
#######################################################
#                                                     #
#                        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   71 (  567),  selected   71 , name one
# Molecule2: number of CA atoms  230 ( 1795),  selected   71 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    71      35_B - 105_B       3.83     3.83
  LCS_AVERAGE:     30.87

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    54      52_B - 105_B       1.66     4.40
  LCS_AVERAGE:     18.73

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32      74_B - 105_B       0.99     4.33
  LCS_AVERAGE:     10.66

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   71
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     D    35_B     D    35_B      8   10   71      3    4    7    7    8   11   11   11   13   15   44   48   56   68   70   70   71   71   71   71 
LCS_GDT     V    36_B     V    36_B      8   10   71      5    7    7    8    9   11   11   11   13   15   44   62   65   68   70   70   71   71   71   71 
LCS_GDT     L    37_B     L    37_B      8   10   71      5    7    7    8    9   11   11   11   13   15   44   48   56   68   70   70   71   71   71   71 
LCS_GDT     P    38_B     P    38_B      8   10   71      5    7    7    8    9   11   11   20   26   35   52   63   65   68   70   70   71   71   71   71 
LCS_GDT     L    39_B     L    39_B      8   10   71      5    7    7    8    9   12   17   33   55   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    40_B     L    40_B      8   10   71      5    7    7    8    9   11   11   11   26   48   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     Q    41_B     Q    41_B      8   10   71      5    7    7    8    9   11   17   20   28   51   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     M    42_B     M    42_B      8   10   71      4    7    7    8    9   11   17   34   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E    43_B     E    43_B      5   10   71      3    4    5    8    8   10   10   13   18   38   45   56   64   68   70   70   71   71   71   71 
LCS_GDT     S    44_B     S    44_B      4   10   71      4    4    4    6    7    9   16   33   37   57   60   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    45_B     L    45_B      4    6   71      4    4    4   12   16   20   44   54   54   57   60   64   65   68   70   70   71   71   71   71 
LCS_GDT     M    46_B     M    46_B      4    6   71      4    4    7   29   49   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     T    47_B     T    47_B      4    6   71      4    4    5    5   18   27   46   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     F    48_B     F    48_B      3    6   71      3    3    5    5    8   14   24   54   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E    49_B     E    49_B      4    6   71      3    4    5    9   16   35   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     A    50_B     A    50_B      4    6   71      3    4    5    8    9   11   11   33   54   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     M    51_B     M    51_B      4    6   71      3    4    4    5    5    6    9   11   13   15   16   17   35   60   67   69   71   71   71   71 
LCS_GDT     A    52_B     A    52_B      4   54   71      3    4    4    7    7   11   27   32   54   55   57   61   62   67   70   70   71   71   71   71 
LCS_GDT     Y    53_B     Y    53_B      4   54   71      3    4    4   14   22   44   53   54   55   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    54_B     L    54_B     19   54   71      3   11   45   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    55_B     R    55_B     31   54   71     14   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     C    56_B     C    56_B     31   54   71      3   25   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     D    57_B     D    57_B     31   54   71     12   29   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     A    58_B     A    58_B     31   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    59_B     L    59_B     31   54   71      7   30   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     V    60_B     V    60_B     31   54   71     14   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E    61_B     E    61_B     31   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    62_B     L    62_B     31   54   71     10   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     G    63_B     G    63_B     31   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     C    64_B     C    64_B     31   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     Y    65_B     Y    65_B     31   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     D    66_B     D    66_B     31   54   71     10   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     G    67_B     G    67_B     31   54   71     12   29   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    68_B     R    68_B     31   54   71      3    6    9   32   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     A    69_B     A    69_B     31   54   71      4   22   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    70_B     L    70_B     31   54   71      8   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E    71_B     E    71_B     31   54   71      9   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     I    72_B     I    72_B     31   54   71     12   28   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     A    73_B     A    73_B     31   54   71      4    5   31   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    74_B     R    74_B     32   54   71      4    5    7   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    75_B     L    75_B     32   54   71      4   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    76_B     L    76_B     32   54   71     10   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     N    77_B     N    77_B     32   54   71      8   27   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     A    78_B     A    78_B     32   54   71     12   29   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    79_B     R    79_B     32   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     Y    80_B     Y    80_B     32   54   71     12   27   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    81_B     L    81_B     32   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     G    82_B     G    82_B     32   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     V    83_B     V    83_B     32   54   71     10   30   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     D    84_B     D    84_B     32   54   71     10   27   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    85_B     L    85_B     32   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     D    86_B     D    86_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     Q    87_B     Q    87_B     32   54   71      6   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    88_B     R    88_B     32   54   71      6   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     A    89_B     A    89_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     I    90_B     I    90_B     32   54   71     15   31   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E    91_B     E    91_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     T    92_B     T    92_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     L    93_B     L    93_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    94_B     R    94_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     T    95_B     T    95_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    96_B     R    96_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     I    97_B     I    97_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E    98_B     E    98_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R    99_B     R    99_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     E   100_B     E   100_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     G   101_B     G   101_B     32   54   71     15   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     M   102_B     M   102_B     32   54   71     15   31   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     S   103_B     S   103_B     32   54   71     14   29   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     D   104_B     D   104_B     32   54   71      6   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_GDT     R   105_B     R   105_B     32   54   71     12   32   46   51   52   52   54   55   57   59   61   64   65   68   70   70   71   71   71   71 
LCS_AVERAGE  LCS_A:  20.08  (  10.66   18.73   30.87 )

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     15     32     46     51     52     52     54     55     57     59     61     64     65     68     70     70     71     71     71     71 
GDT PERCENT_AT   6.52  13.91  20.00  22.17  22.61  22.61  23.48  23.91  24.78  25.65  26.52  27.83  28.26  29.57  30.43  30.43  30.87  30.87  30.87  30.87
GDT RMS_LOCAL    0.31   0.76   0.92   1.08   1.16   1.16   1.43   1.59   1.99   2.27   2.55   2.90   3.05   3.40   3.66   3.66   3.83   3.83   3.83   3.83
GDT RMS_ALL_AT   5.05   4.39   4.36   4.31   4.30   4.30   4.19   4.13   4.01   3.95   3.90   3.87   3.85   3.85   3.84   3.84   3.83   3.83   3.83   3.83

# Checking swapping
#   possible swapping detected:  F    48_B      F    48_B
#   possible swapping detected:  Y    53_B      Y    53_B
#   possible swapping detected:  D    57_B      D    57_B
#   possible swapping detected:  Y    65_B      Y    65_B
#   possible swapping detected:  D    66_B      D    66_B
#   possible swapping detected:  E    71_B      E    71_B
#   possible swapping detected:  Y    80_B      Y    80_B
#   possible swapping detected:  D    84_B      D    84_B
#   possible swapping detected:  E    91_B      E    91_B
#   possible swapping detected:  E   100_B      E   100_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    35_B      D    35_B    10.255     0    0.284   0.351    11.140    0.238    0.119
LGA    V    36_B      V    36_B     8.582     0    0.104   1.054    10.440    2.976    3.401
LGA    L    37_B      L    37_B     9.408     0    0.048   0.977    11.241    2.143    2.381
LGA    P    38_B      P    38_B     8.852     0    0.108   0.102    10.431    4.643    2.789
LGA    L    39_B      L    39_B     7.256     0    0.064   1.262     9.611    9.286    8.095
LGA    L    40_B      L    40_B     8.035     0    0.095   1.433    12.827    6.548    3.631
LGA    Q    41_B      Q    41_B     8.251     0    0.028   1.189    13.768    7.381    3.598
LGA    M    42_B      M    42_B     7.328     0    0.570   1.340    14.237   12.857    7.202
LGA    E    43_B      E    43_B     9.866     0    0.605   1.184    18.339    3.214    1.429
LGA    S    44_B      S    44_B     7.855     0    0.558   0.688     8.805    7.262    6.984
LGA    L    45_B      L    45_B     7.330     0    0.122   0.186    11.996   16.548    8.631
LGA    M    46_B      M    46_B     3.801     0    0.079   1.016     9.120   45.119   28.810
LGA    T    47_B      T    47_B     5.233     0    0.510   0.847     9.141   28.929   18.367
LGA    F    48_B      F    48_B     6.473     0    0.073   1.309     7.503   18.214   20.952
LGA    E    49_B      E    49_B     4.567     0    0.631   1.362     5.092   37.976   42.063
LGA    A    50_B      A    50_B     6.505     0    0.160   0.187     8.995   15.238   12.762
LGA    M    51_B      M    51_B     9.741     0    0.042   0.956    16.942    1.667    0.833
LGA    A    52_B      A    52_B     7.954     0    0.578   0.593     7.954    9.405    9.524
LGA    Y    53_B      Y    53_B     5.943     0    0.625   0.913    12.662   29.762   13.175
LGA    L    54_B      L    54_B     1.536     0    0.676   0.964     7.440   73.214   47.857
LGA    R    55_B      R    55_B     1.264     0    0.361   1.144     8.885   73.214   49.481
LGA    C    56_B      C    56_B     1.550     0    0.067   0.845     3.630   86.190   75.476
LGA    D    57_B      D    57_B     1.466     0    0.272   1.020     4.081   81.429   66.845
LGA    A    58_B      A    58_B     0.979     0    0.059   0.063     1.226   83.690   85.048
LGA    L    59_B      L    59_B     1.128     0    0.089   0.124     2.023   85.952   79.464
LGA    V    60_B      V    60_B     0.298     0    0.188   1.112     3.063   95.238   84.898
LGA    E    61_B      E    61_B     0.508     0    0.077   0.899     3.520   90.476   80.794
LGA    L    62_B      L    62_B     1.128     0    0.073   1.016     3.771   83.690   76.726
LGA    G    63_B      G    63_B     1.141     0    0.056   0.056     1.207   81.429   81.429
LGA    C    64_B      C    64_B     0.771     0    0.027   0.084     0.873   90.476   90.476
LGA    Y    65_B      Y    65_B     1.017     0    0.062   0.310     1.844   85.952   83.016
LGA    D    66_B      D    66_B     0.940     0    0.270   0.959     2.484   81.786   78.452
LGA    G    67_B      G    67_B     1.149     0    0.223   0.223     2.133   77.381   77.381
LGA    R    68_B      R    68_B     3.393     0    0.133   1.135     5.789   51.905   37.056
LGA    A    69_B      A    69_B     1.576     0    0.244   0.240     2.029   77.262   74.762
LGA    L    70_B      L    70_B     0.733     0    0.144   1.393     5.865   97.619   72.262
LGA    E    71_B      E    71_B     0.705     0    0.040   1.126     4.526   92.857   72.381
LGA    I    72_B      I    72_B     0.984     0    0.079   1.436     5.648   85.952   68.333
LGA    A    73_B      A    73_B     2.069     0    0.043   0.046     2.773   68.810   66.476
LGA    R    74_B      R    74_B     2.017     0    0.041   0.924     5.548   70.833   57.056
LGA    L    75_B      L    75_B     0.896     0    0.171   0.858     3.555   92.976   83.571
LGA    L    76_B      L    76_B     0.270     0    0.672   0.635     2.834   86.905   87.619
LGA    N    77_B      N    77_B     1.790     0    0.405   0.836     5.105   67.143   56.012
LGA    A    78_B      A    78_B     1.087     0    0.059   0.065     1.210   81.429   83.238
LGA    R    79_B      R    79_B     0.752     0    0.069   1.340     7.349   83.810   61.169
LGA    Y    80_B      Y    80_B     1.141     0    0.060   0.389     4.795   88.214   65.159
LGA    L    81_B      L    81_B     0.705     0    0.121   0.941     3.852   90.476   78.155
LGA    G    82_B      G    82_B     0.767     0    0.152   0.152     0.902   90.476   90.476
LGA    V    83_B      V    83_B     1.185     0    0.069   1.045     2.491   83.690   76.735
LGA    D    84_B      D    84_B     1.723     0    0.135   0.544     3.588   75.000   69.286
LGA    L    85_B      L    85_B     0.567     0    0.085   1.029     3.783   92.857   83.571
LGA    D    86_B      D    86_B     1.120     0    0.118   1.021     2.418   83.690   80.536
LGA    Q    87_B      Q    87_B     1.162     0    0.034   1.326     6.444   81.429   60.952
LGA    R    88_B      R    88_B     0.982     0    0.060   0.934     3.001   85.952   72.121
LGA    A    89_B      A    89_B     1.000     0    0.049   0.067     1.285   85.952   86.857
LGA    I    90_B      I    90_B     1.398     0    0.080   1.061     4.290   81.429   67.857
LGA    E    91_B      E    91_B     0.924     0    0.036   0.923     4.921   88.214   68.254
LGA    T    92_B      T    92_B     1.051     0    0.057   0.959     2.695   81.429   77.959
LGA    L    93_B      L    93_B     1.223     0    0.042   1.202     3.792   81.429   74.583
LGA    R    94_B      R    94_B     0.628     0    0.035   1.458     6.643   90.476   67.316
LGA    T    95_B      T    95_B     0.565     0    0.033   1.047     2.558   90.476   83.401
LGA    R    96_B      R    96_B     1.084     0    0.033   1.379     5.841   83.690   65.022
LGA    I    97_B      I    97_B     1.065     0    0.046   0.638     2.314   83.690   81.607
LGA    E    98_B      E    98_B     0.849     0    0.064   0.918     5.165   88.214   71.270
LGA    R    99_B      R    99_B     1.039     0    0.059   1.192     7.322   83.690   57.749
LGA    E   100_B      E   100_B     1.090     0    0.182   0.980     2.010   85.952   81.640
LGA    G   101_B      G   101_B     0.814     0    0.229   0.229     0.913   90.476   90.476
LGA    M   102_B      M   102_B     1.246     0    0.188   0.923     2.866   83.690   78.452
LGA    S   103_B      S   103_B     1.398     0    0.021   0.612     2.035   81.429   77.222
LGA    D   104_B      D   104_B     1.082     0    0.112   0.114     1.477   85.952   83.690
LGA    R   105_B      R   105_B     0.099     0    0.249   1.566     8.491   95.238   62.165

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       71     284    284  100.00     567    567  100.00               230
SUMMARY(RMSD_GDC):     3.830          3.692                  4.722           20.088   17.498

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   71  230    4.0     55    1.59    22.609    22.304     3.257

LGA_LOCAL      RMSD:   1.589  Number of atoms:   55  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.135  Number of assigned atoms:   71 
Std_ASGN_ATOMS RMSD:   3.830  Standard rmsd on all 71 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.867854 * X  +  -0.494865 * Y  +   0.044022 * Z  +  30.594496
  Y_new =  -0.467452 * X  +  -0.843357 * Y  +  -0.265024 * Z  + 115.064278
  Z_new =   0.168277 * X  +   0.209424 * Y  +  -0.963237 * Z  +   2.782622 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.494072 -0.169081  2.927508   [DEG:  -28.3082   -9.6876  167.7338 ]
ZXZ:  0.164602  2.869596  0.676885   [DEG:    9.4310  164.4158   38.7827 ]
 
# END of job
