
#######################################################
#                                                     #
#                        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   67 (  575),  selected   67 , name one
# Molecule2: number of CA atoms  124 ( 1059),  selected   67 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:D  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37      88_D - 124_D       4.91    19.32
  LCS_AVERAGE:     23.75

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    30      95_D - 124_D       1.35    20.22
  LCS_AVERAGE:     13.05

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28      97_D - 124_D       0.78    20.80
  LCS_AVERAGE:     11.27

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   67
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     T    58_D     T    58_D      4    4   16      0    3    4    4    4    7    8    8   10   12   12   13   15   18   19   23   25   26   30   37 
LCS_GDT     H    59_D     H    59_D      4    4   16      2    3    4    4    5    7    8    8   10   12   12   13   15   18   19   23   25   26   27   35 
LCS_GDT     D    60_D     D    60_D      4    5   16      3    3    4    4    5    7    8    8   10   12   12   13   15   18   19   23   25   26   27   31 
LCS_GDT     K    61_D     K    61_D      4    5   16      3    4    4    4    5    7    8   11   11   12   12   13   15   18   19   23   25   26   27   31 
LCS_GDT     C    62_D     C    62_D      4    5   16      3    4    4    4    5    7    8    8   10   12   12   15   15   18   19   23   25   30   35   39 
LCS_GDT     E    63_D     E    63_D      4    5   16      3    4    4    4    5    7    8    8   10   12   12   15   15   18   19   23   25   26   34   38 
LCS_GDT     N    64_D     N    64_D      4    5   16      3    4    4    4    5    7    8    8   10   12   12   15   15   18   19   24   26   30   35   40 
LCS_GDT     P    65_D     P    65_D      4    4   16      3    4    4    4    4    6    8    8   10   12   12   15   15   18   20   24   26   32   38   42 
LCS_GDT     K    66_D     K    66_D      4    4   16      3    4    4    4    4    6    7    8   10   12   12   13   15   18   20   23   26   32   38   42 
LCS_GDT     E    67_D     E    67_D      3    4   16      3    3    3    4    5    6    6    8   10   12   12   15   15   18   20   24   26   30   35   42 
LCS_GDT     Q    68_D     Q    68_D      3    4   16      0    3    3    4    5    5    6    8   10   12   15   17   18   19   22   24   26   32   38   42 
LCS_GDT     W    69_D     W    69_D      3    3   16      0    3    3    3    5    5    6    9   12   15   15   17   18   20   22   25   28   36   41   44 
LCS_GDT     V    70_D     V    70_D      3    3   16      3    3    3    3    6    6    7    9   12   15   15   17   18   20   23   27   33   36   41   44 
LCS_GDT     A    71_D     A    71_D      3    4   16      3    3    3    3    4    6    7    9   12   15   15   17   18   20   23   25   27   29   38   42 
LCS_GDT     N    72_D     N    72_D      3    6   16      3    3    3    4    6    6    7   11   12   14   15   17   18   19   21   22   26   29   31   31 
LCS_GDT     Y    73_D     Y    73_D      4    6   16      4    4    4    4    6    6    7   11   12   14   15   17   18   23   25   29   40   45   46   49 
LCS_GDT     Q    74_D     Q    74_D      4    6   14      4    4    4    4    6    6    7   11   12   15   15   17   18   19   23   25   27   29   38   43 
LCS_GDT     N    75_D     N    75_D      4    6   14      4    4    4    4    6    6    7   11   12   14   15   15   17   19   20   22   25   25   27   29 
LCS_GDT     L    76_D     L    76_D      4    6   18      4    4    4    4    6    6    7   11   12   14   15   17   18   19   20   23   26   35   39   42 
LCS_GDT     N    77_D     N    77_D      4    6   18      3    4    4    4    5    6    7   11   12   14   15   17   18   23   29   32   40   45   47   49 
LCS_GDT     N    78_D     N    78_D      4    5   18      3    4    4    5    5    6    7   11   12   15   15   17   22   25   32   40   43   45   47   49 
LCS_GDT     V    79_D     V    79_D      4    5   18      3    4    4    5    5    6    7   11   12   15   15   17   18   23   25   32   40   45   47   49 
LCS_GDT     V    80_D     V    80_D      4    5   18      3    3    4    5    5    6    7   11   12   15   20   29   35   39   39   44   44   45   47   49 
LCS_GDT     F    81_D     F    81_D      4    5   32      3    4    4    5    5    7    9   19   29   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     T    82_D     T    82_D      4    5   33      3    4    6    8   10   16   21   29   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     N    83_D     N    83_D      4    5   33      3    4    6    8   10   14   18   27   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K    84_D     K    84_D      4    5   33      3    4    6    8   10   16   21   29   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     E    85_D     E    85_D      3    4   33      3    3    4    4    4    8   10   14   20   26   29   34   37   39   39   44   44   45   47   49 
LCS_GDT     L    86_D     L    86_D      4    6   33      3    3    4    5    7   10   12   15   19   23   26   29   35   39   39   44   44   45   47   49 
LCS_GDT     E    87_D     E    87_D      4    6   33      3    3    4    5    7   10   12   15   17   19   23   26   28   31   36   40   43   45   47   49 
LCS_GDT     D    88_D     D    88_D      4    6   37      3    3    4    5    7   10   12   15   17   20   24   26   29   33   39   44   44   45   47   49 
LCS_GDT     I    89_D     I    89_D      4    6   37      3    3    4    5    7   10   12   15   18   23   27   34   37   39   39   44   44   45   47   49 
LCS_GDT     Y    90_D     Y    90_D      3    6   37      3    3    3    4    5    7   12   14   17   18   20   24   28   33   39   44   44   45   47   49 
LCS_GDT     D    91_D     D    91_D      4    6   37      4    4    4    4    5    7   12   14   17   18   20   24   28   33   39   44   44   45   47   49 
LCS_GDT     L    92_D     L    92_D      4    4   37      4    4    4    4    5    5    7   11   12   15   19   21   27   34   39   44   44   45   47   49 
LCS_GDT     S    93_D     S    93_D      4    4   37      4    4    4    4    5    5    7   11   12   15   19   21   27   35   39   44   44   45   47   49 
LCS_GDT     N    94_D     N    94_D      4    6   37      4    4    4    4    4   10   12   16   21   32   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K    95_D     K    95_D      6   30   37      5    5   10   19   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     E    96_D     E    96_D      6   30   37      5    5   10   17   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     E    97_D     E    97_D     28   30   37      5    5    9   13   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     T    98_D     T    98_D     28   30   37     18   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K    99_D     K    99_D     28   30   37     19   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     E   100_D     E   100_D     28   30   37     13   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     V   101_D     V   101_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     L   102_D     L   102_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K   103_D     K   103_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K   104_D     K   104_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     F   105_D     F   105_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K   106_D     K   106_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     E   107_D     E   107_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K   108_D     K   108_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     V   109_D     V   109_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     N   110_D     N   110_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     Q   111_D     Q   111_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     F   112_D     F   112_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     Y   113_D     Y   113_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     R   114_D     R   114_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     H   115_D     H   115_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     A   116_D     A   116_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     F   117_D     F   117_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     D   118_D     D   118_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     I   119_D     I   119_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     I   120_D     I   120_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     N   121_D     N   121_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     K   122_D     K   122_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     Y   123_D     Y   123_D     28   30   37     23   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_GDT     G   124_D     G   124_D     28   30   37      3   27   27   27   28   30   30   30   33   34   35   35   37   39   39   44   44   45   47   49 
LCS_AVERAGE  LCS_A:  16.02  (  11.27   13.05   23.75 )

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     23     27     27     27     28     30     30     30     33     34     35     35     37     39     39     44     44     45     47     49 
GDT PERCENT_AT  18.55  21.77  21.77  21.77  22.58  24.19  24.19  24.19  26.61  27.42  28.23  28.23  29.84  31.45  31.45  35.48  35.48  36.29  37.90  39.52
GDT RMS_LOCAL    0.22   0.39   0.39   0.39   0.78   1.35   1.35   1.35   2.55   2.74   3.04   3.04   3.68   4.16   4.16   5.23   5.23   5.36   5.80   6.24
GDT RMS_ALL_AT  20.75  20.63  20.63  20.63  20.80  20.22  20.22  20.22  18.63  18.29  18.31  18.31  17.91  17.64  17.64  17.30  17.30  17.36  16.94  16.46

# Checking swapping
#   possible swapping detected:  E    67_D      E    67_D
#   possible swapping detected:  Y    73_D      Y    73_D
#   possible swapping detected:  E    96_D      E    96_D
#   possible swapping detected:  E    97_D      E    97_D
#   possible swapping detected:  E   100_D      E   100_D
#   possible swapping detected:  F   112_D      F   112_D
#   possible swapping detected:  F   117_D      F   117_D
#   possible swapping detected:  D   118_D      D   118_D
#   possible swapping detected:  Y   123_D      Y   123_D

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    T    58_D      T    58_D    48.051     0    0.680   1.349    48.866    0.000    0.000
LGA    H    59_D      H    59_D    48.830     0    0.437   1.472    48.830    0.000    0.000
LGA    D    60_D      D    60_D    47.384     0    0.543   0.506    49.842    0.000    0.000
LGA    K    61_D      K    61_D    45.369     0    0.381   1.089    46.269    0.000    0.000
LGA    C    62_D      C    62_D    41.239     0    0.137   0.654    42.755    0.000    0.000
LGA    E    63_D      E    63_D    44.080     0    0.614   1.143    45.398    0.000    0.000
LGA    N    64_D      N    64_D    41.720     0    0.177   0.797    46.284    0.000    0.000
LGA    P    65_D      P    65_D    35.467     0    0.651   0.609    37.554    0.000    0.000
LGA    K    66_D      K    66_D    34.771     0    0.616   1.304    40.460    0.000    0.000
LGA    E    67_D      E    67_D    36.370     0    0.616   1.098    40.991    0.000    0.000
LGA    Q    68_D      Q    68_D    31.126     0    0.655   0.804    33.330    0.000    0.000
LGA    W    69_D      W    69_D    27.142     0    0.634   0.933    28.084    0.000    0.000
LGA    V    70_D      V    70_D    27.755     0    0.584   1.408    30.889    0.000    0.000
LGA    A    71_D      A    71_D    27.267     0    0.256   0.255    27.267    0.000    0.000
LGA    N    72_D      N    72_D    26.135     0    0.411   0.846    29.712    0.000    0.000
LGA    Y    73_D      Y    73_D    20.612     0    0.280   1.031    22.478    0.000    0.000
LGA    Q    74_D      Q    74_D    25.050     0    0.135   1.389    32.268    0.000    0.000
LGA    N    75_D      N    75_D    26.839     0    0.181   0.972    30.343    0.000    0.000
LGA    L    76_D      L    76_D    20.620     0    0.608   0.975    22.486    0.000    0.000
LGA    N    77_D      N    77_D    18.088     0    0.220   0.847    20.982    0.000    0.000
LGA    N    78_D      N    78_D    17.989     0    0.416   0.364    19.848    0.000    0.000
LGA    V    79_D      V    79_D    17.838     0    0.080   1.221    20.334    0.000    0.000
LGA    V    80_D      V    80_D    12.416     0    0.614   1.046    14.273    0.000    0.000
LGA    F    81_D      F    81_D     9.207     0    0.533   1.204    10.181    0.833    3.810
LGA    T    82_D      T    82_D     9.007     0    0.639   0.575     9.900    1.548    2.109
LGA    N    83_D      N    83_D     8.661     0    0.303   0.801    11.244    2.500    1.607
LGA    K    84_D      K    84_D     8.445     0    0.585   0.651     9.248    4.524    7.037
LGA    E    85_D      E    85_D    12.843     0    0.594   0.981    21.657    0.000    0.000
LGA    L    86_D      L    86_D    11.608     0    0.650   1.028    11.958    0.000    0.000
LGA    E    87_D      E    87_D    12.311     0    0.579   1.179    15.018    0.000    0.000
LGA    D    88_D      D    88_D    13.237     0    0.374   0.461    16.314    0.000    0.000
LGA    I    89_D      I    89_D    11.202     0    0.196   1.310    12.563    0.119    0.060
LGA    Y    90_D      Y    90_D    12.633     0    0.608   1.393    16.565    0.000    0.000
LGA    D    91_D      D    91_D    13.983     0    0.666   1.250    18.527    0.000    0.000
LGA    L    92_D      L    92_D    15.653     0    0.016   0.897    20.328    0.000    0.000
LGA    S    93_D      S    93_D    13.757     0    0.399   0.664    15.049    0.000    0.000
LGA    N    94_D      N    94_D     9.379     0    0.258   0.453    10.310    7.976    6.964
LGA    K    95_D      K    95_D     3.922     0    0.591   1.024    13.386   42.976   23.280
LGA    E    96_D      E    96_D     3.694     0    0.014   1.436     7.686   48.452   30.476
LGA    E    97_D      E    97_D     2.761     0    0.105   0.667     3.974   61.190   55.820
LGA    T    98_D      T    98_D     0.890     0    0.218   1.193     2.796   88.214   78.231
LGA    K    99_D      K    99_D     0.938     0    0.035   0.695     1.885   85.952   85.503
LGA    E   100_D      E   100_D     1.172     0    0.007   1.076     5.596   81.429   63.333
LGA    V   101_D      V   101_D     1.523     0    0.015   0.086     1.658   75.000   75.306
LGA    L   102_D      L   102_D     1.421     0    0.025   0.807     3.887   81.429   72.500
LGA    K   103_D      K   103_D     1.279     0    0.021   0.820     2.853   83.690   77.831
LGA    K   104_D      K   104_D     1.097     0    0.022   0.978     5.952   81.429   67.037
LGA    F   105_D      F   105_D     0.947     0    0.020   0.197     1.119   88.214   87.186
LGA    K   106_D      K   106_D     0.848     0    0.034   0.966     5.243   90.476   73.280
LGA    E   107_D      E   107_D     0.803     0    0.016   0.151     1.284   90.476   87.460
LGA    K   108_D      K   108_D     0.662     0    0.043   0.625     2.180   90.476   84.656
LGA    V   109_D      V   109_D     0.486     0    0.013   0.096     0.696   97.619   95.918
LGA    N   110_D      N   110_D     0.539     0    0.019   1.081     2.709   95.238   86.488
LGA    Q   111_D      Q   111_D     0.481     0    0.027   0.199     1.156   97.619   92.646
LGA    F   112_D      F   112_D     0.220     0    0.023   0.121     0.442  100.000  100.000
LGA    Y   113_D      Y   113_D     0.253     0    0.053   0.108     0.699  100.000   96.825
LGA    R   114_D      R   114_D     0.098     0    0.022   0.404     1.191  100.000   93.203
LGA    H   115_D      H   115_D     0.423     0    0.057   1.116     2.621   97.619   86.524
LGA    A   116_D      A   116_D     0.597     0    0.020   0.031     0.772   92.857   92.381
LGA    F   117_D      F   117_D     0.357     0    0.015   0.164     1.234  100.000   91.472
LGA    D   118_D      D   118_D     0.348     0    0.059   0.867     4.120  100.000   79.345
LGA    I   119_D      I   119_D     0.523     0    0.035   0.135     0.791   97.619   94.048
LGA    I   120_D      I   120_D     0.469     0    0.085   1.595     4.214   95.238   78.810
LGA    N   121_D      N   121_D     0.405     0    0.034   1.404     3.557  100.000   83.274
LGA    K   122_D      K   122_D     0.811     0    0.068   1.213     6.596   90.476   69.524
LGA    Y   123_D      Y   123_D     0.938     0    0.280   0.282     2.021   81.786   87.579
LGA    G   124_D      G   124_D     1.140     0    0.699   0.699     2.960   75.476   75.476

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       67     268    268  100.00     575    575  100.00               124
SUMMARY(RMSD_GDC):    11.335         11.274                 12.005           21.197   19.250

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   67  124    4.0     30    1.35    25.806    22.355     2.068

LGA_LOCAL      RMSD:   1.351  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  20.219  Number of assigned atoms:   67 
Std_ASGN_ATOMS RMSD:  11.335  Standard rmsd on all 67 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.462956 * X  +   0.309688 * Y  +   0.830521 * Z  + -39.027260
  Y_new =   0.095219 * X  +  -0.914181 * Y  +   0.393962 * Z  + -78.596321
  Z_new =   0.881252 * X  +   0.261468 * Y  +   0.393738 * Z  +   2.916654 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.938746 -1.078504  0.586201   [DEG:  168.3777  -61.7938   33.5868 ]
ZXZ:  2.013718  1.166102  1.282369   [DEG:  115.3776   66.8127   73.4743 ]
 
# END of job
