
#######################################################
#                                                     #
#                        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        1.39     1.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.39     1.39
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    63      23_A - 85_A        0.88     1.41
  LCS_AVERAGE:     96.97

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   64   64      3    3    3    3    4    4    8    8   48   52   58   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     63   64   64      3    4    5   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     63   64   64      3    4    5   23   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     63   64   64      3   14   20   29   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     63   64   64     35   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     63   64   64     34   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     63   64   64     35   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     63   64   64     21   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     63   64   64     48   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     63   64   64     20   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     63   64   64     46   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     63   64   64     15   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     63   64   64     13   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     63   64   64     12   41   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     63   64   64     13   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     63   64   64     49   59   60   61   61   62   63   63   63   63   63   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  98.99  (  96.97  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     49     59     60     61     61     62     63     63     63     63     63     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  76.56  92.19  93.75  95.31  95.31  96.88  98.44  98.44  98.44  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.41   0.43   0.64   0.60   0.78   0.88   0.88   0.88   0.88   0.88   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39
GDT RMS_ALL_AT   1.44   1.43   1.43   1.41   1.45   1.40   1.41   1.41   1.41   1.41   1.41   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39   1.39

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     8.855     0    0.634   0.582    10.173    8.571    6.857
LGA    D    23_A      D    23_A     3.635     0    0.498   0.418     5.023   39.167   41.429
LGA    G    24_A      G    24_A     3.453     0    0.269   0.269     3.453   57.381   57.381
LGA    D    25_A      D    25_A     3.225     0    0.431   1.009     5.149   45.833   39.405
LGA    G    26_A      G    26_A     0.324     0    0.052   0.052     0.724   97.619   97.619
LGA    Q    27_A      Q    27_A     0.280     0    0.031   0.692     1.894  100.000   94.921
LGA    G    28_A      G    28_A     0.199     0    0.034   0.034     0.294  100.000  100.000
LGA    L    29_A      L    29_A     0.260     0    0.031   0.078     0.416  100.000  100.000
LGA    Y    30_A      Y    30_A     0.292     0    0.021   0.078     0.381  100.000  100.000
LGA    A    31_A      A    31_A     0.306     0    0.033   0.039     0.335  100.000  100.000
LGA    A    32_A      A    32_A     0.217     0    0.018   0.030     0.301  100.000  100.000
LGA    N    33_A      N    33_A     0.298     0    0.013   0.077     0.421  100.000  100.000
LGA    C    34_A      C    34_A     0.342     0    0.038   0.090     0.462  100.000  100.000
LGA    A    35_A      A    35_A     0.502     0    0.017   0.021     0.800   92.857   94.286
LGA    A    36_A      A    36_A     0.615     0    0.016   0.024     0.853   90.476   90.476
LGA    C    37_A      C    37_A     0.638     0    0.017   0.056     0.829   90.476   90.476
LGA    H    38_A      H    38_A     0.551     0    0.010   0.130     0.797   90.476   92.381
LGA    G    39_A      G    39_A     0.757     0    0.068   0.068     0.757   95.238   95.238
LGA    A    40_A      A    40_A     0.403     0    0.033   0.036     0.601  100.000   98.095
LGA    L    41_A      L    41_A     0.403     0    0.015   0.027     0.524   97.619   98.810
LGA    A    42_A      A    42_A     0.605     0    0.036   0.043     0.654   90.476   90.476
LGA    T    43_A      T    43_A     0.587     0    0.132   0.110     0.882   90.476   90.476
LGA    S    44_A      S    44_A     0.671     0    0.059   0.077     0.671   92.857   92.063
LGA    E    45_A      E    45_A     0.992     0    0.019   0.647     4.033   90.476   67.143
LGA    K    46_A      K    46_A     0.272     0    0.095   0.220     1.758   95.238   90.688
LGA    K    47_A      K    47_A     0.293     0    0.017   0.162     0.551  100.000   98.942
LGA    G    48_A      G    48_A     0.292     0    0.046   0.046     0.346  100.000  100.000
LGA    T    49_A      T    49_A     0.297     0    0.080   0.106     0.410  100.000  100.000
LGA    T    50_A      T    50_A     0.302     0    0.017   0.077     0.753  100.000   95.918
LGA    L    51_A      L    51_A     0.269     0    0.030   0.089     0.813  100.000   98.810
LGA    A    52_A      A    52_A     0.399     0    0.015   0.020     0.556  100.000   98.095
LGA    R    53_A      R    53_A     0.366     0    0.018   0.430     1.878  100.000   90.693
LGA    L    54_A      L    54_A     0.230     0    0.050   0.080     0.409  100.000  100.000
LGA    Q    55_A      Q    55_A     0.238     0    0.040   0.223     0.541  100.000   98.942
LGA    S    56_A      S    56_A     0.364     0    0.033   0.035     0.540  100.000   98.413
LGA    A    57_A      A    57_A     0.165     0    0.015   0.021     0.258  100.000  100.000
LGA    V    58_A      V    58_A     0.333     0    0.027   0.037     0.601  100.000   98.639
LGA    S    59_A      S    59_A     0.269     0    0.014   0.739     2.213  100.000   94.127
LGA    A    60_A      A    60_A     0.157     0    0.014   0.034     0.325  100.000  100.000
LGA    N    61_A      N    61_A     0.400     0    0.037   0.172     1.300  100.000   94.107
LGA    A    62_A      A    62_A     0.177     0    0.012   0.020     0.456  100.000  100.000
LGA    G    63_A      G    63_A     0.241     0    0.050   0.050     0.826   95.238   95.238
LGA    G    64_A      G    64_A     0.764     0    0.052   0.052     0.859   90.476   90.476
LGA    M    65_A      M    65_A     0.783     0    0.038   0.191     0.884   90.476   90.476
LGA    G    66_A      G    66_A     0.611     0    0.014   0.014     0.753   90.476   90.476
LGA    F    67_A      F    67_A     1.254     0    0.047   0.164     2.237   81.429   75.281
LGA    L    68_A      L    68_A     1.042     0    0.064   0.088     1.701   85.952   81.548
LGA    S    69_A      S    69_A     0.419     0    0.029   0.052     0.733   95.238   95.238
LGA    S    70_A      S    70_A     0.620     0    0.011   0.012     0.837   92.857   92.063
LGA    L    71_A      L    71_A     0.535     0    0.027   0.069     0.678   90.476   90.476
LGA    T    72_A      T    72_A     0.595     0    0.042   0.051     0.779   95.238   93.197
LGA    S    73_A      S    73_A     0.335     0    0.019   0.619     2.466  100.000   94.127
LGA    A    74_A      A    74_A     0.097     0    0.049   0.062     0.220  100.000  100.000
LGA    Q    75_A      Q    75_A     0.325     0    0.023   0.063     0.697  100.000   96.825
LGA    L    76_A      L    76_A     0.211     0    0.006   0.056     0.397  100.000  100.000
LGA    Q    77_A      Q    77_A     0.331     0    0.076   0.172     0.589  100.000   98.942
LGA    A    78_A      A    78_A     0.380     0    0.025   0.032     0.398  100.000  100.000
LGA    I    79_A      I    79_A     0.223     0    0.026   0.048     0.302  100.000  100.000
LGA    V    80_A      V    80_A     0.221     0    0.020   0.056     0.314  100.000  100.000
LGA    D    81_A      D    81_A     0.351     0    0.060   0.076     0.933  100.000   95.238
LGA    V    82_A      V    82_A     0.368     0    0.029   1.248     2.634  100.000   87.483
LGA    L    83_A      L    83_A     0.324     0    0.071   0.072     0.475  100.000  100.000
LGA    A    84_A      A    84_A     0.442     0    0.122   0.139     0.714   97.619   98.095
LGA    V    85_A      V    85_A     0.444     0    0.234   1.304     2.745   95.357   86.190

# 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):     1.385          1.295                  1.415           93.220   91.348

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    0.88    96.484    97.711     6.418

LGA_LOCAL      RMSD:   0.882  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.411  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.385  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.358662 * X  +   0.725565 * Y  +  -0.587297 * Z  +  22.402449
  Y_new =   0.688274 * X  +   0.219462 * Y  +   0.691459 * Z  +  -9.982608
  Z_new =   0.630587 * X  +  -0.652221 * Y  +  -0.420675 * Z  + -10.712841 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.090409 -0.682310 -2.143640   [DEG:   62.4758  -39.0935 -122.8215 ]
ZXZ: -2.437471  2.004985  2.373057   [DEG: -139.6568  114.8772  135.9662 ]
 
# END of job
