
#######################################################
#                                                     #
#                        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        3.43     3.43
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      43_A - 67_A        1.98     6.01
  LONGEST_CONTINUOUS_SEGMENT:    25      44_A - 68_A        1.97     6.11
  LCS_AVERAGE:     34.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      44_A - 63_A        0.92     6.51
  LCS_AVERAGE:     25.46

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    4    4    4    4    6    7   10   12   14   14   44   57   62   63   63   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      1   11   16   20   24   30   35   46   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   18   64      3    4   17   28   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     D    25_A     D    25_A     15   18   64      3    3    9   31   36   42   49   53   56   57   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    26_A     G    26_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    28_A     G    28_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    29_A     L    29_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    31_A     A    31_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    32_A     A    32_A     15   18   64     15   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     N    33_A     N    33_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     C    34_A     C    34_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    35_A     A    35_A     15   18   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    36_A     A    36_A     15   18   64     12   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     C    37_A     C    37_A     15   18   64     13   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     H    38_A     H    38_A     15   18   64     10   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    39_A     G    39_A     15   18   64     15   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    40_A     A    40_A     15   24   64      3    4   21   32   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    41_A     L    41_A      5   24   64      3    4    8   18   34   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    42_A     A    42_A      5   24   64      3    4    6   12   21   31   38   49   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     T    43_A     T    43_A      5   25   64      3    4    8   18   33   39   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     S    44_A     S    44_A     20   25   64      3    4   15   19   21   25   29   39   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     E    45_A     E    45_A     20   25   64      8   17   19   20   22   28   49   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     K    46_A     K    46_A     20   25   64      7   17   19   20   25   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     K    47_A     K    47_A     20   25   64      4   17   19   20   23   27   35   46   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    48_A     G    48_A     20   25   64      4   17   19   20   23   28   41   54   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     T    49_A     T    49_A     20   25   64      8   17   19   20   25   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     T    50_A     T    50_A     20   25   64     13   17   19   20   25   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    51_A     L    51_A     20   25   64     13   17   19   24   27   37   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    52_A     A    52_A     20   25   64     13   17   20   26   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     R    53_A     R    53_A     20   25   64     13   17   20   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    54_A     L    54_A     20   25   64     13   17   20   24   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     20   25   64     13   17   20   24   36   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     S    56_A     S    56_A     20   25   64     13   17   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    57_A     A    57_A     20   25   64     13   17   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     V    58_A     V    58_A     20   25   64     13   17   19   21   36   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     S    59_A     S    59_A     20   25   64     13   17   19   20   35   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    60_A     A    60_A     20   25   64     13   17   19   20   35   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     N    61_A     N    61_A     20   25   64     13   17   19   20   35   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    62_A     A    62_A     20   25   64     13   17   19   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    63_A     G    63_A     20   25   64      4   24   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    64_A     G    64_A     17   25   64      4    5   13   26   37   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     M    65_A     M    65_A     16   25   64      4    5   14   26   38   43   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     G    66_A     G    66_A      5   25   64      4    5    5    9   11   25   37   48   51   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     F    67_A     F    67_A     17   25   64      4   14   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    68_A     L    68_A     18   25   64      4   22   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     S    69_A     S    69_A     18   24   64     12   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     S    70_A     S    70_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    71_A     L    71_A     18   24   64      7   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     T    72_A     T    72_A     18   24   64     10   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     S    73_A     S    73_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    74_A     A    74_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    76_A     L    76_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    78_A     A    78_A     18   24   64     16   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     I    79_A     I    79_A     18   24   64     14   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     V    80_A     V    80_A     18   24   64      9   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     D    81_A     D    81_A     18   24   64      9   27   29   34   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     V    82_A     V    82_A     18   24   64      9   20   27   33   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     L    83_A     L    83_A     18   24   64      9   20   26   33   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     A    84_A     A    84_A     18   24   64      9   20   27   33   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_GDT     V    85_A     V    85_A     18   24   64      3   20   26   33   38   44   52   56   59   61   62   63   63   63   63   63   63   64   64   64 
LCS_AVERAGE  LCS_A:  53.43  (  25.46   34.81  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     16     27     29     34     38     44     52     56     59     61     62     63     63     63     63     63     63     64     64     64 
GDT PERCENT_AT  25.00  42.19  45.31  53.12  59.38  68.75  81.25  87.50  92.19  95.31  96.88  98.44  98.44  98.44  98.44  98.44  98.44 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.57   0.75   1.06   1.34   1.85   2.26   2.51   2.80   2.97   2.99   3.09   3.09   3.09   3.09   3.09   3.09   3.43   3.43   3.43
GDT RMS_ALL_AT   4.01   4.02   4.02   4.11   3.89   3.71   3.68   3.57   3.47   3.44   3.48   3.45   3.45   3.45   3.45   3.45   3.45   3.43   3.43   3.43

# 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    13.682     0    0.423   0.439    14.713    0.000    0.000
LGA    D    23_A      D    23_A     7.460     0    0.684   0.685     9.298   14.762   14.226
LGA    G    24_A      G    24_A     2.621     0    0.447   0.447     4.493   54.762   54.762
LGA    D    25_A      D    25_A     4.058     0    0.223   1.081     8.581   43.690   25.595
LGA    G    26_A      G    26_A     1.182     0    0.180   0.180     1.606   79.286   79.286
LGA    Q    27_A      Q    27_A     1.254     0    0.071   1.047     5.494   79.286   59.947
LGA    G    28_A      G    28_A     1.660     0    0.071   0.071     1.660   79.286   79.286
LGA    L    29_A      L    29_A     1.346     0    0.012   0.135     1.403   81.429   81.429
LGA    Y    30_A      Y    30_A     1.286     0    0.062   0.237     1.731   81.429   78.571
LGA    A    31_A      A    31_A     1.385     0    0.014   0.014     1.473   81.429   81.429
LGA    A    32_A      A    32_A     1.454     0    0.032   0.034     1.454   81.429   81.429
LGA    N    33_A      N    33_A     1.110     0    0.060   0.137     1.352   81.429   81.429
LGA    C    34_A      C    34_A     1.123     0    0.018   0.148     1.618   81.429   80.000
LGA    A    35_A      A    35_A     1.393     0    0.015   0.016     1.532   79.286   78.000
LGA    A    36_A      A    36_A     1.652     0    0.036   0.035     1.735   72.857   72.857
LGA    C    37_A      C    37_A     1.269     0    0.025   0.089     1.385   81.429   81.429
LGA    H    38_A      H    38_A     1.566     0    0.073   0.995     4.094   75.000   69.810
LGA    G    39_A      G    39_A     1.587     0    0.272   0.272     1.587   77.262   77.262
LGA    A    40_A      A    40_A     1.914     0    0.698   0.635     2.920   75.000   71.429
LGA    L    41_A      L    41_A     3.822     0    0.583   1.510     6.706   45.119   42.619
LGA    A    42_A      A    42_A     6.314     0    0.318   0.310     6.711   24.048   21.905
LGA    T    43_A      T    43_A     4.814     0    0.608   1.332     5.806   28.810   28.571
LGA    S    44_A      S    44_A     6.652     0    0.273   0.371     7.801   16.190   13.651
LGA    E    45_A      E    45_A     5.311     0    0.156   0.774     6.796   29.048   23.016
LGA    K    46_A      K    46_A     3.940     0    0.129   0.137     5.075   31.786   53.175
LGA    K    47_A      K    47_A     6.657     0    0.070   0.817    11.861   17.262    8.836
LGA    G    48_A      G    48_A     6.171     0    0.144   0.144     6.487   24.405   24.405
LGA    T    49_A      T    49_A     3.886     0    0.197   0.972     4.873   40.357   39.048
LGA    T    50_A      T    50_A     3.662     0    0.032   0.055     3.686   45.000   48.163
LGA    L    51_A      L    51_A     3.872     0    0.013   1.370     7.549   46.667   32.202
LGA    A    52_A      A    52_A     2.532     0    0.015   0.016     2.996   60.952   61.714
LGA    R    53_A      R    53_A     1.646     0    0.015   0.618     3.021   72.857   65.758
LGA    L    54_A      L    54_A     2.820     0    0.016   1.397     7.120   57.262   41.488
LGA    Q    55_A      Q    55_A     3.272     0    0.012   0.208     4.971   51.786   47.249
LGA    S    56_A      S    56_A     2.223     0    0.047   0.050     2.547   62.857   66.190
LGA    A    57_A      A    57_A     2.150     0    0.009   0.019     2.817   60.952   61.714
LGA    V    58_A      V    58_A     3.524     0    0.022   0.056     4.363   45.000   43.401
LGA    S    59_A      S    59_A     3.758     0    0.009   0.740     5.971   41.786   38.651
LGA    A    60_A      A    60_A     3.281     0    0.020   0.025     3.376   50.000   51.429
LGA    N    61_A      N    61_A     3.424     0    0.093   0.963     5.942   53.571   42.083
LGA    A    62_A      A    62_A     2.034     0    0.051   0.062     2.626   66.905   68.095
LGA    G    63_A      G    63_A     1.354     0    0.643   0.643     1.529   79.286   79.286
LGA    G    64_A      G    64_A     4.225     0    0.039   0.039     4.732   37.262   37.262
LGA    M    65_A      M    65_A     3.753     0    0.289   0.770     4.050   43.452   52.679
LGA    G    66_A      G    66_A     6.027     0    0.553   0.553     6.027   26.667   26.667
LGA    F    67_A      F    67_A     1.495     0    0.628   1.280     7.192   75.357   50.130
LGA    L    68_A      L    68_A     0.690     0    0.011   0.070     1.620   90.476   84.881
LGA    S    69_A      S    69_A     0.778     0    0.071   0.075     1.143   90.595   90.556
LGA    S    70_A      S    70_A     1.208     0    0.076   0.114     1.966   81.548   81.508
LGA    L    71_A      L    71_A     1.488     0    0.606   1.412     3.907   69.762   70.595
LGA    T    72_A      T    72_A     1.982     0    0.077   0.135     2.265   72.857   69.388
LGA    S    73_A      S    73_A     2.011     0    0.005   0.628     3.597   66.786   62.540
LGA    A    74_A      A    74_A     2.119     0    0.041   0.047     2.286   68.810   68.000
LGA    Q    75_A      Q    75_A     1.437     0    0.082   0.937     3.110   75.000   74.127
LGA    L    76_A      L    76_A     1.656     0    0.071   1.179     3.783   72.857   72.440
LGA    Q    77_A      Q    77_A     1.609     0    0.041   0.193     1.853   72.857   72.857
LGA    A    78_A      A    78_A     1.634     0    0.027   0.034     1.656   72.857   72.857
LGA    I    79_A      I    79_A     1.707     0    0.032   0.126     1.890   72.857   73.929
LGA    V    80_A      V    80_A     2.054     0    0.020   0.070     2.304   68.810   67.075
LGA    D    81_A      D    81_A     1.768     0    0.041   0.085     2.123   70.833   73.988
LGA    V    82_A      V    82_A     2.294     0    0.094   0.874     3.484   64.762   62.721
LGA    L    83_A      L    83_A     2.641     0    0.173   0.281     3.370   60.952   58.155
LGA    A    84_A      A    84_A     2.706     0    0.099   0.105     2.824   57.143   57.143
LGA    V    85_A      V    85_A     2.657     0    0.292   1.336     3.491   57.143   58.367

# 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):     3.434          3.321                  3.654           59.719   57.636

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     56    2.51    70.312    64.522     2.144

LGA_LOCAL      RMSD:   2.511  Number of atoms:   56  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.569  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.434  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.526629 * X  +  -0.752934 * Y  +  -0.394656 * Z  +  25.167883
  Y_new =  -0.672257 * X  +   0.084706 * Y  +   0.735456 * Z  + -19.525526
  Z_new =  -0.520319 * X  +   0.652622 * Y  +  -0.550774 * Z  + -12.546521 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.235317  0.547225  2.271761   [DEG: -128.0742   31.3537  130.1623 ]
ZXZ: -2.649085  2.154087 -0.673077   [DEG: -151.7814  123.4201  -38.5645 ]
 
# END of job
