
#######################################################
#                                                     #
#                        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   64 (  496),  selected   64 , name one
# Molecule2: number of CA atoms   67 (  519),  selected   64 , 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:    64       3_A - 66_A        0.85     0.85
  LCS_AVERAGE:     95.52

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64       3_A - 66_A        0.85     0.85
  LCS_AVERAGE:     95.52

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64       3_A - 66_A        0.85     0.85
  LCS_AVERAGE:     95.52

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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     P     3_A     P     3_A     64   64   64     10   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E     4_A     E     4_A     64   64   64     13   44   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E     5_A     E     5_A     64   64   64     10   27   57   61   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q     6_A     Q     6_A     64   64   64     13   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K     7_A     K     7_A     64   64   64     22   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q     8_A     Q     8_A     64   64   64     13   47   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M     9_A     M     9_A     64   64   64     12   47   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    10_A     L    10_A     64   64   64     21   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    11_A     G    11_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    12_A     E    12_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    13_A     A    13_A     64   64   64     29   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    14_A     I    14_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    15_A     Y    15_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     P    16_A     P    16_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    17_A     K    17_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    18_A     V    18_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    19_A     A    19_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    20_A     A    20_A     64   64   64     23   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    21_A     S    21_A     64   64   64     34   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    22_A     Q    22_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     P    23_A     P    23_A     64   64   64     33   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    24_A     E    24_A     64   64   64     23   53   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    25_A     L    25_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    26_A     A    26_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    27_A     G    27_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    28_A     K    28_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    30_A     T    30_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    31_A     G    31_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    32_A     M    32_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    33_A     I    33_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    34_A     L    34_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    35_A     E    35_A     64   64   64     27   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    36_A     L    36_A     64   64   64      9   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     P    37_A     P    37_A     64   64   64     33   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    38_A     V    38_A     64   64   64     27   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    39_A     T    39_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    40_A     E    40_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    42_A     L    42_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    43_A     H    43_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    44_A     L    44_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    45_A     L    45_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    46_A     E    46_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    47_A     E    47_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    48_A     S    48_A     64   64   64     33   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    49_A     E    49_A     64   64   64     22   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    50_A     A    50_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    52_A     D    52_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    53_A     A    53_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    54_A     K    54_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    55_A     V    55_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    56_A     N    56_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    57_A     E    57_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    58_A     A    58_A     64   64   64     35   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    59_A     L    59_A     64   64   64     33   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    60_A     E    60_A     64   64   64     20   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    61_A     V    61_A     64   64   64     14   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    62_A     L    62_A     64   64   64     14   54   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    63_A     K    63_A     64   64   64     14   26   59   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    64_A     E    64_A     64   64   64     14   26   55   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    65_A     Y    65_A     64   64   64     14   26   55   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    66_A     Q    66_A     64   64   64      3   26   50   63   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  95.52  (  95.52   95.52   95.52 )

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     35     54     59     63     64     64     64     64     64     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  52.24  80.60  88.06  94.03  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52  95.52
GDT RMS_LOCAL    0.33   0.53   0.66   0.82   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85
GDT RMS_ALL_AT   0.98   0.92   0.88   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85   0.85

# Checking swapping
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    57_A      E    57_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    P     3_A      P     3_A     0.858     0    0.449   0.434     3.035   83.810   70.340
LGA    E     4_A      E     4_A     1.796     0    0.048   0.965     5.993   72.857   54.709
LGA    E     5_A      E     5_A     2.072     0    0.099   0.939     4.434   75.119   57.619
LGA    Q     6_A      Q     6_A     0.955     0    0.042   0.869     3.300   88.214   81.058
LGA    K     7_A      K     7_A     0.674     0    0.029   1.012     2.973   90.476   79.101
LGA    Q     8_A      Q     8_A     1.446     0    0.024   0.898     5.517   81.429   63.492
LGA    M     9_A      M     9_A     1.327     0    0.031   1.084     2.603   83.690   76.369
LGA    L    10_A      L    10_A     0.569     0    0.045   0.136     1.311   95.238   90.595
LGA    G    11_A      G    11_A     0.343     0    0.024   0.024     0.373  100.000  100.000
LGA    E    12_A      E    12_A     0.271     0    0.061   0.120     0.705   97.619   93.651
LGA    A    13_A      A    13_A     0.588     0    0.055   0.052     0.827   92.857   92.381
LGA    I    14_A      I    14_A     0.519     0    0.028   1.221     3.469   95.238   80.417
LGA    Y    15_A      Y    15_A     0.448     0    0.034   0.240     1.138  100.000   92.143
LGA    P    16_A      P    16_A     0.535     0    0.034   0.364     1.723   92.857   89.320
LGA    K    17_A      K    17_A     0.684     0    0.029   1.295     5.775   90.476   74.603
LGA    V    18_A      V    18_A     0.415     0    0.033   0.978     2.458   92.857   87.007
LGA    A    19_A      A    19_A     0.786     0    0.065   0.064     1.071   88.214   88.667
LGA    A    20_A      A    20_A     1.087     0    0.121   0.125     1.755   81.548   81.524
LGA    S    21_A      S    21_A     0.873     0    0.166   0.651     1.544   92.857   89.127
LGA    Q    22_A      Q    22_A     0.637     0    0.151   0.126     1.121   92.857   87.513
LGA    P    23_A      P    23_A     1.152     0    0.066   0.372     1.364   83.690   85.306
LGA    E    24_A      E    24_A     1.291     0    0.030   0.854     5.406   81.429   58.942
LGA    L    25_A      L    25_A     0.866     0    0.099   0.118     1.033   88.214   88.214
LGA    A    26_A      A    26_A     0.706     0    0.025   0.039     0.795   90.476   90.476
LGA    G    27_A      G    27_A     0.765     0    0.026   0.026     0.796   90.476   90.476
LGA    K    28_A      K    28_A     0.733     0    0.016   1.012     3.795   90.476   76.032
LGA    L    29_A      L    29_A     0.473     0    0.048   0.188     0.895   92.857   92.857
LGA    T    30_A      T    30_A     0.631     0    0.057   1.078     2.905   90.476   83.197
LGA    G    31_A      G    31_A     0.670     0    0.033   0.033     0.691   90.476   90.476
LGA    M    32_A      M    32_A     0.491     0    0.022   0.100     0.632   97.619   94.048
LGA    I    33_A      I    33_A     0.460     0    0.015   0.984     3.046  100.000   83.810
LGA    L    34_A      L    34_A     0.406     0    0.078   0.126     0.752  100.000   95.238
LGA    E    35_A      E    35_A     0.507     0    0.037   1.147     3.825   92.857   82.381
LGA    L    36_A      L    36_A     0.765     0    0.052   1.022     4.160   92.857   80.655
LGA    P    37_A      P    37_A     0.431     0    0.081   0.367     1.206  100.000   94.626
LGA    V    38_A      V    38_A     0.521     0    0.023   0.178     0.972   97.619   94.558
LGA    T    39_A      T    39_A     0.472     0    0.032   1.026     2.205  100.000   89.728
LGA    E    40_A      E    40_A     0.294     0    0.050   0.988     2.857  100.000   88.201
LGA    L    41_A      L    41_A     0.330     0    0.028   0.895     2.403  100.000   92.083
LGA    L    42_A      L    42_A     0.348     0    0.035   1.412     3.464  100.000   85.000
LGA    H    43_A      H    43_A     0.446     0    0.034   1.123     2.832  100.000   88.524
LGA    L    44_A      L    44_A     0.378     0    0.053   1.033     2.874   97.619   89.048
LGA    L    45_A      L    45_A     0.100     0    0.048   0.261     1.283  100.000   97.679
LGA    E    46_A      E    46_A     0.366     0    0.052   0.823     2.588  100.000   83.492
LGA    E    47_A      E    47_A     0.446     0    0.057   0.388     1.303  100.000   94.762
LGA    S    48_A      S    48_A     0.400     0    0.029   0.626     1.945   95.238   92.302
LGA    E    49_A      E    49_A     0.865     0    0.098   0.950     3.250   90.476   79.153
LGA    A    50_A      A    50_A     0.598     0    0.024   0.036     0.600   92.857   92.381
LGA    L    51_A      L    51_A     0.385     0    0.051   1.061     2.981  100.000   90.060
LGA    D    52_A      D    52_A     0.568     0    0.036   0.955     3.628   90.476   75.357
LGA    A    53_A      A    53_A     0.755     0    0.047   0.048     0.917   90.476   90.476
LGA    K    54_A      K    54_A     0.531     0    0.033   0.842     4.446   90.476   75.450
LGA    V    55_A      V    55_A     0.573     0    0.031   0.894     2.398   90.476   84.286
LGA    N    56_A      N    56_A     0.539     0    0.022   0.209     1.363   95.238   90.595
LGA    E    57_A      E    57_A     0.243     0    0.036   0.612     1.826  100.000   89.841
LGA    A    58_A      A    58_A     0.243     0    0.030   0.041     0.271  100.000  100.000
LGA    L    59_A      L    59_A     0.300     0    0.033   0.576     1.818  100.000   94.226
LGA    E    60_A      E    60_A     0.707     0    0.048   1.086     5.673   88.214   66.455
LGA    V    61_A      V    61_A     0.902     0    0.028   0.122     1.282   88.214   87.891
LGA    L    62_A      L    62_A     0.787     0    0.032   1.383     2.919   85.952   77.679
LGA    K    63_A      K    63_A     1.342     0    0.035   0.906     1.854   77.143   77.619
LGA    E    64_A      E    64_A     1.866     0    0.068   1.212     6.711   69.048   48.942
LGA    Y    65_A      Y    65_A     1.894     0    0.052   1.353     7.880   70.833   49.206
LGA    Q    66_A      Q    66_A     2.000     0    0.711   0.638     2.671   64.881   68.413

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     496    496  100.00                67
SUMMARY(RMSD_GDC):     0.852          0.858                  1.761           87.244   79.847

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   64   67    4.0     64    0.85    91.418    93.683     6.721

LGA_LOCAL      RMSD:   0.852  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.852  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   0.852  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.847420 * X  +   0.239718 * Y  +  -0.473724 * Z  +   2.309415
  Y_new =   0.507306 * X  +  -0.102440 * Y  +   0.855656 * Z  + -11.222189
  Z_new =   0.156588 * X  +  -0.965423 * Y  +  -0.208420 * Z  +   1.703491 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.539424 -0.157235 -1.783418   [DEG:   30.9067   -9.0089 -102.1823 ]
ZXZ: -2.635961  1.780756  2.980797   [DEG: -151.0294  102.0298  170.7871 ]
 
# END of job
