
#######################################################
#                                                     #
#                        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        1.38     1.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    64      22_A - 85_A        1.38     1.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62      23_A - 84_A        0.95     1.41
  LONGEST_CONTINUOUS_SEGMENT:    62      24_A - 85_A        0.94     1.42
  LCS_AVERAGE:     95.43

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    3    4    7   16   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A     62   64   64      3    3    8   16   32   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A     62   64   64      3    3    4    7   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     62   64   64      3    5   15   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     62   64   64     30   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     62   64   64     28   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     62   64   64     28   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     62   64   64     28   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     62   64   64     19   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A     62   64   64     33   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A     62   64   64     25   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A     62   64   64     33   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     62   64   64     26   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     62   64   64     17   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     62   64   64     34   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     62   64   64     28   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     62   64   64     15   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A     62   64   64     33   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     62   64   64     13   29   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     62   64   64     15   33   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     62   64   64     17   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     62   64   64     35   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     62   64   64     25   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     62   64   64     13   57   59   59   61   62   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     62   64   64      3    3    3    3   35   60   62   63   63   64   64   64   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  98.48  (  95.43  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     35     57     59     59     61     62     62     63     63     64     64     64     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  54.69  89.06  92.19  92.19  95.31  96.88  96.88  98.44  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.52   0.56   0.56   0.78   0.95   0.95   1.09   1.09   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38
GDT RMS_ALL_AT   1.43   1.42   1.43   1.43   1.42   1.41   1.41   1.40   1.40   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38

# Checking swapping
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     7.075     0    0.042   0.040     9.068   20.833   16.952
LGA    D    23_A      D    23_A     4.289     0    0.087   0.084     9.626   39.167   23.929
LGA    G    24_A      G    24_A     3.118     0    0.596   0.596     3.118   57.262   57.262
LGA    D    25_A      D    25_A     2.724     0    0.596   1.228     4.855   50.714   47.143
LGA    G    26_A      G    26_A     0.364     0    0.070   0.070     0.515   97.619   97.619
LGA    Q    27_A      Q    27_A     0.386     0    0.014   1.425     5.785  100.000   77.037
LGA    G    28_A      G    28_A     0.385     0    0.012   0.012     0.418  100.000  100.000
LGA    L    29_A      L    29_A     0.155     0    0.015   1.250     2.675  100.000   90.238
LGA    Y    30_A      Y    30_A     0.165     0    0.026   0.111     0.270  100.000  100.000
LGA    A    31_A      A    31_A     0.296     0    0.019   0.022     0.576   97.619   98.095
LGA    A    32_A      A    32_A     0.443     0    0.008   0.013     0.491  100.000  100.000
LGA    N    33_A      N    33_A     0.251     0    0.013   0.085     0.393  100.000  100.000
LGA    C    34_A      C    34_A     0.295     0    0.012   0.074     0.457  100.000  100.000
LGA    A    35_A      A    35_A     0.603     0    0.036   0.042     1.035   90.595   90.571
LGA    A    36_A      A    36_A     0.906     0    0.010   0.009     1.156   88.214   88.667
LGA    C    37_A      C    37_A     0.919     0    0.014   0.021     1.070   88.214   88.968
LGA    H    38_A      H    38_A     0.896     0    0.035   0.225     1.314   88.214   87.762
LGA    G    39_A      G    39_A     0.938     0    0.074   0.074     0.963   90.476   90.476
LGA    A    40_A      A    40_A     0.319     0    0.018   0.024     0.583  100.000   98.095
LGA    L    41_A      L    41_A     0.555     0    0.034   0.050     1.000   92.857   91.667
LGA    A    42_A      A    42_A     0.727     0    0.012   0.015     0.765   90.476   90.476
LGA    T    43_A      T    43_A     0.523     0    0.102   0.089     0.767   90.476   94.558
LGA    S    44_A      S    44_A     0.673     0    0.019   0.030     0.786   92.857   92.063
LGA    E    45_A      E    45_A     1.036     0    0.062   0.776     4.451   88.214   66.825
LGA    K    46_A      K    46_A     0.212     0    0.088   0.578     3.349   97.619   88.148
LGA    K    47_A      K    47_A     0.378     0    0.011   0.086     1.183  100.000   93.757
LGA    G    48_A      G    48_A     0.390     0    0.117   0.117     0.738   97.619   97.619
LGA    T    49_A      T    49_A     0.402     0    0.051   0.090     0.537  100.000   98.639
LGA    T    50_A      T    50_A     0.518     0    0.034   0.106     1.160   95.238   91.905
LGA    L    51_A      L    51_A     0.261     0    0.013   0.072     0.517  100.000   98.810
LGA    A    52_A      A    52_A     0.407     0    0.004   0.004     0.553  100.000   98.095
LGA    R    53_A      R    53_A     0.673     0    0.008   0.993     4.810   90.476   77.403
LGA    L    54_A      L    54_A     0.519     0    0.013   0.118     0.700   90.476   94.048
LGA    Q    55_A      Q    55_A     0.579     0    0.023   0.231     0.695   90.476   93.651
LGA    S    56_A      S    56_A     0.697     0    0.021   0.638     2.731   90.476   84.921
LGA    A    57_A      A    57_A     0.536     0    0.025   0.028     0.640   92.857   94.286
LGA    V    58_A      V    58_A     0.622     0    0.019   1.336     3.074   92.857   82.381
LGA    S    59_A      S    59_A     0.611     0    0.016   0.529     2.382   90.476   86.190
LGA    A    60_A      A    60_A     0.621     0    0.018   0.024     0.821   92.857   92.381
LGA    N    61_A      N    61_A     0.463     0    0.061   0.153     1.386  100.000   94.107
LGA    A    62_A      A    62_A     0.516     0    0.025   0.033     0.572   90.476   92.381
LGA    G    63_A      G    63_A     0.760     0    0.039   0.039     1.045   88.214   88.214
LGA    G    64_A      G    64_A     0.882     0    0.051   0.051     1.049   88.214   88.214
LGA    M    65_A      M    65_A     0.619     0    0.029   0.171     0.899   90.476   91.667
LGA    G    66_A      G    66_A     0.692     0    0.008   0.008     0.935   90.476   90.476
LGA    F    67_A      F    67_A     1.500     0    0.039   0.207     2.377   79.286   75.281
LGA    L    68_A      L    68_A     1.409     0    0.087   1.246     4.080   81.429   71.667
LGA    S    69_A      S    69_A     0.811     0    0.038   0.043     1.038   88.214   88.968
LGA    S    70_A      S    70_A     0.374     0    0.013   0.037     0.572   97.619   95.238
LGA    L    71_A      L    71_A     0.547     0    0.032   1.232     3.050   97.619   85.774
LGA    T    72_A      T    72_A     0.348     0    0.013   0.047     0.570  100.000   98.639
LGA    S    73_A      S    73_A     0.189     0    0.011   0.033     0.505  100.000   98.413
LGA    A    74_A      A    74_A     0.421     0    0.011   0.012     0.593  100.000   98.095
LGA    Q    75_A      Q    75_A     0.337     0    0.023   0.146     0.760  100.000   97.884
LGA    L    76_A      L    76_A     0.208     0    0.012   1.238     2.525  100.000   90.238
LGA    Q    77_A      Q    77_A     0.171     0    0.010   0.162     0.478  100.000  100.000
LGA    A    78_A      A    78_A     0.119     0    0.008   0.009     0.144  100.000  100.000
LGA    I    79_A      I    79_A     0.116     0    0.012   0.036     0.268  100.000  100.000
LGA    V    80_A      V    80_A     0.289     0    0.041   1.341     2.548  100.000   88.844
LGA    D    81_A      D    81_A     0.368     0    0.010   0.033     0.922  100.000   95.238
LGA    V    82_A      V    82_A     0.377     0    0.083   1.255     2.766   97.619   86.122
LGA    L    83_A      L    83_A     0.690     0    0.171   1.221     2.881   88.452   83.274
LGA    A    84_A      A    84_A     0.745     0    0.061   0.068     2.325   82.024   83.714
LGA    V    85_A      V    85_A     4.232     0    0.486   0.803     6.715   33.452   28.503

# 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):     1.380          1.361                  1.742           90.294   87.056

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     63    1.09    94.922    97.170     5.297

LGA_LOCAL      RMSD:   1.089  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.396  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   1.380  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.302290 * X  +  -0.313995 * Y  +  -0.900015 * Z  +  25.019779
  Y_new =   0.898150 * X  +   0.222443 * Y  +  -0.379269 * Z  + -12.094118
  Z_new =   0.319291 * X  +  -0.922999 * Y  +   0.214772 * Z  + -15.648028 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.895457 -0.324981 -1.342175   [DEG:  108.6017  -18.6200  -76.9010 ]
ZXZ: -1.171976  1.354338  2.808550   [DEG:  -67.1493   77.5978  160.9181 ]
 
# END of job
