
#######################################################
#                                                     #
#                        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   72 (  612),  selected   72 , name one
# Molecule2: number of CA atoms  104 (  843),  selected   72 , 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:    34      23_A - 56_A        4.94    26.15
  LONGEST_CONTINUOUS_SEGMENT:    34      24_A - 57_A        4.92    25.83
  LCS_AVERAGE:     30.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      60_A - 81_A        1.94    19.47
  LCS_AVERAGE:     13.13

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      23_A - 35_A        0.87    25.72
  LCS_AVERAGE:      8.01

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   72
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     V    23_A     V    23_A     13   14   34      3   10   13   17   18   22   24   25   26   26   26   26   27   28   31   32   34   34   35   38 
LCS_GDT     H    24_A     H    24_A     13   14   34      3   10   14   21   21   23   24   25   26   26   26   26   28   30   31   32   34   34   35   38 
LCS_GDT     N    25_A     N    25_A     13   14   34      3   10   14   21   21   23   24   25   26   26   26   26   28   30   31   32   34   34   35   38 
LCS_GDT     I    26_A     I    26_A     13   14   34      7   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     K    27_A     K    27_A     13   14   34      7   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     C    28_A     C    28_A     13   14   34      7   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   38   41 
LCS_GDT     H    29_A     H    29_A     13   14   34      7   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     F    30_A     F    30_A     13   14   34      7   10   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   38   41 
LCS_GDT     D    31_A     D    31_A     13   14   34      7   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     N    32_A     N    32_A     13   14   34      4   10   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     C    33_A     C    33_A     13   14   34      7   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     N    34_A     N    34_A     13   14   34      5   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     R    35_A     R    35_A     13   14   34      6   11   18   21   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     K    36_A     K    36_A     11   14   34      3    6   16   20   22   23   24   25   26   26   28   28   29   30   31   32   34   34   35   38 
LCS_GDT     I    37_A     I    37_A      3    8   34      3    3    4    5    7    8    8   17   22   25   28   28   29   30   31   32   34   34   36   38 
LCS_GDT     H    38_A     H    38_A      4    8   34      3    4    4    5    7   10   13   16   23   25   28   28   29   30   31   32   34   34   37   41 
LCS_GDT     W    39_A     W    39_A      4    8   34      3    4    4    5    7    8   12   14   19   24   28   28   29   30   31   32   37   39   41   44 
LCS_GDT     K    40_A     K    40_A      5    8   34      5    5    5    5    7    8   12   14   19   25   28   28   29   30   31   32   37   39   41   44 
LCS_GDT     I    41_A     I    41_A      5    8   34      5    5    5    5    7    8    9   10   12   18   24   28   29   30   33   37   38   40   43   45 
LCS_GDT     R    42_A     R    42_A      5    8   34      5    5    5    5    7    8    8    9   11   13   14   15   15   23   27   33   38   40   43   44 
LCS_GDT     Y    43_A     Y    43_A      5    8   34      5    5    5    5    7    8    8    9   13   14   14   18   27   30   31   33   38   40   43   45 
LCS_GDT     G    44_A     G    44_A      5   10   34      5    5    5    5    9   10   13   19   23   25   28   28   29   30   34   37   39   42   43   45 
LCS_GDT     K    45_A     K    45_A      4   12   34      4    4    6    8   22   23   23   25   26   26   28   28   29   30   31   32   39   42   43   45 
LCS_GDT     L    46_A     L    46_A      8   12   34      4    4    8   11   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     R    47_A     R    47_A      9   12   34      4    9   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     L    48_A     L    48_A      9   12   34      4   10   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     V    49_A     V    49_A      9   12   34      4    8   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     D    50_A     D    50_A      9   12   34      4    8   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     H    51_A     H    51_A      9   12   34      6   11   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     A    52_A     A    52_A      9   12   34      4   11   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     L    53_A     L    53_A      9   12   34      4    8   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     S    54_A     S    54_A      9   12   34      6   11   18   21   22   23   24   25   26   26   28   28   29   30   32   36   38   41   43   45 
LCS_GDT     H    55_A     H    55_A      9   12   34      4    5   18   21   22   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     Q    56_A     Q    56_A      6   12   34      4    4    6   20   21   23   24   25   26   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     E    57_A     E    57_A      4    7   34      3    4    4    6    8   11   15   19   22   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     E    58_A     E    58_A      4    7   33      3    4    4    5    8   11   15   19   22   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     K    59_A     K    59_A      4    8   33      3    4    6    6    8   13   15   19   22   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     S    60_A     S    60_A      7   22   33      3    5    7   14   18   20   23   23   23   24   27   30   34   36   37   38   40   42   43   45 
LCS_GDT     I    61_A     I    61_A     11   22   33      5   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     D    62_A     D    62_A     11   22   33      5   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     C    63_A     C    63_A     11   22   33      5   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     Q    64_A     Q    64_A     11   22   33      3    6    9   14   17   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     K    65_A     K    65_A     11   22   33      4   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     C    66_A     C    66_A     11   22   33      3   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     E    67_A     E    67_A     11   22   33      3   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     Y    68_A     Y    68_A     11   22   33      5   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     S    69_A     S    69_A     11   22   33      5   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     C    70_A     C    70_A     11   22   33      4   10   13   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     Q    71_A     Q    71_A     11   22   33      5   10   14   16   19   20   23   23   23   24   27   30   34   36   37   38   40   42   43   45 
LCS_GDT     T    72_A     T    72_A      9   22   33      3    4   14   16   19   20   23   23   23   24   26   30   31   33   37   38   40   42   43   45 
LCS_GDT     T    73_A     T    73_A      9   22   33      3    7    9   15   19   20   23   23   23   24   26   28   30   33   36   37   39   42   43   45 
LCS_GDT     R    74_A     R    74_A      9   22   33      3    7    9   15   19   20   23   23   23   24   27   30   31   35   37   38   40   42   43   45 
LCS_GDT     Q    75_A     Q    75_A      9   22   33      5    8   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     M    76_A     M    76_A      9   22   33      4   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     R    77_A     R    77_A      9   22   33      5    7   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     Y    78_A     Y    78_A      9   22   33      5   10   14   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     H    79_A     H    79_A      9   22   33      5   10   13   16   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     Y    80_A     Y    80_A      7   22   33      3    3    6   15   19   20   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     K    81_A     K    81_A      3   22   33      3    3    4    6    7   18   23   23   23   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     K    82_A     K    82_A      5    5   31      4    4    5    5    7   14   14   19   22   24   25   29   30   36   36   38   40   42   43   45 
LCS_GDT     I    83_A     I    83_A      5    5   31      4    4    5    5    5   18   23   23   23   24   26   30   32   36   36   38   40   42   43   45 
LCS_GDT     H    84_A     H    84_A      5    5   31      4    4    5    5    5    7   11   18   22   26   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     A    85_A     A    85_A      5    5   31      4    4    6    6    8   11   15   19   22   24   28   30   34   36   37   38   40   42   43   45 
LCS_GDT     N    86_A     N    86_A      5    5   31      3    4    6    6    8   10   12   16   19   20   24   28   30   33   37   38   40   42   43   45 
LCS_GDT     L    87_A     L    87_A      4    4   31      3    4    6    6    8   10   12   16   19   20   23   28   30   32   34   38   40   42   43   45 
LCS_GDT     K    88_A     K    88_A      4    6   18      3    4    5    5    5    7    8   10   14   19   21   23   25   27   31   36   38   40   43   45 
LCS_GDT     M    89_A     M    89_A      5    6   14      3    3    5    6    6    6    8   10   11   12   15   18   20   21   23   27   30   34   38   43 
LCS_GDT     E    90_A     E    90_A      5    6   14      3    5    5    6    6    6    8   10   11   14   16   18   20   23   27   29   30   34   38   41 
LCS_GDT     G    91_A     G    91_A      5    6   14      3    5    5    6    6    6    8   10   11   15   18   21   23   23   27   30   32   35   39   43 
LCS_GDT     F    92_A     F    92_A      5    6   14      3    5    5    6    6    6    8   10   11   12   15   16   20   21   22   25   28   32   35   38 
LCS_GDT     G    93_A     G    93_A      5    6   14      3    5    5    6    6    6    8   10   11   11   15   16   17   18   22   25   26   32   35   38 
LCS_GDT     I    94_A     I    94_A      5    6   14      3    5    5    6    6    6    8   10   11   11   15   16   20   21   22   25   28   32   35   38 
LCS_AVERAGE  LCS_A:  17.15  (   8.01   13.13   30.32 )

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      7     11     18     21     22     23     24     25     26     26     28     30     34     36     37     38     40     42     43     45 
GDT PERCENT_AT   6.73  10.58  17.31  20.19  21.15  22.12  23.08  24.04  25.00  25.00  26.92  28.85  32.69  34.62  35.58  36.54  38.46  40.38  41.35  43.27
GDT RMS_LOCAL    0.28   0.66   0.99   1.25   1.47   1.47   1.59   1.79   2.00   2.00   3.56   4.09   4.49   4.67   4.94   4.95   5.31   5.65   5.73   6.09
GDT RMS_ALL_AT  25.14  26.12  25.92  26.28  25.28  26.12  26.31  26.07  25.87  25.87  25.30  15.51  15.21  15.26  15.21  15.36  15.07  14.79  14.81  14.52

# Checking swapping
#   possible swapping detected:  Y    80_A      Y    80_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    V    23_A      V    23_A     3.530     0    0.164   1.168     6.691   48.333   38.571
LGA    H    24_A      H    24_A     2.364     0    0.169   0.873     2.760   62.857   69.000
LGA    N    25_A      N    25_A     2.329     0    0.158   1.154     3.261   68.810   63.988
LGA    I    26_A      I    26_A     0.590     0    0.240   1.356     5.052   88.214   73.988
LGA    K    27_A      K    27_A     0.514     0    0.029   0.218     1.154   90.476   89.471
LGA    C    28_A      C    28_A     0.722     0    0.035   0.077     1.025   90.476   88.968
LGA    H    29_A      H    29_A     0.922     0    0.035   1.182     3.309   85.952   76.810
LGA    F    30_A      F    30_A     1.487     0    0.039   0.614     3.412   83.690   74.286
LGA    D    31_A      D    31_A     0.907     0    0.119   0.696     4.486   90.595   71.548
LGA    N    32_A      N    32_A     1.849     0    0.116   0.989     5.358   75.000   57.440
LGA    C    33_A      C    33_A     0.963     0    0.054   0.732     3.281   85.952   80.714
LGA    N    34_A      N    34_A     0.913     0    0.129   0.598     1.725   86.071   83.810
LGA    R    35_A      R    35_A     0.632     0    0.610   1.013     8.124   82.262   57.965
LGA    K    36_A      K    36_A     2.731     0    0.627   1.299     5.971   49.643   49.418
LGA    I    37_A      I    37_A     8.933     0    0.583   1.135    13.203    4.167    2.083
LGA    H    38_A      H    38_A    11.584     0    0.551   1.142    12.485    0.000    0.000
LGA    W    39_A      W    39_A    11.787     0    0.429   0.983    20.357    0.000    0.000
LGA    K    40_A      K    40_A    12.225     0    0.645   0.810    12.592    0.000    0.000
LGA    I    41_A      I    41_A    13.556     0    0.068   0.135    18.228    0.000    0.000
LGA    R    42_A      R    42_A    14.864     0    0.112   1.251    23.886    0.000    0.000
LGA    Y    43_A      Y    43_A    11.524     0    0.121   1.496    12.143    0.000    0.000
LGA    G    44_A      G    44_A     8.662     0    0.113   0.113     9.611   10.714   10.714
LGA    K    45_A      K    45_A     5.100     0    0.202   1.268     6.554   30.000   28.783
LGA    L    46_A      L    46_A     4.175     0    0.083   1.381     8.497   45.357   29.345
LGA    R    47_A      R    47_A     1.609     0    0.138   0.991     4.947   75.476   64.459
LGA    L    48_A      L    48_A     1.024     0    0.042   1.365     5.917   88.333   65.595
LGA    V    49_A      V    49_A     1.203     0    0.019   0.135     2.166   83.929   78.027
LGA    D    50_A      D    50_A     1.589     0    0.029   0.792     4.800   79.286   65.179
LGA    H    51_A      H    51_A     0.289     0    0.027   0.278     1.587   92.857   88.810
LGA    A    52_A      A    52_A     0.980     0    0.108   0.114     1.344   85.952   85.048
LGA    L    53_A      L    53_A     1.408     0    0.122   1.382     5.844   85.952   66.429
LGA    S    54_A      S    54_A     0.685     0    0.136   0.261     1.251   90.595   87.540
LGA    H    55_A      H    55_A     1.416     0    0.331   1.082     4.241   66.548   66.333
LGA    Q    56_A      Q    56_A     2.874     0    0.663   1.008     7.254   38.333   54.233
LGA    E    57_A      E    57_A     9.169     4    0.158   0.153    13.765    3.690    1.799
LGA    E    58_A      E    58_A    13.655     4    0.206   0.226    14.701    0.000    0.000
LGA    K    59_A      K    59_A    18.671     0    0.548   0.982    25.512    0.000    0.000
LGA    S    60_A      S    60_A    21.293     0    0.655   0.865    22.165    0.000    0.000
LGA    I    61_A      I    61_A    23.467     0    0.162   1.554    27.382    0.000    0.000
LGA    D    62_A      D    62_A    30.314     0    0.146   1.202    33.210    0.000    0.000
LGA    C    63_A      C    63_A    32.727     0    0.160   0.211    36.608    0.000    0.000
LGA    Q    64_A      Q    64_A    36.675     0    0.117   1.639    40.807    0.000    0.000
LGA    K    65_A      K    65_A    40.055     0    0.061   0.696    44.198    0.000    0.000
LGA    C    66_A      C    66_A    43.658     0    0.711   0.642    43.818    0.000    0.000
LGA    E    67_A      E    67_A    42.807     4    0.440   0.417    45.035    0.000    0.000
LGA    Y    68_A      Y    68_A    38.381     0    0.083   1.376    39.615    0.000    0.000
LGA    S    69_A      S    69_A    32.931     0    0.116   0.580    35.245    0.000    0.000
LGA    C    70_A      C    70_A    27.366     0    0.246   0.671    28.790    0.000    0.000
LGA    Q    71_A      Q    71_A    22.412     0    0.648   1.167    24.668    0.000    0.000
LGA    T    72_A      T    72_A    19.417     0    0.137   0.261    22.567    0.000    0.000
LGA    T    73_A      T    73_A    19.083     0    0.042   1.057    21.471    0.000    0.000
LGA    R    74_A      R    74_A    23.909     0    0.620   1.366    33.770    0.000    0.000
LGA    Q    75_A      Q    75_A    27.300     0    0.225   0.843    30.048    0.000    0.000
LGA    M    76_A      M    76_A    24.793     0    0.061   1.252    25.679    0.000    0.000
LGA    R    77_A      R    77_A    24.010     0    0.060   1.056    26.933    0.000    0.000
LGA    Y    78_A      Y    78_A    30.066     0    0.055   1.386    41.390    0.000    0.000
LGA    H    79_A      H    79_A    31.860     0    0.545   0.626    37.153    0.000    0.000
LGA    Y    80_A      Y    80_A    30.911     0    0.199   0.648    32.690    0.000    0.000
LGA    K    81_A      K    81_A    33.804     0    0.605   1.294    37.314    0.000    0.000
LGA    K    82_A      K    82_A    39.202     0    0.282   0.540    43.757    0.000    0.000
LGA    I    83_A      I    83_A    43.954     0    0.652   0.993    46.177    0.000    0.000
LGA    H    84_A      H    84_A    46.376     0    0.200   0.230    48.383    0.000    0.000
LGA    A    85_A      A    85_A    46.208     0    0.602   0.547    47.196    0.000    0.000
LGA    N    86_A      N    86_A    50.558     3    0.254   0.245    53.358    0.000    0.000
LGA    L    87_A      L    87_A    47.554     0    0.631   1.354    48.447    0.000    0.000
LGA    K    88_A      K    88_A    46.276     0    0.643   1.510    48.653    0.000    0.000
LGA    M    89_A      M    89_A    47.106     0    0.167   1.073    47.595    0.000    0.000
LGA    E    90_A      E    90_A    46.694     0    0.316   0.992    49.592    0.000    0.000
LGA    G    91_A      G    91_A    43.537     0    0.375   0.375    44.246    0.000    0.000
LGA    F    92_A      F    92_A    44.025     0    0.454   1.098    52.573    0.000    0.000
LGA    G    93_A      G    93_A    42.724     0    0.584   0.584    43.895    0.000    0.000
LGA    I    94_A      I    94_A    39.474     0    0.696   1.026    40.090    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       72     288    288  100.00     597    597  100.00               104
SUMMARY(RMSD_GDC):    10.757         10.630                 11.817           18.938   17.023

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   72  104    4.0     25    1.79    22.837    20.910     1.321

LGA_LOCAL      RMSD:   1.792  Number of atoms:   25  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  26.068  Number of assigned atoms:   72 
Std_ASGN_ATOMS RMSD:  10.757  Standard rmsd on all 72 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.735858 * X  +  -0.453598 * Y  +  -0.502754 * Z  + -11.059057
  Y_new =  -0.449893 * X  +   0.227394 * Y  +  -0.863648 * Z  +   6.047800
  Z_new =   0.506072 * X  +   0.861708 * Y  +  -0.036741 * Z  +  -8.715611 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.548749 -0.530624  1.613408   [DEG:  -31.4410  -30.4025   92.4415 ]
ZXZ: -0.527175  1.607545  0.531021   [DEG:  -30.2049   92.1056   30.4253 ]
 
# END of job
