
#######################################################
#                                                     #
#                        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   66 (  516),  selected   66 , name one
# Molecule2: number of CA atoms   78 (  613),  selected   66 , 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:    66      25_A - 90_A        1.85     1.85
  LCS_AVERAGE:     84.62

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    66      25_A - 90_A        1.85     1.85
  LCS_AVERAGE:     84.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    33      30_A - 62_A        1.00     2.08
  LONGEST_CONTINUOUS_SEGMENT:    33      31_A - 63_A        1.00     2.08
  LCS_AVERAGE:     38.46

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   66
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    25_A     Q    25_A     23   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    26_A     D    26_A     26   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     K    27_A     K    27_A     26   66   66      8   19   47   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    28_A     L    28_A     29   66   66      8   29   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    29_A     V    29_A     29   66   66      8   29   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    30_A     L    30_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     R    31_A     R    31_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    32_A     V    32_A     33   66   66      5   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    33_A     D    33_A     33   66   66      5   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    34_A     G    34_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     I    35_A     I    35_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    36_A     L    36_A     33   66   66      3   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     N    37_A     N    37_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    38_A     E    38_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    39_A     L    39_A     33   66   66      4   23   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    40_A     D    40_A     33   66   66      4   21   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     A    41_A     A    41_A     33   66   66      8   12   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q    42_A     Q    42_A     33   66   66      8   21   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    43_A     V    43_A     33   66   66      8   28   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    44_A     L    44_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    45_A     E    45_A     33   66   66      8   23   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    46_A     G    46_A     33   66   66      6   19   47   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     I    47_A     I    47_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    48_A     L    48_A     33   66   66      8   13   43   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     T    49_A     T    49_A     33   66   66      6   13   43   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     R    50_A     R    50_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    51_A     L    51_A     33   66   66      6   28   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     N    52_A     N    52_A     33   66   66      5   14   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    53_A     G    53_A     33   66   66      6   29   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    54_A     V    54_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     R    55_A     R    55_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     Q    56_A     Q    56_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     F    57_A     F    57_A     33   66   66      6   29   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     R    58_A     R    58_A     33   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    59_A     L    59_A     33   66   66      8   29   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    60_A     D    60_A     33   66   66      4   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     R    61_A     R    61_A     33   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     I    62_A     I    62_A     33   66   66      4   26   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     S    63_A     S    63_A     33   66   66      4   26   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    64_A     G    64_A     31   66   66      4   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    65_A     E    65_A     31   66   66      4   28   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    66_A     L    66_A     31   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    67_A     E    67_A     31   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    68_A     V    68_A     31   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    69_A     V    69_A     31   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     F    70_A     F    70_A     31   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    71_A     D    71_A     31   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     P    72_A     P    72_A     31   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    73_A     E    73_A     31   66   66      8   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    74_A     V    74_A     31   66   66      9   30   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    75_A     V    75_A     31   66   66      5   23   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     S    76_A     S    76_A     31   66   66      7   23   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     S    77_A     S    77_A     31   66   66      7   26   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     R    78_A     R    78_A     31   66   66      5   21   44   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     S    79_A     S    79_A     31   66   66      7   16   41   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     L    80_A     L    80_A     31   66   66      7   23   45   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     V    81_A     V    81_A     31   66   66      7   23   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    82_A     D    82_A     31   66   66      7   23   49   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    83_A     G    83_A     31   66   66      7   18   41   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     I    84_A     I    84_A     25   66   66      7   22   44   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    85_A     E    85_A     25   66   66      8   23   48   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     E    86_A     E    86_A     21   66   66      7   22   42   59   62   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     D    87_A     D    87_A     14   66   66      7   13   17   42   58   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    88_A     G    88_A     14   66   66      4   13   15   26   54   64   64   64   64   65   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     F    89_A     F    89_A      3   66   66      3    3    3    3    9   12   16   39   52   63   66   66   66   66   66   66   66   66   66   66 
LCS_GDT     G    90_A     G    90_A      3   66   66      0    3    5    7   10   15   24   47   63   65   66   66   66   66   66   66   66   66   66   66 
LCS_AVERAGE  LCS_A:  69.23  (  38.46   84.62   84.62 )

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      9     30     49     59     62     64     64     64     64     65     66     66     66     66     66     66     66     66     66     66 
GDT PERCENT_AT  11.54  38.46  62.82  75.64  79.49  82.05  82.05  82.05  82.05  83.33  84.62  84.62  84.62  84.62  84.62  84.62  84.62  84.62  84.62  84.62
GDT RMS_LOCAL    0.36   0.72   1.02   1.24   1.29   1.44   1.44   1.44   1.44   1.65   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85
GDT RMS_ALL_AT   1.98   1.95   1.96   1.92   1.91   1.88   1.88   1.88   1.88   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85   1.85

# Checking swapping
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  D    60_A      D    60_A
#   possible swapping detected:  E    67_A      E    67_A
#   possible swapping detected:  E    86_A      E    86_A
#   possible swapping detected:  D    87_A      D    87_A
#   possible swapping detected:  F    89_A      F    89_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    Q    25_A      Q    25_A     0.552     0    0.056   0.294     2.023   92.857   83.757
LGA    D    26_A      D    26_A     1.178     0    0.076   0.778     2.515   85.952   80.655
LGA    K    27_A      K    27_A     1.850     0    0.133   0.834     4.887   66.905   55.926
LGA    L    28_A      L    28_A     1.432     0    0.033   1.338     4.975   83.690   69.345
LGA    V    29_A      V    29_A     1.200     0    0.030   0.080     2.132   83.690   77.891
LGA    L    30_A      L    30_A     0.771     0    0.100   0.811     2.414   88.214   83.929
LGA    R    31_A      R    31_A     0.508     0    0.086   0.913     4.252   92.857   69.437
LGA    V    32_A      V    32_A     0.966     0    0.046   0.120     1.257   85.952   86.599
LGA    D    33_A      D    33_A     1.342     0    0.138   0.851     3.527   81.429   68.631
LGA    G    34_A      G    34_A     0.892     0    0.082   0.082     0.897   90.476   90.476
LGA    I    35_A      I    35_A     0.906     0    0.081   0.105     1.068   90.476   89.345
LGA    L    36_A      L    36_A     0.959     0    0.031   0.050     1.722   90.476   84.881
LGA    N    37_A      N    37_A     1.355     0    0.038   1.212     2.850   81.429   75.238
LGA    E    38_A      E    38_A     0.848     0    0.035   0.850     3.298   85.952   79.048
LGA    L    39_A      L    39_A     1.419     0    0.025   0.900     3.694   77.143   68.452
LGA    D    40_A      D    40_A     1.682     0    0.046   0.101     1.768   72.857   72.857
LGA    A    41_A      A    41_A     1.536     0    0.094   0.095     1.597   75.000   74.571
LGA    Q    42_A      Q    42_A     1.677     0    0.025   0.300     3.018   72.857   69.418
LGA    V    43_A      V    43_A     1.367     0    0.111   0.113     1.538   79.286   80.204
LGA    L    44_A      L    44_A     1.112     0    0.071   0.157     2.145   79.286   76.131
LGA    E    45_A      E    45_A     1.617     0    0.081   0.823     3.255   72.976   69.524
LGA    G    46_A      G    46_A     2.038     0    0.048   0.048     2.038   70.833   70.833
LGA    I    47_A      I    47_A     1.233     0    0.026   0.694     2.575   77.143   79.643
LGA    L    48_A      L    48_A     2.044     0    0.067   0.119     2.526   66.786   64.821
LGA    T    49_A      T    49_A     2.166     0    0.062   0.119     2.822   68.810   65.986
LGA    R    50_A      R    50_A     1.006     0    0.085   1.304     6.164   81.429   67.056
LGA    L    51_A      L    51_A     1.559     0    0.042   1.274     3.610   79.286   73.452
LGA    N    52_A      N    52_A     1.952     0    0.015   1.000     4.639   70.833   61.726
LGA    G    53_A      G    53_A     1.382     0    0.037   0.037     1.554   81.548   81.548
LGA    V    54_A      V    54_A     0.781     0    0.046   0.098     1.089   90.476   89.184
LGA    R    55_A      R    55_A     0.467     0    0.101   1.271     9.629   97.619   56.104
LGA    Q    56_A      Q    56_A     0.620     0    0.055   1.153     5.383   92.857   75.397
LGA    F    57_A      F    57_A     1.228     0    0.107   0.808     4.727   83.690   65.238
LGA    R    58_A      R    58_A     0.953     0    0.166   1.250     7.684   85.952   60.390
LGA    L    59_A      L    59_A     1.428     0    0.098   0.945     3.456   81.429   77.500
LGA    D    60_A      D    60_A     1.011     0    0.093   1.032     5.412   85.952   66.488
LGA    R    61_A      R    61_A     0.606     0    0.089   1.540     8.648   90.476   54.978
LGA    I    62_A      I    62_A     0.808     0    0.129   1.267     3.432   86.190   72.917
LGA    S    63_A      S    63_A     1.147     0    0.044   0.648     1.642   88.214   83.095
LGA    G    64_A      G    64_A     0.916     0    0.131   0.131     1.585   88.452   88.452
LGA    E    65_A      E    65_A     1.341     0    0.094   0.279     3.497   81.429   68.942
LGA    L    66_A      L    66_A     0.938     0    0.098   1.056     3.832   85.952   74.762
LGA    E    67_A      E    67_A     0.758     0    0.121   0.882     1.906   90.476   82.593
LGA    V    68_A      V    68_A     0.660     0    0.033   0.114     0.807   90.476   91.837
LGA    V    69_A      V    69_A     0.587     0    0.042   0.119     0.939   95.238   94.558
LGA    F    70_A      F    70_A     0.614     0    0.042   0.264     0.717   90.476   93.074
LGA    D    71_A      D    71_A     0.721     0    0.021   0.243     1.448   90.476   89.345
LGA    P    72_A      P    72_A     0.645     0    0.033   0.128     1.377   92.857   90.544
LGA    E    73_A      E    73_A     0.916     0    0.050   0.418     3.548   88.214   76.455
LGA    V    74_A      V    74_A     0.655     0    0.146   0.149     0.970   90.476   90.476
LGA    V    75_A      V    75_A     1.266     0    0.009   0.057     1.796   85.952   82.789
LGA    S    76_A      S    76_A     1.511     0    0.015   0.091     2.091   79.286   75.794
LGA    S    77_A      S    77_A     1.052     0    0.014   0.025     1.627   81.429   80.000
LGA    R    78_A      R    78_A     1.957     0    0.059   1.107     5.980   72.857   58.268
LGA    S    79_A      S    79_A     2.165     0    0.023   0.042     2.736   66.786   64.841
LGA    L    80_A      L    80_A     1.702     0    0.044   0.977     1.924   75.000   79.524
LGA    V    81_A      V    81_A     1.214     0    0.057   0.068     1.406   81.429   81.429
LGA    D    82_A      D    82_A     1.424     0    0.074   0.171     2.506   77.143   73.036
LGA    G    83_A      G    83_A     2.112     0    0.045   0.045     2.139   68.810   68.810
LGA    I    84_A      I    84_A     1.622     0    0.042   0.166     2.107   72.857   72.917
LGA    E    85_A      E    85_A     1.325     0    0.041   0.419     1.887   77.143   82.540
LGA    E    86_A      E    86_A     1.993     0    0.062   0.115     3.094   66.905   62.381
LGA    D    87_A      D    87_A     3.599     0    0.045   0.780     7.062   43.452   34.940
LGA    G    88_A      G    88_A     3.719     0    0.205   0.205     4.352   41.905   41.905
LGA    F    89_A      F    89_A     7.271     0    0.554   1.211    10.979   14.881    5.887
LGA    G    90_A      G    90_A     6.879     0    0.738   0.738     7.863   10.238   10.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       66     264    264  100.00     516    516  100.00                78
SUMMARY(RMSD_GDC):     1.845          1.834                  2.592           66.793   61.398

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   66   78    4.0     64    1.44    70.192    77.761     4.156

LGA_LOCAL      RMSD:   1.440  Number of atoms:   64  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.878  Number of assigned atoms:   66 
Std_ASGN_ATOMS RMSD:   1.845  Standard rmsd on all 66 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.180275 * X  +  -0.578244 * Y  +  -0.795698 * Z  +   9.803024
  Y_new =  -0.464192 * X  +   0.663189 * Y  +  -0.587116 * Z  + -12.471582
  Z_new =   0.867195 * X  +   0.475199 * Y  +  -0.148860 * Z  +  -8.608326 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.200363 -1.049541  1.874372   [DEG:  -68.7757  -60.1343  107.3936 ]
ZXZ: -0.935108  1.720212  1.069511   [DEG:  -53.5777   98.5609   61.2785 ]
 
# END of job
