
#######################################################
#                                                     #
#                        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   81 (  556),  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:    39      47_A - 85_A        4.99     5.67
  LCS_AVERAGE:     51.78

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      64_A - 85_A        1.95     6.18
  LCS_AVERAGE:     26.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      68_A - 85_A        0.91     6.42
  LCS_AVERAGE:     19.48

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   24      1    4    4    6    6    6    7    7   14   16   18   26   33   38   45   55   58   61   61   61 
LCS_GDT     D    23_A     D    23_A      4    5   24      0    4    5   12   14   16   20   28   36   47   54   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    24_A     G    24_A      4   17   24      3    4    8   13   28   43   46   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     D    25_A     D    25_A     15   17   24      3    4   10   36   40   42   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    26_A     G    26_A     15   17   24     10   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     Q    27_A     Q    27_A     15   17   24      6   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    28_A     G    28_A     15   17   24      8   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    29_A     L    29_A     15   17   24     10   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     Y    30_A     Y    30_A     15   17   24     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    31_A     A    31_A     15   17   24     12   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    32_A     A    32_A     15   17   24     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     N    33_A     N    33_A     15   17   24     10   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     C    34_A     C    34_A     15   17   24     10   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    35_A     A    35_A     15   17   24     10   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    36_A     A    36_A     15   17   24     10   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     C    37_A     C    37_A     15   17   24     10   16   27   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     H    38_A     H    38_A     15   17   24     10   15   25   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    39_A     G    39_A     15   17   24      3    3   27   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    40_A     A    40_A      3   17   24      3    3   19   30   37   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    41_A     L    41_A      3    6   24      3    3    4    5   10   15   20   38   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    42_A     A    42_A      3    6   24      3    3    5    7   14   18   39   51   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     T    43_A     T    43_A      4    6   24      3    4    4    5   10   14   21   38   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     S    44_A     S    44_A      4    6   24      3    4    4    4    5    7    8   11   13   16   20   31   51   58   59   60   60   61   61   61 
LCS_GDT     E    45_A     E    45_A      4    6   24      3    4    4    5    6    8    8   19   20   24   27   36   48   55   59   60   60   61   61   61 
LCS_GDT     K    46_A     K    46_A      4    6   24      3    4    4    5    5    7    8    8    9   13   15   15   17   19   20   27   28   29   35   47 
LCS_GDT     K    47_A     K    47_A      3    4   39      3    3    3    4    4    4    8    8    9   13   15   15   17   19   20   21   25   29   30   47 
LCS_GDT     G    48_A     G    48_A      3    4   39      3    3    3    5    5    7    8    8    9   12   15   15   17   19   22   23   25   31   35   36 
LCS_GDT     T    49_A     T    49_A     13   16   39      7   12   12   13   15   32   44   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     T    50_A     T    50_A     13   16   39     10   12   12   13   30   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    51_A     L    51_A     13   16   39     10   12   12   20   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    52_A     A    52_A     13   16   39     10   18   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     R    53_A     R    53_A     13   16   39     10   12   24   33   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    54_A     L    54_A     13   16   39     10   12   17   27   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     Q    55_A     Q    55_A     13   16   39     10   12   24   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     S    56_A     S    56_A     13   16   39     10   12   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    57_A     A    57_A     13   16   39     10   18   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     V    58_A     V    58_A     13   16   39     10   12   17   26   35   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     S    59_A     S    59_A     13   16   39     10   12   12   13   15   20   46   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    60_A     A    60_A     13   16   39      6   12   12   13   17   42   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     N    61_A     N    61_A     13   16   39      3   14   26   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    62_A     A    62_A      5   16   39      3    4    5    5    8   21   40   50   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    63_A     G    63_A      5   16   39      3    4    5    5    9   16   39   46   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    64_A     G    64_A      5   22   39      3    4   10   15   27   41   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     M    65_A     M    65_A      3   22   39      3    3    3    5   27   37   43   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     G    66_A     G    66_A      3   22   39      3    3    3    6   19   34   43   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     F    67_A     F    67_A     16   22   39      3    6   13   20   34   39   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    68_A     L    68_A     18   22   39      8   18   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     S    69_A     S    69_A     18   22   39      8   18   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     S    70_A     S    70_A     18   22   39      8   18   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    71_A     L    71_A     18   22   39      9   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     T    72_A     T    72_A     18   22   39     12   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     S    73_A     S    73_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    74_A     A    74_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     Q    75_A     Q    75_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    76_A     L    76_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     Q    77_A     Q    77_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    78_A     A    78_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     I    79_A     I    79_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     V    80_A     V    80_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     D    81_A     D    81_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     V    82_A     V    82_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     L    83_A     L    83_A     18   22   39     12   22   27   35   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     A    84_A     A    84_A     18   22   39     13   22   28   36   40   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_GDT     V    85_A     V    85_A     18   22   39      0   12   20   30   39   43   47   52   53   57   57   57   58   58   59   60   60   61   61   61 
LCS_AVERAGE  LCS_A:  32.44  (  19.48   26.05   51.78 )

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     13     22     28     36     40     43     47     52     53     57     57     57     58     58     59     60     60     61     61     61 
GDT PERCENT_AT  20.31  34.38  43.75  56.25  62.50  67.19  73.44  81.25  82.81  89.06  89.06  89.06  90.62  90.62  92.19  93.75  93.75  95.31  95.31  95.31
GDT RMS_LOCAL    0.35   0.63   0.98   1.27   1.43   1.73   1.91   2.29   2.37   2.78   2.78   2.78   2.99   2.99   3.26   3.55   3.55   4.00   4.00   4.00
GDT RMS_ALL_AT   6.22   6.15   6.07   6.06   6.06   6.00   6.05   6.00   5.97   5.82   5.82   5.82   5.78   5.78   5.71   5.63   5.63   5.59   5.59   5.59

# 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    16.500     0    0.127   0.133    18.454    0.000    0.000
LGA    D    23_A      D    23_A     9.689     0    0.580   0.820    12.083    5.238    4.821
LGA    G    24_A      G    24_A     5.041     0    0.546   0.546     6.896   30.238   30.238
LGA    D    25_A      D    25_A     2.431     0    0.306   1.130     6.310   58.690   42.083
LGA    G    26_A      G    26_A     1.185     0    0.097   0.097     1.187   81.429   81.429
LGA    Q    27_A      Q    27_A     1.154     0    0.023   1.439     6.463   85.952   65.291
LGA    G    28_A      G    28_A     0.941     0    0.012   0.012     1.035   88.214   88.214
LGA    L    29_A      L    29_A     0.846     0    0.042   1.356     3.745   88.214   74.226
LGA    Y    30_A      Y    30_A     1.127     0    0.024   0.156     2.063   81.429   77.183
LGA    A    31_A      A    31_A     1.546     0    0.010   0.013     1.943   75.000   74.571
LGA    A    32_A      A    32_A     1.626     0    0.021   0.029     1.833   75.000   74.571
LGA    N    33_A      N    33_A     1.357     0    0.030   0.064     1.837   77.143   79.286
LGA    C    34_A      C    34_A     1.592     0    0.017   0.124     1.881   75.000   74.286
LGA    A    35_A      A    35_A     1.975     0    0.039   0.042     2.559   66.905   68.095
LGA    A    36_A      A    36_A     2.246     0    0.018   0.016     2.544   62.857   63.238
LGA    C    37_A      C    37_A     2.225     0    0.044   0.039     2.425   64.762   66.111
LGA    H    38_A      H    38_A     2.491     0    0.543   0.453     4.249   55.952   60.476
LGA    G    39_A      G    39_A     1.117     0    0.021   0.021     2.650   73.214   73.214
LGA    A    40_A      A    40_A     2.971     0    0.624   0.583     3.589   59.286   56.095
LGA    L    41_A      L    41_A     6.476     0    0.204   1.364    11.304   17.262    9.583
LGA    A    42_A      A    42_A     6.916     0    0.282   0.279     7.253   13.452   13.429
LGA    T    43_A      T    43_A     6.792     0    0.568   1.378     7.617   13.690   16.054
LGA    S    44_A      S    44_A    11.138     0    0.093   0.131    15.018    0.000    0.000
LGA    E    45_A      E    45_A    12.199     0    0.711   1.223    15.762    0.000    0.053
LGA    K    46_A      K    46_A    18.877     0    0.313   0.882    24.570    0.000    0.000
LGA    K    47_A      K    47_A    20.158     0    0.063   0.813    23.754    0.000    0.000
LGA    G    48_A      G    48_A    20.807     0    0.529   0.529    22.466    0.000    0.000
LGA    T    49_A      T    49_A     4.920     0    0.308   0.960     7.172   24.762   25.374
LGA    T    50_A      T    50_A     3.312     0    0.035   0.065     3.774   51.905   51.156
LGA    L    51_A      L    51_A     2.545     0    0.020   0.870     4.727   62.976   56.905
LGA    A    52_A      A    52_A     1.554     0    0.014   0.018     1.848   72.857   72.857
LGA    R    53_A      R    53_A     2.178     0    0.044   1.060     8.103   70.833   45.238
LGA    L    54_A      L    54_A     2.274     0    0.030   1.393     6.856   66.786   47.024
LGA    Q    55_A      Q    55_A     2.155     0    0.060   0.165     3.511   68.810   63.333
LGA    S    56_A      S    56_A     1.836     0    0.044   0.045     2.206   70.833   70.159
LGA    A    57_A      A    57_A     1.341     0    0.036   0.037     1.895   77.143   76.286
LGA    V    58_A      V    58_A     3.189     0    0.067   0.087     4.628   48.810   44.762
LGA    S    59_A      S    59_A     3.788     0    0.010   0.723     6.089   42.024   38.095
LGA    A    60_A      A    60_A     3.383     0    0.377   0.355     4.295   55.476   51.810
LGA    N    61_A      N    61_A     2.067     0    0.037   0.099     7.097   75.119   47.798
LGA    A    62_A      A    62_A     5.066     0    0.264   0.297     6.675   29.881   26.571
LGA    G    63_A      G    63_A     5.721     0    0.598   0.598     5.721   33.571   33.571
LGA    G    64_A      G    64_A     3.292     0    0.634   0.634     3.845   50.119   50.119
LGA    M    65_A      M    65_A     3.842     0    0.616   1.250     6.389   40.357   39.762
LGA    G    66_A      G    66_A     3.955     0    0.686   0.686     5.259   40.714   40.714
LGA    F    67_A      F    67_A     3.791     0    0.683   0.454     9.209   55.595   28.095
LGA    L    68_A      L    68_A     1.160     0    0.251   0.248     2.072   79.524   82.738
LGA    S    69_A      S    69_A     1.033     0    0.020   0.057     1.249   85.952   84.444
LGA    S    70_A      S    70_A     0.367     0    0.071   0.070     0.580   95.238   96.825
LGA    L    71_A      L    71_A     0.551     0    0.026   0.141     1.034   90.595   92.917
LGA    T    72_A      T    72_A     1.420     0    0.026   0.084     1.582   81.429   77.755
LGA    S    73_A      S    73_A     1.724     0    0.009   0.631     2.041   77.143   74.365
LGA    A    74_A      A    74_A     1.206     0    0.054   0.055     1.413   85.952   85.048
LGA    Q    75_A      Q    75_A     1.048     0    0.039   0.060     1.228   83.690   83.439
LGA    L    76_A      L    76_A     1.308     0    0.009   1.405     3.384   81.429   75.357
LGA    Q    77_A      Q    77_A     1.279     0    0.056   0.160     1.700   83.690   79.577
LGA    A    78_A      A    78_A     0.734     0    0.039   0.046     0.951   90.476   90.476
LGA    I    79_A      I    79_A     1.184     0    0.031   1.054     3.465   81.429   77.500
LGA    V    80_A      V    80_A     1.326     0    0.027   0.043     1.578   81.429   80.204
LGA    D    81_A      D    81_A     0.821     0    0.033   0.040     1.253   85.952   90.595
LGA    V    82_A      V    82_A     1.325     0    0.125   0.910     2.682   77.143   75.578
LGA    L    83_A      L    83_A     2.071     0    0.171   0.206     2.863   68.810   65.833
LGA    A    84_A      A    84_A     1.733     0    0.655   0.602     3.031   67.143   68.286
LGA    V    85_A      V    85_A     3.159     0    0.267   1.110     6.743   47.143   36.327

# 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):     5.440          5.448                  5.961           58.307   54.991

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   81   64    4.0     52    2.29    66.406    59.000     2.173

LGA_LOCAL      RMSD:   2.293  Number of atoms:   52  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.998  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   5.440  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.793697 * X  +  -0.608114 * Y  +   0.015559 * Z  +   9.655005
  Y_new =   0.581328 * X  +  -0.750706 * Y  +   0.313845 * Z  + -19.910969
  Z_new =  -0.179173 * X  +   0.258142 * Y  +   0.949347 * Z  + -57.581417 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.509431  0.180146  0.265497   [DEG:  143.7798   10.3216   15.2118 ]
ZXZ:  3.092059  0.319646 -0.606747   [DEG:  177.1619   18.3143  -34.7640 ]
 
# END of job
