.026   0.754     5.102   70.952   55.541
LGA    L    59_A      L    59_A     1.459     0    0.048   0.864     2.594   72.976   67.976
LGA    D    60_A      D    60_A     1.127     0    0.077   0.283     1.763   85.952   87.202
LGA    R    61_A      R    61_A     1.491     0    0.091   1.018     4.671   77.262   57.446
LGA    I    62_A      I    62_A     1.516     0    0.000   0.043     2.481   77.143   72.976
LGA    S    63_A      S    63_A     1.128     0    0.017   0.035     1.330   85.952   84.444
LGA    G    64_A      G    64_A     0.781     0    0.187   0.187     1.653   88.452   88.452
LGA    E    65_A      E    65_A     1.283     0    0.075   0.203     3.278   88.214   73.598
LGA    L    66_A      L    66_A     0.805     0    0.119   0.184     0.988   90.476   90.476
LGA    E    67_A      E    67_A     1.182     0    0.159   0.702     2.551   81.429   72.222
LGA    V    68_A      V    68_A     0.964     0    0.034   1.120     2.801   88.214   80.612
LGA    V    69_A      V    69_A     0.508     0    0.036   0.044     0.793   95.238   94.558
LGA    F    70_A      F    70_A     0.361     0    0.027   0.104     1.037   97.619   95.714
LGA    D    71_A      D    71_A     0.539     0    0.089   0.568     1.725   90.595   88.333
LGA    P    72_A      P    72_A     1.257     0    0.095   0.102     1.387   83.690   84.014
LGA    E    73_A      E    73_A     1.435     0    0.142   0.310     2.305   75.119   75.767
LGA    V    74_A      V    74_A     1.139     0    0.064   0.082     1.443   81.429   81.429
LGA    V    75_A      V    75_A     0.646     0    0.086   1.171     2.704   90.476   82.041
LGA    S    76_A      S    76_A     0.729     0    0.049   0.105     0.838   90.476   90.476
LGA    S    77_A      S    77_A     0.903     0    0.091   0.131     1.335   90.476   87.460
LGA    R    78_A      R    78_A     0.891     0    0.086   1.076     4.821   90.476   74.935
LGA    S    79_A      S    79_A     1.038     0    0.023   0.034     1.547   83.690   81.508
LGA    L    80_A      L    80_A     1.428     0    0.000   0.839     1.747   81.429   81.488
LGA    V    81_A      V    81_A     1.242     0    0.046   0.050     1.607   81.429   78.980
LGA    D    82_A      D    82_A     0.789     0    0.000   0.121     1.462   90.476   88.214
LGA    G    83_A      G    83_A     1.342     0    0.016   0.016     1.689   81.548   81.548
LGA    I    84_A      I    84_A     1.822     0    0.021   0.072     2.594   72.976   67.917
LGA    E    85_A      E    85_A     1.347     0    0.113   0.143     1.508   79.286   79.524
LGA    E    86_A      E    86_A     1.069     0    0.069   0.964     3.758   81.548   66.720
LGA    D    87_A      D    87_A     3.150     0    0.094   0.103     4.867   52.024   44.643
LGA    G    88_A      G    88_A     3.415     0    0.162   0.162     4.153   46.905   46.905
LGA    F    89_A      F    89_A     7.161     0    0.480   1.279    11.326   13.333    5.281
LGA    G    90_A      G    90_A     6.795     0    0.607   0.607     7.699   10.238   10.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     525    525  100.00                78
SUMMARY(RMSD_GDC):     2.105          2.121                  2.661           65.314   61.228

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   78    4.0     64    1.56    66.987    76.378     3.862

LGA_LOCAL      RMSD:   1.557  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.133  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   2.105  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.380481 * X  +  -0.639090 * Y  +  -0.668429 * Z  + 213.188568
  Y_new =   0.807373 * X  +  -0.582028 * Y  +   0.096911 * Z  + -35.267464
  Z_new =  -0.450980 * X  +  -0.502799 * Y  +   0.737435 * Z  +  -9.411594 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.011187  0.467863 -0.598421   [DEG:  115.2325   26.8066  -34.2870 ]
ZXZ: -1.714776  0.741531 -2.410472   [DEG:  -98.2495   42.4866 -138.1099 ]
 
# END of job
