
#######################################################
#                                                     #
#                        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        3.82     3.82
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      47_A - 66_A        1.95     6.82
  LONGEST_CONTINUOUS_SEGMENT:    20      48_A - 67_A        2.00     5.96
  LONGEST_CONTINUOUS_SEGMENT:    20      61_A - 80_A        2.00     4.38
  LONGEST_CONTINUOUS_SEGMENT:    20      62_A - 81_A        1.98     4.32
  LCS_AVERAGE:     28.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      25_A - 40_A        0.72     5.05
  LONGEST_CONTINUOUS_SEGMENT:    16      69_A - 84_A        0.95     4.62
  LCS_AVERAGE:     19.80

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      4    5   64      3    4    4    5    8    8   21   23   25   29   32   39   49   58   61   62   63   64   64   64 
LCS_GDT     D    23_A     D    23_A      4    5   64      3    4    4    9   18   27   30   40   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    24_A     G    24_A      4   19   64      3    6   16   28   35   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     D    25_A     D    25_A     16   19   64      3    7   17   33   38   44   47   51   54   57   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    26_A     G    26_A     16   19   64      9   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    28_A     G    28_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    29_A     L    29_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    31_A     A    31_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    32_A     A    32_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     N    33_A     N    33_A     16   19   64     12   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     C    34_A     C    34_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    35_A     A    35_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    36_A     A    36_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     C    37_A     C    37_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     H    38_A     H    38_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    39_A     G    39_A     16   19   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    40_A     A    40_A     16   19   64      3   24   28   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    41_A     L    41_A      5   19   64      3    4    6   13   25   40   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    42_A     A    42_A      5   19   64      3    5    6    8   11   22   33   37   55   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     T    43_A     T    43_A      5    7   64      3    5    6   16   19   31   44   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     S    44_A     S    44_A      5    7   64      3   10   14   16   18   20   23   31   41   52   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     E    45_A     E    45_A      5    7   64      3    7    9   11   16   17   19   21   28   34   52   60   62   63   63   63   63   64   64   64 
LCS_GDT     K    46_A     K    46_A      5   18   64      3    8   10   13   16   20   23   32   45   55   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     K    47_A     K    47_A      4   20   64      3    3    5    6    6   17   34   49   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    48_A     G    48_A      4   20   64      3    4    5    6    7   26   37   51   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     T    49_A     T    49_A     13   20   64      4    7   10   13   16   20   23   32   48   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     T    50_A     T    50_A     14   20   64      4   11   14   16   19   37   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    51_A     L    51_A     14   20   64      6   11   14   16   37   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    52_A     A    52_A     14   20   64      6   11   26   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     R    53_A     R    53_A     14   20   64      6   11   17   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    54_A     L    54_A     14   20   64      6   11   14   20   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     14   20   64      6   11   14   27   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     S    56_A     S    56_A     14   20   64      6   11   25   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    57_A     A    57_A     14   20   64      5   11   25   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     V    58_A     V    58_A     14   20   64      5   11   14   21   36   43   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     S    59_A     S    59_A     14   20   64      4   11   14   17   31   43   46   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    60_A     A    60_A     14   20   64      4   11   14   16   31   43   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     N    61_A     N    61_A     14   20   64      4   11   18   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    62_A     A    62_A     14   20   64      3   21   28   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    63_A     G    63_A     14   20   64      3   25   28   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    64_A     G    64_A      6   20   64      3    4   22   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     M    65_A     M    65_A      6   20   64      3   13   28   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     G    66_A     G    66_A      6   20   64      3    5   14   29   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     F    67_A     F    67_A      3   20   64      3    3    4   13   27   42   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    68_A     L    68_A      4   20   64      4    4   12   15   19   27   41   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     S    69_A     S    69_A     16   20   64      4   16   29   31   36   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     S    70_A     S    70_A     16   20   64      4    7   21   33   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    71_A     L    71_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     T    72_A     T    72_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     S    73_A     S    73_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    74_A     A    74_A     16   20   64      9   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     16   20   64     15   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    76_A     L    76_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    78_A     A    78_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     I    79_A     I    79_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     V    80_A     V    80_A     16   20   64     18   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     D    81_A     D    81_A     16   20   64      6   26   29   34   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     V    82_A     V    82_A     16   19   64      6   16   29   33   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     L    83_A     L    83_A     16   19   64      7   23   29   33   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     A    84_A     A    84_A     16   19   64      7   26   29   33   38   44   49   52   56   58   60   61   62   63   63   63   63   64   64   64 
LCS_GDT     V    85_A     V    85_A     15   19   64      0    6   12   16   31   33   41   49   54   55   59   61   62   63   63   63   63   64   64   64 
LCS_AVERAGE  LCS_A:  49.58  (  19.80   28.96  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     18     26     29     34     38     44     49     52     56     58     60     61     62     63     63     63     63     64     64     64 
GDT PERCENT_AT  28.12  40.62  45.31  53.12  59.38  68.75  76.56  81.25  87.50  90.62  93.75  95.31  96.88  98.44  98.44  98.44  98.44 100.00 100.00 100.00
GDT RMS_LOCAL    0.35   0.55   0.73   1.19   1.33   1.66   2.17   2.27   2.86   3.04   3.21   3.21   3.34   3.50   3.50   3.50   3.50   3.82   3.82   3.82
GDT RMS_ALL_AT   4.49   4.53   4.59   4.42   4.41   4.37   4.14   4.16   3.90   3.86   3.86   3.87   3.84   3.84   3.84   3.84   3.84   3.82   3.82   3.82

# 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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A    14.304     0    0.033   0.051    15.708    0.000    0.000
LGA    D    23_A      D    23_A     7.934     0    0.597   0.682    10.096   11.429   15.714
LGA    G    24_A      G    24_A     3.975     0    0.503   0.503     5.487   48.095   48.095
LGA    D    25_A      D    25_A     3.166     0    0.699   1.225     8.271   59.286   34.226
LGA    G    26_A      G    26_A     2.017     0    0.116   0.116     2.470   73.095   73.095
LGA    Q    27_A      Q    27_A     1.127     0    0.077   0.964     3.143   85.952   76.190
LGA    G    28_A      G    28_A     0.740     0    0.039   0.039     0.952   92.857   92.857
LGA    L    29_A      L    29_A     0.815     0    0.029   1.156     3.706   90.476   80.119
LGA    Y    30_A      Y    30_A     0.498     0    0.089   0.481     2.960   97.619   84.286
LGA    A    31_A      A    31_A     0.209     0    0.040   0.049     0.506   97.619   98.095
LGA    A    32_A      A    32_A     0.751     0    0.118   0.115     1.435   88.214   88.667
LGA    N    33_A      N    33_A     1.339     0    0.183   0.334     2.662   75.476   75.238
LGA    C    34_A      C    34_A     0.920     0    0.043   0.148     1.141   88.214   88.968
LGA    A    35_A      A    35_A     1.036     0    0.039   0.038     1.116   85.952   85.048
LGA    A    36_A      A    36_A     1.011     0    0.106   0.104     1.170   85.952   85.048
LGA    C    37_A      C    37_A     1.345     0    0.156   0.157     1.777   79.286   80.000
LGA    H    38_A      H    38_A     1.274     0    0.218   0.171     2.026   77.262   75.524
LGA    G    39_A      G    39_A     1.222     0    0.132   0.132     1.251   85.952   85.952
LGA    A    40_A      A    40_A     1.334     0    0.547   0.573     1.876   79.405   78.095
LGA    L    41_A      L    41_A     4.716     0    0.551   1.498     6.083   26.786   27.321
LGA    A    42_A      A    42_A     7.998     0    0.672   0.634    10.453   11.905    9.524
LGA    T    43_A      T    43_A     7.341     0    0.521   0.546     9.805    7.262    6.327
LGA    S    44_A      S    44_A     9.677     0    0.162   0.210    10.596    2.381    1.667
LGA    E    45_A      E    45_A    10.421     0    0.266   0.970    15.886    0.714    0.317
LGA    K    46_A      K    46_A     7.889     0    0.174   0.913    15.218   11.190    4.974
LGA    K    47_A      K    47_A     7.614     0    0.445   1.033    13.632   11.071    5.767
LGA    G    48_A      G    48_A     7.373     0    0.578   0.578     7.819   23.333   23.333
LGA    T    49_A      T    49_A     6.863     0    0.568   1.337    11.495   19.048   11.020
LGA    T    50_A      T    50_A     4.056     0    0.087   0.200     5.166   37.500   37.415
LGA    L    51_A      L    51_A     2.592     0    0.076   1.005     5.656   60.952   50.536
LGA    A    52_A      A    52_A     1.415     0    0.042   0.048     1.860   79.286   79.714
LGA    R    53_A      R    53_A     1.807     0    0.058   1.547     6.175   70.833   57.489
LGA    L    54_A      L    54_A     2.828     0    0.043   1.157     7.719   59.048   42.024
LGA    Q    55_A      Q    55_A     2.462     0    0.042   0.710     2.462   64.762   79.365
LGA    S    56_A      S    56_A     1.680     0    0.092   0.677     2.085   70.833   72.937
LGA    A    57_A      A    57_A     1.757     0    0.037   0.049     2.554   66.905   68.095
LGA    V    58_A      V    58_A     3.533     0    0.034   1.156     6.396   45.238   40.680
LGA    S    59_A      S    59_A     3.915     0    0.091   0.734     6.140   40.357   36.984
LGA    A    60_A      A    60_A     3.446     0    0.731   0.694     5.984   41.190   44.381
LGA    N    61_A      N    61_A     2.215     0    0.599   1.246     3.354   65.119   63.155
LGA    A    62_A      A    62_A     0.944     0    0.115   0.110     1.601   83.810   83.333
LGA    G    63_A      G    63_A     0.873     0    0.709   0.709     2.371   84.048   84.048
LGA    G    64_A      G    64_A     2.517     0    0.247   0.247     2.517   64.881   64.881
LGA    M    65_A      M    65_A     2.098     0    0.655   1.175     4.182   59.405   58.869
LGA    G    66_A      G    66_A     2.652     0    0.661   0.661     2.652   62.857   62.857
LGA    F    67_A      F    67_A     3.841     0    0.384   1.084     5.463   40.357   47.446
LGA    L    68_A      L    68_A     4.354     0    0.303   1.000    10.404   45.119   25.298
LGA    S    69_A      S    69_A     3.083     0    0.121   0.632     3.766   53.810   53.889
LGA    S    70_A      S    70_A     2.526     0    0.128   0.655     3.224   62.976   59.841
LGA    L    71_A      L    71_A     1.134     0    0.069   0.096     1.698   79.286   84.881
LGA    T    72_A      T    72_A     1.519     0    0.061   1.144     3.084   75.000   73.265
LGA    S    73_A      S    73_A     2.114     0    0.065   0.607     3.931   68.810   63.889
LGA    A    74_A      A    74_A     1.707     0    0.048   0.047     1.764   72.857   72.857
LGA    Q    75_A      Q    75_A     1.234     0    0.043   0.089     1.333   81.429   82.434
LGA    L    76_A      L    76_A     1.537     0    0.033   0.065     1.800   75.000   73.929
LGA    Q    77_A      Q    77_A     1.539     0    0.039   1.117     3.450   75.000   74.127
LGA    A    78_A      A    78_A     1.367     0    0.041   0.042     1.405   81.429   81.429
LGA    I    79_A      I    79_A     1.385     0    0.048   0.113     1.618   77.143   79.286
LGA    V    80_A      V    80_A     1.725     0    0.053   0.107     1.941   75.000   74.082
LGA    D    81_A      D    81_A     1.627     0    0.043   0.193     2.312   68.810   69.821
LGA    V    82_A      V    82_A     2.670     0    0.028   1.015     3.370   57.262   57.279
LGA    L    83_A      L    83_A     3.007     0    0.124   0.160     3.952   55.357   51.071
LGA    A    84_A      A    84_A     2.272     0    0.111   0.107     3.273   55.476   58.952
LGA    V    85_A      V    85_A     4.559     0    0.616   1.164     7.196   43.690   31.361

# 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):     3.819          3.655                  4.352           59.635   57.459

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     52    2.27    68.359    61.625     2.198

LGA_LOCAL      RMSD:   2.265  Number of atoms:   52  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.159  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.819  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.947281 * X  +   0.235921 * Y  +   0.216793 * Z  +  -0.430701
  Y_new =   0.146561 * X  +   0.282631 * Y  +  -0.947966 * Z  + -38.528133
  Z_new =  -0.284917 * X  +   0.929764 * Y  +   0.233154 * Z  + -43.159771 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.153500  0.288920  1.325096   [DEG:    8.7949   16.5539   75.9224 ]
ZXZ:  0.224827  1.335476 -0.297355   [DEG:   12.8816   76.5172  -17.0372 ]
 
# END of job
