
#######################################################
#                                                     #
#                        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        4.54     4.54
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.98     5.08
  LCS_AVERAGE:     29.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.93     5.44
  LCS_AVERAGE:     18.85

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      3    3   64      3    3    4    7    7   11   15   21   29   38   45   56   58   60   61   62   63   63   63   63 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    5    5    7    7   18   22   33   43   53   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    24_A     G    24_A      3   16   64      3    8   16   30   37   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     D    25_A     D    25_A     14   16   64      3    5    9   28   38   42   47   51   52   54   54   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    26_A     G    26_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     Q    27_A     Q    27_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    28_A     G    28_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    29_A     L    29_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     Y    30_A     Y    30_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    31_A     A    31_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    32_A     A    32_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     N    33_A     N    33_A     14   16   64     11   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     C    34_A     C    34_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    35_A     A    35_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    36_A     A    36_A     14   16   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     C    37_A     C    37_A     14   16   64      4   25   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     H    38_A     H    38_A     14   16   64      4   25   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     14   16   64      4    8   20   30   37   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    40_A     A    40_A      4    7   64      4    4    4    7   13   19   23   37   49   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    41_A     L    41_A      4    6   64      4    4    4    5    6    6    8   13   18   22   29   34   47   52   60   61   63   63   63   63 
LCS_GDT     A    42_A     A    42_A      4    6   64      4    4    4    5    6    6    8    8   15   21   22   26   29   32   38   42   48   60   62   63 
LCS_GDT     T    43_A     T    43_A      4    6   64      4    4    4    5    6    6   12   17   23   26   29   38   48   54   60   62   63   63   63   63 
LCS_GDT     S    44_A     S    44_A      4    6   64      3    4    4    7   11   17   20   23   28   39   48   57   59   60   61   62   63   63   63   63 
LCS_GDT     E    45_A     E    45_A      4    6   64      3    4    4    6   17   32   44   50   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     K    46_A     K    46_A      4   18   64      0    4   10   16   18   19   23   27   45   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     K    47_A     K    47_A      4   18   64      3    4    4    4    6    9   13   18   24   39   51   57   59   60   61   62   63   63   63   63 
LCS_GDT     G    48_A     G    48_A      4   20   64      3    4    4    5   11   18   20   24   38   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     T    49_A     T    49_A     14   20   64      8   12   13   15   17   19   40   50   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     T    50_A     T    50_A     14   20   64     10   12   14   16   18   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    51_A     L    51_A     14   20   64     10   12   14   18   22   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    52_A     A    52_A     14   20   64     10   12   19   30   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     R    53_A     R    53_A     14   20   64     10   12   21   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    54_A     L    54_A     14   20   64     10   12   14   18   32   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     Q    55_A     Q    55_A     14   20   64     10   12   14   18   30   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   20   64     10   12   19   30   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    57_A     A    57_A     14   20   64     10   12   21   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     V    58_A     V    58_A     14   20   64     10   12   14   16   25   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     S    59_A     S    59_A     14   20   64     10   12   14   16   20   32   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    60_A     A    60_A     14   20   64      7   12   14   16   25   41   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     N    61_A     N    61_A     14   25   64      3   10   20   30   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    62_A     A    62_A     14   25   64      8   20   28   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    63_A     G    63_A     14   25   64      3    6   13   30   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    64_A     G    64_A      4   25   64      3    3   27   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     M    65_A     M    65_A      4   25   64      3    9   28   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     G    66_A     G    66_A      3   25   64      3    5   19   30   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     F    67_A     F    67_A      3   25   64      3    3    4    5   16   27   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    68_A     L    68_A      4   25   64      4    4    5    5   24   29   41   50   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     S    69_A     S    69_A     17   25   64      4   25   29   30   34   41   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     S    70_A     S    70_A     17   25   64      4    5    8   21   37   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    71_A     L    71_A     17   25   64      8   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     T    72_A     T    72_A     17   25   64     12   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     S    73_A     S    73_A     17   25   64      9   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    74_A     A    74_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     Q    75_A     Q    75_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    76_A     L    76_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     Q    77_A     Q    77_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    78_A     A    78_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     I    79_A     I    79_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     V    80_A     V    80_A     17   25   64     17   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     D    81_A     D    81_A     17   25   64     15   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     V    82_A     V    82_A     17   25   64      5   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     L    83_A     L    83_A     17   25   64     12   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     A    84_A     A    84_A     17   25   64     12   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_GDT     V    85_A     V    85_A     17   25   64      4   26   29   31   38   42   48   51   53   54   57   58   59   60   61   62   63   63   63   63 
LCS_AVERAGE  LCS_A:  49.55  (  18.85   29.81  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     17     26     29     31     38     42     48     51     53     54     57     58     59     60     61     62     63     63     63     63 
GDT PERCENT_AT  26.56  40.62  45.31  48.44  59.38  65.62  75.00  79.69  82.81  84.38  89.06  90.62  92.19  93.75  95.31  96.88  98.44  98.44  98.44  98.44
GDT RMS_LOCAL    0.33   0.52   0.66   0.96   1.48   1.77   2.10   2.24   2.48   2.51   3.16   3.19   3.35   3.56   3.69   3.99   4.21   4.21   4.21   4.21
GDT RMS_ALL_AT   5.35   5.37   5.32   5.31   5.33   5.45   5.19   5.22   5.05   5.08   4.77   4.79   4.73   4.66   4.65   4.58   4.55   4.55   4.55   4.55

# Checking swapping
#   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    10.155     0    0.021   0.029    11.945    1.667    1.333
LGA    D    23_A      D    23_A     8.700     0    0.109   1.152    13.117    9.762    4.940
LGA    G    24_A      G    24_A     3.610     0    0.492   0.492     5.634   45.238   45.238
LGA    D    25_A      D    25_A     3.170     0    0.276   0.878     9.709   51.905   30.833
LGA    G    26_A      G    26_A     1.258     0    0.101   0.101     1.371   81.429   81.429
LGA    Q    27_A      Q    27_A     1.149     0    0.032   1.512     5.691   83.690   68.624
LGA    G    28_A      G    28_A     1.008     0    0.038   0.038     1.121   85.952   85.952
LGA    L    29_A      L    29_A     0.522     0    0.039   1.352     4.012   95.238   79.762
LGA    Y    30_A      Y    30_A     0.412     0    0.047   0.097     0.781  100.000   95.238
LGA    A    31_A      A    31_A     0.726     0    0.050   0.052     0.885   90.476   90.476
LGA    A    32_A      A    32_A     0.934     0    0.117   0.115     1.554   83.810   85.143
LGA    N    33_A      N    33_A     1.221     0    0.201   1.138     3.174   75.476   75.655
LGA    C    34_A      C    34_A     0.889     0    0.039   0.173     0.889   90.476   92.063
LGA    A    35_A      A    35_A     0.759     0    0.098   0.095     0.873   92.857   92.381
LGA    A    36_A      A    36_A     0.576     0    0.093   0.090     1.070   90.476   88.667
LGA    C    37_A      C    37_A     2.178     0    0.096   0.099     2.952   64.881   62.302
LGA    H    38_A      H    38_A     2.229     0    0.157   1.105     5.534   64.762   55.952
LGA    G    39_A      G    39_A     3.145     0    0.132   0.132     6.840   35.476   35.476
LGA    A    40_A      A    40_A     9.542     0    0.630   0.592    11.443    3.452    2.762
LGA    L    41_A      L    41_A    14.095     0    0.028   1.387    18.518    0.000    0.000
LGA    A    42_A      A    42_A    17.280     0    0.128   0.129    19.003    0.000    0.000
LGA    T    43_A      T    43_A    15.201     0    0.623   0.619    18.503    0.000    0.000
LGA    S    44_A      S    44_A    12.075     0    0.149   0.574    13.946    0.000    0.000
LGA    E    45_A      E    45_A     6.519     0    0.573   1.354     8.329   13.214   21.429
LGA    K    46_A      K    46_A     8.667     0    0.582   1.207    10.446    2.619    1.587
LGA    K    47_A      K    47_A    10.368     0    0.058   1.401    10.952    2.976    1.323
LGA    G    48_A      G    48_A     8.705     0    0.663   0.663     9.893   12.976   12.976
LGA    T    49_A      T    49_A     5.251     0    0.363   0.512     9.860   21.786   15.374
LGA    T    50_A      T    50_A     3.629     0    0.044   1.051     4.029   45.119   49.252
LGA    L    51_A      L    51_A     3.386     0    0.058   1.405     7.331   53.571   38.095
LGA    A    52_A      A    52_A     1.825     0    0.034   0.042     2.246   70.833   72.952
LGA    R    53_A      R    53_A     1.634     0    0.030   0.604     6.140   72.857   52.078
LGA    L    54_A      L    54_A     2.965     0    0.035   0.233     4.341   55.357   49.405
LGA    Q    55_A      Q    55_A     3.259     0    0.036   1.170     3.328   51.786   58.466
LGA    S    56_A      S    56_A     2.153     0    0.061   0.060     2.378   64.762   67.460
LGA    A    57_A      A    57_A     1.642     0    0.043   0.049     2.195   68.810   71.333
LGA    V    58_A      V    58_A     3.380     0    0.032   1.011     5.331   48.452   45.782
LGA    S    59_A      S    59_A     4.246     0    0.103   0.569     4.886   37.262   36.270
LGA    A    60_A      A    60_A     3.625     0    0.729   0.689     5.678   37.857   40.286
LGA    N    61_A      N    61_A     1.791     0    0.617   1.254     4.952   65.476   59.167
LGA    A    62_A      A    62_A     0.273     0    0.227   0.250     2.484   84.167   81.905
LGA    G    63_A      G    63_A     2.551     0    0.540   0.540     2.551   69.048   69.048
LGA    G    64_A      G    64_A     2.112     0    0.031   0.031     2.857   64.881   64.881
LGA    M    65_A      M    65_A     1.882     0    0.695   0.626     3.767   65.476   68.214
LGA    G    66_A      G    66_A     2.130     0    0.676   0.676     2.782   64.881   64.881
LGA    F    67_A      F    67_A     4.013     0    0.308   1.047     5.843   38.810   43.074
LGA    L    68_A      L    68_A     4.256     0    0.302   0.911    10.508   46.786   27.024
LGA    S    69_A      S    69_A     3.373     0    0.146   0.619     4.469   50.476   46.032
LGA    S    70_A      S    70_A     3.320     0    0.137   0.642     4.084   53.810   49.286
LGA    L    71_A      L    71_A     1.302     0    0.086   0.932     2.364   72.976   75.298
LGA    T    72_A      T    72_A     1.841     0    0.063   0.066     1.851   72.857   74.082
LGA    S    73_A      S    73_A     2.357     0    0.058   0.086     2.642   64.762   63.492
LGA    A    74_A      A    74_A     1.570     0    0.038   0.040     1.720   75.000   76.286
LGA    Q    75_A      Q    75_A     0.764     0    0.058   0.236     1.313   90.476   90.529
LGA    L    76_A      L    76_A     1.253     0    0.030   0.084     1.623   81.429   79.286
LGA    Q    77_A      Q    77_A     1.483     0    0.029   1.475     7.476   79.286   56.032
LGA    A    78_A      A    78_A     1.240     0    0.035   0.038     1.361   81.429   81.429
LGA    I    79_A      I    79_A     1.187     0    0.032   0.139     1.374   81.429   82.560
LGA    V    80_A      V    80_A     1.716     0    0.030   0.095     2.087   75.000   72.925
LGA    D    81_A      D    81_A     1.734     0    0.060   0.538     3.096   72.857   68.988
LGA    V    82_A      V    82_A     1.904     0    0.109   0.978     3.716   72.857   70.000
LGA    L    83_A      L    83_A     1.931     0    0.145   0.924     4.015   75.000   68.452
LGA    A    84_A      A    84_A     2.285     0    0.093   0.091     2.426   64.762   64.762
LGA    V    85_A      V    85_A     2.248     0    0.266   0.285     2.331   64.762   64.762

# 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):     4.536          4.443                  4.920           56.812   54.229

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     51    2.24    66.406    59.913     2.177

LGA_LOCAL      RMSD:   2.242  Number of atoms:   51  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.225  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   4.536  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.170442 * X  +  -0.984151 * Y  +  -0.048952 * Z  +  67.922821
  Y_new =  -0.791613 * X  +   0.166342 * Y  +  -0.587945 * Z  +  23.074808
  Z_new =   0.586769 * X  +  -0.061459 * Y  +  -0.807418 * Z  +  22.973442 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.782869 -0.627063 -3.065621   [DEG: -102.1508  -35.9281 -175.6471 ]
ZXZ: -0.083068  2.510560  1.675158   [DEG:   -4.7594  143.8445   95.9795 ]
 
# END of job
