
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  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      22_A - 85_A        3.36     3.36
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      60_A - 85_A        2.00     3.87
  LCS_AVERAGE:     36.87

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      67_A - 85_A        0.97     3.75
  LCS_AVERAGE:     24.98

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     A    22_A     A    22_A      3    4   64      0    3    3    4    4    4    6    9   13   15   17   36   51   58   61   63   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      2    9   13   18   22   29   35   44   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   22   64      3    4    9   20   36   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     16   22   64      3    4    9   31   41   43   48   55   57   60   61   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     16   22   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     16   22   64      5   22   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     16   22   64     12   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     16   22   64     14   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     16   22   64      5   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     16   22   64     11   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     16   22   64      4   24   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      6   22   64      3    7   13   27   32   35   40   49   56   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      6   22   64      4   18   29   34   35   43   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      4   22   64      0    3    4    7   16   31   44   52   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     15   24   64      4    9   16   18   39   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     18   24   64      4   12   17   18   22   43   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     18   24   64      4   13   17   18   20   26   32   51   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     18   24   64      4    6   11   18   19   25   32   46   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     18   24   64      3   14   17   18   31   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     18   24   64     12   14   17   20   31   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     18   24   64     12   14   17   20   30   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     18   24   64     12   14   17   26   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     18   24   64     12   14   17   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     18   24   64     12   14   17   20   33   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     18   24   64     11   14   17   18   30   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     18   25   64     12   14   24   32   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     18   25   64     12   14   24   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     18   25   64     12   14   17   18   29   40   52   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     18   25   64     12   14   17   18   24   35   47   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     18   26   64     12   14   17   18   24   37   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     18   26   64     12   14   17   18   27   41   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     18   26   64     12   14   24   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     18   26   64      4   15   26   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     16   26   64      3    5    5   15   30   40   49   54   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      5   26   64      3    5   16   25   34   44   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      5   26   64      1    5    6    8   11   22   35   48   54   60   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     19   26   64      6   11   24   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     19   26   64      6   12   28   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     19   26   64      7   25   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     19   26   64      7   22   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     19   26   64     20   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     19   26   64     16   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     19   26   64     22   28   31   34   41   45   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     19   26   64     14   28   31   34   41   44   53   55   57   61   62   63   63   63   63   63   64   64   64   64 
LCS_AVERAGE  LCS_A:  53.95  (  24.98   36.87  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     22     28     31     34     41     45     53     55     57     61     62     63     63     63     63     63     64     64     64     64 
GDT PERCENT_AT  34.38  43.75  48.44  53.12  64.06  70.31  82.81  85.94  89.06  95.31  96.88  98.44  98.44  98.44  98.44  98.44 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.46   0.61   0.88   1.45   1.92   2.26   2.33   2.45   2.92   3.00   3.02   3.02   3.02   3.02   3.02   3.36   3.36   3.36   3.36
GDT RMS_ALL_AT   4.02   4.01   4.02   3.95   3.74   3.53   3.48   3.50   3.51   3.37   3.36   3.37   3.37   3.37   3.37   3.37   3.36   3.36   3.36   3.36

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A    13.411     0    0.538   0.551    14.889    0.000    0.000
LGA    D    23_A      D    23_A     8.257     0    0.694   0.704    10.703   10.952    7.440
LGA    G    24_A      G    24_A     4.224     0    0.548   0.548     5.841   36.786   36.786
LGA    D    25_A      D    25_A     3.076     0    0.241   1.074     7.029   54.167   36.071
LGA    G    26_A      G    26_A     1.006     0    0.103   0.103     1.007   85.952   85.952
LGA    Q    27_A      Q    27_A     0.893     0    0.030   0.807     2.622   90.476   80.899
LGA    G    28_A      G    28_A     0.753     0    0.079   0.079     0.753   92.857   92.857
LGA    L    29_A      L    29_A     0.718     0    0.012   0.088     1.118   90.476   88.214
LGA    Y    30_A      Y    30_A     0.846     0    0.075   0.133     1.061   88.214   88.214
LGA    A    31_A      A    31_A     0.653     0    0.010   0.012     0.887   90.476   90.476
LGA    A    32_A      A    32_A     1.023     0    0.038   0.040     1.265   83.690   83.238
LGA    N    33_A      N    33_A     1.227     0    0.029   0.077     1.432   81.429   81.429
LGA    C    34_A      C    34_A     1.286     0    0.045   0.092     1.503   81.429   80.000
LGA    A    35_A      A    35_A     1.241     0    0.024   0.023     1.829   77.143   78.000
LGA    A    36_A      A    36_A     2.319     0    0.020   0.018     2.805   64.881   63.333
LGA    C    37_A      C    37_A     2.143     0    0.018   0.052     2.341   64.762   64.762
LGA    H    38_A      H    38_A     1.737     0    0.075   0.113     1.843   72.857   72.857
LGA    G    39_A      G    39_A     1.785     0    0.131   0.131     1.824   77.143   77.143
LGA    A    40_A      A    40_A     1.060     0    0.036   0.043     1.936   81.548   79.810
LGA    L    41_A      L    41_A     1.881     0    0.625   1.438     3.422   72.976   71.190
LGA    A    42_A      A    42_A     5.630     0    0.176   0.190     6.381   27.619   25.524
LGA    T    43_A      T    43_A     3.873     0    0.634   0.668     4.236   41.786   42.449
LGA    S    44_A      S    44_A     5.368     0    0.487   0.688     6.215   26.310   23.968
LGA    E    45_A      E    45_A     3.076     0    0.508   0.875     6.238   57.976   40.159
LGA    K    46_A      K    46_A     4.185     0    0.049   0.576     4.899   34.286   54.656
LGA    K    47_A      K    47_A     6.431     0    0.659   0.581     9.967   22.857   12.751
LGA    G    48_A      G    48_A     7.176     0    0.042   0.042     7.465   16.905   16.905
LGA    T    49_A      T    49_A     3.943     0    0.117   1.207     5.780   37.500   38.776
LGA    T    50_A      T    50_A     3.532     0    0.056   0.065     3.532   48.333   50.068
LGA    L    51_A      L    51_A     3.767     0    0.014   1.349     7.460   46.667   32.560
LGA    A    52_A      A    52_A     2.462     0    0.014   0.015     2.914   62.857   63.238
LGA    R    53_A      R    53_A     1.781     0    0.017   1.035     3.306   68.810   65.671
LGA    L    54_A      L    54_A     2.950     0    0.011   1.400     7.209   53.571   39.643
LGA    Q    55_A      Q    55_A     3.334     0    0.017   1.065     5.743   50.000   42.593
LGA    S    56_A      S    56_A     2.243     0    0.055   0.061     2.634   62.857   66.190
LGA    A    57_A      A    57_A     2.230     0    0.007   0.019     2.979   60.952   61.714
LGA    V    58_A      V    58_A     3.962     0    0.054   0.096     5.095   41.905   38.299
LGA    S    59_A      S    59_A     4.248     0    0.010   0.098     4.647   37.262   36.270
LGA    A    60_A      A    60_A     3.618     0    0.030   0.034     3.677   43.333   44.667
LGA    N    61_A      N    61_A     3.664     0    0.092   0.985     5.777   50.238   39.643
LGA    A    62_A      A    62_A     1.831     0    0.052   0.056     2.588   68.929   69.714
LGA    G    63_A      G    63_A     1.896     0    0.629   0.629     2.236   72.976   72.976
LGA    G    64_A      G    64_A     5.238     0    0.045   0.045     5.604   29.048   29.048
LGA    M    65_A      M    65_A     3.786     0    0.643   1.084     4.863   37.262   54.167
LGA    G    66_A      G    66_A     6.400     0    0.647   0.647     6.400   24.048   24.048
LGA    F    67_A      F    67_A     2.012     0    0.589   1.395     6.993   63.095   49.654
LGA    L    68_A      L    68_A     1.098     0    0.055   0.131     1.618   85.952   81.548
LGA    S    69_A      S    69_A     0.845     0    0.037   0.062     1.647   85.952   83.016
LGA    S    70_A      S    70_A     1.600     0    0.043   0.086     1.974   75.000   75.714
LGA    L    71_A      L    71_A     1.158     0    0.022   0.101     1.567   79.286   84.881
LGA    T    72_A      T    72_A     1.888     0    0.042   0.041     1.914   72.857   72.857
LGA    S    73_A      S    73_A     2.129     0    0.031   0.637     3.024   68.810   65.000
LGA    A    74_A      A    74_A     1.577     0    0.023   0.026     1.766   77.143   78.000
LGA    Q    75_A      Q    75_A     1.337     0    0.024   0.051     1.555   81.429   80.476
LGA    L    76_A      L    76_A     1.697     0    0.028   0.104     2.210   72.857   71.845
LGA    Q    77_A      Q    77_A     1.740     0    0.106   0.192     3.258   72.857   65.026
LGA    A    78_A      A    78_A     1.189     0    0.016   0.027     1.345   81.429   81.429
LGA    I    79_A      I    79_A     1.395     0    0.010   0.060     1.447   81.429   81.429
LGA    V    80_A      V    80_A     1.678     0    0.037   0.071     2.231   72.857   70.544
LGA    D    81_A      D    81_A     1.735     0    0.063   0.131     2.345   72.857   71.845
LGA    V    82_A      V    82_A     1.449     0    0.085   0.849     2.724   79.286   78.027
LGA    L    83_A      L    83_A     1.550     0    0.140   0.158     1.606   75.000   73.929
LGA    A    84_A      A    84_A     2.194     0    0.111   0.118     2.362   64.762   64.762
LGA    V    85_A      V    85_A     2.512     0    0.292   1.337     4.921   60.952   61.769

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     3.356          3.268                  3.493           61.661   59.939

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     55    2.33    70.312    65.672     2.267

LGA_LOCAL      RMSD:   2.326  Number of atoms:   55  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.503  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.356  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.387239 * X  +   0.865576 * Y  +  -0.317528 * Z  +  23.240698
  Y_new =   0.404545 * X  +  -0.149957 * Y  +  -0.902140 * Z  + -23.000044
  Z_new =  -0.828486 * X  +  -0.477798 * Y  +  -0.292095 * Z  + -12.583398 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.334342  0.976399 -2.119510   [DEG:  133.7479   55.9436 -121.4390 ]
ZXZ: -0.338430  1.867213 -2.093916   [DEG:  -19.3906  106.9834 -119.9726 ]
 
# END of job
