
#######################################################
#                                                     #
#                        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 (  519),  selected   67 , name one
# Molecule2: number of CA atoms   67 (  519),  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       2_A - 68_A        0.70     0.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.70     0.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    67       2_A - 68_A        0.70     0.70
  LCS_AVERAGE:    100.00

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     S     2_A     S     2_A     67   67   67     10   35   61   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P     3_A     P     3_A     67   67   67     21   58   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     4_A     E     4_A     67   67   67     20   58   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E     5_A     E     5_A     67   67   67     27   61   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     6_A     Q     6_A     67   67   67     36   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K     7_A     K     7_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q     8_A     Q     8_A     67   67   67     36   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M     9_A     M     9_A     67   67   67     37   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    10_A     L    10_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    11_A     G    11_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    12_A     E    12_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    13_A     A    13_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    14_A     I    14_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    15_A     Y    15_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    16_A     P    16_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    17_A     K    17_A     67   67   67     36   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    18_A     V    18_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    19_A     A    19_A     67   67   67     36   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    20_A     A    20_A     67   67   67     29   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    21_A     S    21_A     67   67   67      4   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    22_A     Q    22_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    23_A     P    23_A     67   67   67     36   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    24_A     E    24_A     67   67   67     36   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    25_A     L    25_A     67   67   67     41   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    26_A     A    26_A     67   67   67     32   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    27_A     G    27_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    28_A     K    28_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    29_A     L    29_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    30_A     T    30_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     G    31_A     G    31_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     M    32_A     M    32_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     I    33_A     I    33_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    34_A     L    34_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    35_A     E    35_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    36_A     L    36_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     P    37_A     P    37_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    38_A     V    38_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     T    39_A     T    39_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    40_A     E    40_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    41_A     L    41_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    42_A     L    42_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     H    43_A     H    43_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    44_A     L    44_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    45_A     L    45_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    46_A     E    46_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    47_A     E    47_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     S    48_A     S    48_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    49_A     E    49_A     67   67   67     40   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    50_A     A    50_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    51_A     L    51_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     D    52_A     D    52_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    53_A     A    53_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    54_A     K    54_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    55_A     V    55_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    56_A     N    56_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    57_A     E    57_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     A    58_A     A    58_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    59_A     L    59_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    60_A     E    60_A     67   67   67     22   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     V    61_A     V    61_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     L    62_A     L    62_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     K    63_A     K    63_A     67   67   67     22   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     E    64_A     E    64_A     67   67   67     17   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Y    65_A     Y    65_A     67   67   67     39   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    66_A     Q    66_A     67   67   67     17   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     Q    67_A     Q    67_A     67   67   67     44   62   65   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_GDT     N    68_A     N    68_A     67   67   67      4   32   63   66   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67   67 
LCS_AVERAGE  LCS_A: 100.00  ( 100.00  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     44     62     65     66     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67     67 
GDT PERCENT_AT  65.67  92.54  97.01  98.51 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.50   0.58   0.64   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70
GDT RMS_ALL_AT   0.77   0.75   0.72   0.71   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70   0.70

# Checking swapping
#   possible swapping detected:  Y    15_A      Y    15_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  E    46_A      E    46_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  Y    65_A      Y    65_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     2_A      S     2_A     2.339     0    0.047   0.051     2.606   66.905   64.921
LGA    P     3_A      P     3_A     1.291     0    0.038   0.190     2.048   81.548   79.116
LGA    E     4_A      E     4_A     1.167     0    0.015   0.675     4.368   85.952   68.836
LGA    E     5_A      E     5_A     0.867     0    0.060   0.463     3.621   92.857   75.926
LGA    Q     6_A      Q     6_A     0.663     0    0.055   0.562     1.559   95.238   89.630
LGA    K     7_A      K     7_A     0.395     0    0.021   0.536     1.490  100.000   93.757
LGA    Q     8_A      Q     8_A     0.527     0    0.074   0.182     0.781   97.619   96.825
LGA    M     9_A      M     9_A     0.439     0    0.031   0.768     1.930  100.000   90.833
LGA    L    10_A      L    10_A     0.401     0    0.037   0.137     1.100  100.000   94.107
LGA    G    11_A      G    11_A     0.370     0    0.020   0.020     0.568   97.619   97.619
LGA    E    12_A      E    12_A     0.321     0    0.047   0.133     0.644  100.000   98.942
LGA    A    13_A      A    13_A     0.266     0    0.032   0.037     0.319  100.000  100.000
LGA    I    14_A      I    14_A     0.281     0    0.038   0.057     0.573  100.000   98.810
LGA    Y    15_A      Y    15_A     0.308     0    0.026   0.209     0.567   97.619   96.825
LGA    P    16_A      P    16_A     0.383     0    0.023   0.165     0.711   95.238   95.918
LGA    K    17_A      K    17_A     0.577     0    0.013   0.941     3.117   90.476   84.974
LGA    V    18_A      V    18_A     0.482     0    0.010   0.042     0.839   95.238   97.279
LGA    A    19_A      A    19_A     0.678     0    0.052   0.052     0.800   90.476   90.476
LGA    A    20_A      A    20_A     0.795     0    0.112   0.134     1.197   88.214   88.667
LGA    S    21_A      S    21_A     0.663     0    0.098   0.647     1.331   97.619   92.222
LGA    Q    22_A      Q    22_A     0.359     0    0.062   0.065     0.660   97.619   93.651
LGA    P    23_A      P    23_A     0.750     0    0.057   0.317     0.969   90.476   91.837
LGA    E    24_A      E    24_A     0.894     0    0.026   0.718     2.348   90.476   83.651
LGA    L    25_A      L    25_A     0.725     0    0.023   0.103     0.997   90.476   90.476
LGA    A    26_A      A    26_A     0.740     0    0.026   0.024     0.881   92.857   92.381
LGA    G    27_A      G    27_A     0.612     0    0.045   0.045     0.683   90.476   90.476
LGA    K    28_A      K    28_A     0.514     0    0.023   0.263     0.794   95.238   92.593
LGA    L    29_A      L    29_A     0.297     0    0.015   0.099     0.547  100.000   98.810
LGA    T    30_A      T    30_A     0.502     0    0.021   0.064     0.558   92.857   91.837
LGA    G    31_A      G    31_A     0.637     0    0.031   0.031     0.637   90.476   90.476
LGA    M    32_A      M    32_A     0.336     0    0.035   0.069     0.489  100.000  100.000
LGA    I    33_A      I    33_A     0.173     0    0.033   0.067     0.316  100.000  100.000
LGA    L    34_A      L    34_A     0.369     0    0.054   0.075     0.432  100.000  100.000
LGA    E    35_A      E    35_A     0.414     0    0.051   1.192     4.359  100.000   74.974
LGA    L    36_A      L    36_A     0.392     0    0.052   0.083     0.467  100.000  100.000
LGA    P    37_A      P    37_A     0.447     0    0.094   0.334     1.270   97.619   94.626
LGA    V    38_A      V    38_A     0.584     0    0.028   0.087     1.035   90.476   89.184
LGA    T    39_A      T    39_A     0.547     0    0.019   0.048     0.705   95.238   93.197
LGA    E    40_A      E    40_A     0.357     0    0.031   0.798     2.947  100.000   87.249
LGA    L    41_A      L    41_A     0.244     0    0.040   0.083     0.669  100.000   98.810
LGA    L    42_A      L    42_A     0.327     0    0.067   0.111     0.386  100.000  100.000
LGA    H    43_A      H    43_A     0.450     0    0.012   0.059     0.855  100.000   94.286
LGA    L    44_A      L    44_A     0.414     0    0.034   0.184     0.889  100.000   96.429
LGA    L    45_A      L    45_A     0.304     0    0.051   0.118     0.368  100.000  100.000
LGA    E    46_A      E    46_A     0.318     0    0.012   0.892     3.350  100.000   81.005
LGA    E    47_A      E    47_A     0.405     0    0.030   0.169     0.721  100.000   94.709
LGA    S    48_A      S    48_A     0.429     0    0.087   0.664     2.011   97.619   90.952
LGA    E    49_A      E    49_A     0.734     0    0.089   0.829     2.393   92.857   83.704
LGA    A    50_A      A    50_A     0.509     0    0.009   0.010     0.542   95.238   96.190
LGA    L    51_A      L    51_A     0.415     0    0.019   0.096     0.546  100.000   98.810
LGA    D    52_A      D    52_A     0.446     0    0.021   0.074     0.514   97.619   98.810
LGA    A    53_A      A    53_A     0.551     0    0.045   0.048     0.551   90.476   90.476
LGA    K    54_A      K    54_A     0.505     0    0.031   0.240     1.143   97.619   94.762
LGA    V    55_A      V    55_A     0.349     0    0.019   0.058     0.504  100.000   98.639
LGA    N    56_A      N    56_A     0.462     0    0.080   0.139     0.846  100.000   95.238
LGA    E    57_A      E    57_A     0.343     0    0.022   0.641     2.351  100.000   84.339
LGA    A    58_A      A    58_A     0.358     0    0.041   0.038     0.426  100.000  100.000
LGA    L    59_A      L    59_A     0.346     0    0.051   0.569     1.792  100.000   90.774
LGA    E    60_A      E    60_A     0.791     0    0.119   1.116     4.640   88.214   72.169
LGA    V    61_A      V    61_A     0.731     0    0.024   0.041     0.794   90.476   90.476
LGA    L    62_A      L    62_A     0.493     0    0.019   1.285     2.787   95.238   85.476
LGA    K    63_A      K    63_A     0.877     0    0.012   0.854     3.530   85.952   75.714
LGA    E    64_A      E    64_A     1.230     0    0.022   0.935     4.304   81.429   63.810
LGA    Y    65_A      Y    65_A     1.022     0    0.031   0.240     1.911   83.690   81.548
LGA    Q    66_A      Q    66_A     1.110     0    0.042   0.121     2.521   88.214   77.090
LGA    Q    67_A      Q    67_A     0.664     0    0.251   0.560     3.503   88.214   77.513
LGA    N    68_A      N    68_A     2.121     0    0.645   1.020     6.328   48.690   43.750

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     519    519  100.00                67
SUMMARY(RMSD_GDC):     0.703          0.810                  1.233           94.156   89.650

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67   67    4.0     67    0.70    97.761    99.084     8.341

LGA_LOCAL      RMSD:   0.703  Number of atoms:   67  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   0.703  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:   0.703  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.457153 * X  +   0.701917 * Y  +   0.546190 * Z  +   1.293622
  Y_new =  -0.508598 * X  +  -0.710116 * Y  +   0.486891 * Z  +   3.878218
  Z_new =   0.729616 * X  +  -0.055207 * Y  +   0.681625 * Z  +  16.604431 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.302976 -0.817760 -0.080817   [DEG: -131.9508  -46.8542   -4.6305 ]
ZXZ:  2.298858  0.820814  1.646318   [DEG:  131.7148   47.0292   94.3271 ]
 
# END of job
