
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    45      32_A - 76_A        4.87    11.31
  LCS_AVERAGE:     62.32

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      55_A - 76_A        1.84    10.87
  LCS_AVERAGE:     28.35

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      63_A - 76_A        0.81    11.79
  LCS_AVERAGE:     17.33

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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    32_A     A    32_A      3   11   45      4   13   15   20   23   24   26   27   30   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     T    33_A     T    33_A      5   13   45      3    4    5    9   23   23   25   26   27   29   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     M    34_A     M    34_A      8   13   45      3    5    8   10   14   17   24   28   31   33   35   37   38   39   39   42   43   44   45   45 
LCS_GDT     A    35_A     A    35_A      9   14   45      4    7   11   13   17   21   24   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     D    36_A     D    36_A      9   14   45      3    7   11   13   18   21   26   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     L    37_A     L    37_A      9   14   45      4    7   11   13   17   23   26   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     K    38_A     K    38_A      9   14   45      4    7   14   20   23   24   26   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     M    39_A     M    39_A      9   14   45      4    8   11   13   17   21   24   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     Q    40_A     Q    40_A      9   14   45      3    8   11   13   14   21   24   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     A    41_A     A    41_A      9   14   45      4    8   11   13   14   17   19   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     V    42_A     V    42_A      9   14   45      3    8   12   17   21   24   26   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     K    43_A     K    43_A      9   14   45      4    8   11   13   17   21   24   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     E    44_A     E    44_A      9   14   45      4    8   11   13   14   17   24   28   31   33   35   37   37   39   39   42   42   43   45   45 
LCS_GDT     I    45_A     I    45_A      9   14   45      5    8   11   13   18   21   24   26   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     C    46_A     C    46_A      9   14   45      5    8    9   13   17   21   24   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     Y    47_A     Y    47_A      9   14   45      5    8    9   12   17   21   24   28   31   33   35   37   37   39   40   42   43   44   45   45 
LCS_GDT     E    48_A     E    48_A      9   14   45      6    8   11   15   18   21   24   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     V    49_A     V    49_A      9   13   45      6    8    9   11   11   13   18   24   29   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     A    50_A     A    50_A      9   13   45      6    8    9   11   11   13   15   17   22   31   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     L    51_A     L    51_A      9   13   45      6    8    9   11   11   13   15   17   22   31   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     A    52_A     A    52_A      9   13   45      6    8    9   11   11   18   22   25   30   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     D    53_A     D    53_A      9   13   45      6    8    9   11   11   13   14   18   21   24   30   33   36   38   40   42   43   44   45   45 
LCS_GDT     F    54_A     F    54_A      3   17   45      3    3    5    8   11   16   22   28   31   33   35   37   37   39   40   42   43   44   45   45 
LCS_GDT     R    55_A     R    55_A      3   22   45      3    6   11   15   18   23   25   28   31   33   35   37   38   39   40   42   43   44   45   45 
LCS_GDT     H    56_A     H    56_A      3   22   45      3    3    5   18   23   24   26   27   31   33   35   37   38   38   40   42   43   44   45   45 
LCS_GDT     G    57_A     G    57_A     13   22   45      9   11   15   19   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     R    58_A     R    58_A     13   22   45      9   11   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     A    59_A     A    59_A     13   22   45      9   11   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     E    60_A     E    60_A     13   22   45      9   11   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     I    61_A     I    61_A     13   22   45      9   11   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     E    62_A     E    62_A     13   22   45      9   11   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     A    63_A     A    63_A     14   22   45      9   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     L    64_A     L    64_A     14   22   45      9   11   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     A    65_A     A    65_A     14   22   45      9   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     A    66_A     A    66_A     14   22   45      4   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     L    67_A     L    67_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     K    68_A     K    68_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     M    69_A     M    69_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     R    70_A     R    70_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     E    71_A     E    71_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     L    72_A     L    72_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     C    73_A     C    73_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     R    74_A     R    74_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     T    75_A     T    75_A     14   22   45      7   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     Y    76_A     Y    76_A     14   22   45      5   13   15   20   23   24   26   27   30   33   35   36   38   38   40   42   43   44   45   45 
LCS_GDT     G    83_A     G    83_A      3   16   24      3    3    3    6   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     D    84_A     D    84_A      7   16   18      4    4    7    9   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     A    85_A     A    85_A      9   16   18      4    6   11   12   13   20   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     W    86_A     W    86_A     12   16   18      4    7   11   12   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     R    87_A     R    87_A     12   16   18      6   10   11   13   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     A    88_A     A    88_A     12   16   18      6   10   11   13   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     V    89_A     V    89_A     12   16   18      6   10   11   13   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   45 
LCS_GDT     A    90_A     A    90_A     12   16   18      6   10   11   13   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     R    91_A     R    91_A     12   16   18      6   10   11   13   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     D    92_A     D    92_A     12   16   18      6   10   11   13   16   20   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     V    93_A     V    93_A     12   16   18      6   10   11   13   17   20   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     W    94_A     W    94_A     12   16   18      6   10   11   13   17   21   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     D    95_A     D    95_A     12   16   18      6   10   11   13   16   19   24   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     T    96_A     T    96_A     12   16   18      6   10   11   13   15   16   23   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     V    97_A     V    97_A     12   16   18      4   10   11   13   15   16   23   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_GDT     G    98_A     G    98_A     12   16   18      4    4   10   12   15   16   23   28   31   33   35   37   37   39   39   40   40   40   42   43 
LCS_AVERAGE  LCS_A:  36.00  (  17.33   28.35   62.32 )

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      9     13     15     20     23     24     26     28     31     33     35     37     38     39     40     42     43     44     45     45 
GDT PERCENT_AT  14.75  21.31  24.59  32.79  37.70  39.34  42.62  45.90  50.82  54.10  57.38  60.66  62.30  63.93  65.57  68.85  70.49  72.13  73.77  73.77
GDT RMS_LOCAL    0.32   0.65   0.79   1.36   1.58   1.71   1.99   2.71   2.92   3.06   3.30   3.56   3.70   3.81   4.03   4.34   4.52   4.70   4.87   4.87
GDT RMS_ALL_AT  10.84  12.11  11.80  11.07  10.89  10.97  11.09  10.86  10.84  10.93  11.49  10.86  11.59  11.13  11.53  11.37  11.28  11.22  11.31  11.31

# Checking swapping
#   possible swapping detected:  Y    47_A      Y    47_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  Y    76_A      Y    76_A
#   possible swapping detected:  D    95_A      D    95_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     7.066     0    0.331   0.319     9.339   17.262   16.476
LGA    T    33_A      T    33_A     6.171     0    0.598   0.512    10.170   22.976   13.605
LGA    M    34_A      M    34_A     4.281     0    0.107   1.498     5.961   47.619   38.274
LGA    A    35_A      A    35_A     1.189     0    0.183   0.186     2.231   75.119   74.667
LGA    D    36_A      D    36_A     1.992     0    0.145   0.174     4.526   77.143   59.583
LGA    L    37_A      L    37_A     1.003     0    0.032   1.040     2.968   77.381   76.369
LGA    K    38_A      K    38_A     2.429     0    0.090   1.109     6.005   62.976   50.106
LGA    M    39_A      M    39_A     2.474     0    0.122   0.870     4.510   60.952   55.060
LGA    Q    40_A      Q    40_A     3.357     0    0.032   1.409     6.826   46.905   37.196
LGA    A    41_A      A    41_A     4.600     0    0.045   0.044     5.116   33.095   32.762
LGA    V    42_A      V    42_A     3.934     0    0.192   0.307     4.423   46.667   44.354
LGA    K    43_A      K    43_A     2.719     0    0.089   0.845     3.248   57.262   67.143
LGA    E    44_A      E    44_A     4.018     0    0.158   1.246     5.590   40.238   36.825
LGA    I    45_A      I    45_A     4.616     0    0.125   0.176     6.878   38.810   29.167
LGA    C    46_A      C    46_A     3.249     0    0.078   0.844     3.879   55.714   53.810
LGA    Y    47_A      Y    47_A     1.630     0    0.047   0.203     8.844   68.929   40.595
LGA    E    48_A      E    48_A     1.851     0    0.087   0.981     5.272   59.762   51.852
LGA    V    49_A      V    49_A     5.790     0    0.032   0.998     8.376   19.762   16.327
LGA    A    50_A      A    50_A     7.447     0    0.065   0.077     9.102    8.929    9.810
LGA    L    51_A      L    51_A     7.165     0    0.192   1.394     8.896    8.333    8.810
LGA    A    52_A      A    52_A     7.925     0    0.283   0.276     9.007    5.357    5.714
LGA    D    53_A      D    53_A    11.290     0    0.085   1.198    15.193    0.357    0.179
LGA    F    54_A      F    54_A     4.856     0    0.647   1.150     6.874   36.190   35.801
LGA    R    55_A      R    55_A     3.602     0    0.676   1.277     8.417   32.857   21.948
LGA    H    56_A      H    56_A     6.858     0    0.040   1.362     8.984   14.524    8.333
LGA    G    57_A      G    57_A    12.824     0    0.337   0.337    14.061    0.000    0.000
LGA    R    58_A      R    58_A    17.281     0    0.043   1.057    25.727    0.000    0.000
LGA    A    59_A      A    59_A    22.167     0    0.024   0.029    24.334    0.000    0.000
LGA    E    60_A      E    60_A    18.185     0    0.038   1.218    19.135    0.000    0.000
LGA    I    61_A      I    61_A    13.028     0    0.027   0.126    14.806    0.000    0.774
LGA    E    62_A      E    62_A    18.368     0    0.043   1.272    23.513    0.000    0.000
LGA    A    63_A      A    63_A    21.526     0    0.057   0.077    23.134    0.000    0.000
LGA    L    64_A      L    64_A    15.771     0    0.136   0.564    17.413    0.000    0.000
LGA    A    65_A      A    65_A    13.538     0    0.062   0.077    15.221    0.000    0.000
LGA    A    66_A      A    66_A    19.601     0    0.079   0.098    22.404    0.000    0.000
LGA    L    67_A      L    67_A    19.838     0    0.075   0.914    23.456    0.000    0.000
LGA    K    68_A      K    68_A    13.301     0    0.041   1.011    15.383    0.000    0.529
LGA    M    69_A      M    69_A    14.405     0    0.073   1.247    16.271    0.000    0.000
LGA    R    70_A      R    70_A    20.431     0    0.074   1.244    24.779    0.000    0.000
LGA    E    71_A      E    71_A    19.452     0    0.034   0.671    19.452    0.000    0.000
LGA    L    72_A      L    72_A    14.086     0    0.059   0.824    15.650    0.000    0.595
LGA    C    73_A      C    73_A    17.178     0    0.092   0.282    19.531    0.000    0.000
LGA    R    74_A      R    74_A    22.985     0    0.305   1.447    30.308    0.000    0.000
LGA    T    75_A      T    75_A    20.722     0    0.096   0.225    22.048    0.000    0.000
LGA    Y    76_A      Y    76_A    18.082     0    0.505   1.442    19.106    0.000    0.000
LGA    G    83_A      G    83_A     3.353     0    0.114   0.114     3.633   48.333   48.333
LGA    D    84_A      D    84_A     3.031     0    0.349   0.510     3.074   51.786   58.452
LGA    A    85_A      A    85_A     3.637     0    0.031   0.033     4.718   54.048   49.524
LGA    W    86_A      W    86_A     2.155     0    0.186   0.822     9.263   70.952   36.735
LGA    R    87_A      R    87_A     2.044     0    0.056   0.118     6.222   73.214   47.662
LGA    A    88_A      A    88_A     2.090     0    0.101   0.102     2.651   68.810   66.476
LGA    V    89_A      V    89_A     1.484     0    0.051   0.093     3.043   83.690   72.381
LGA    A    90_A      A    90_A     1.377     0    0.055   0.055     2.198   83.690   79.905
LGA    R    91_A      R    91_A     1.970     0    0.045   1.382    10.493   72.976   39.740
LGA    D    92_A      D    92_A     2.537     0    0.074   0.288     4.024   61.190   54.881
LGA    V    93_A      V    93_A     1.807     0    0.048   0.118     2.508   75.000   70.680
LGA    W    94_A      W    94_A     1.186     0    0.031   1.166     7.065   75.357   55.374
LGA    D    95_A      D    95_A     3.309     0    0.202   0.925     4.916   47.381   61.607
LGA    T    96_A      T    96_A     3.892     0    0.181   0.976     5.579   37.976   38.503
LGA    V    97_A      V    97_A     3.852     0    0.052   1.194     4.672   45.000   41.701
LGA    G    98_A      G    98_A     4.678     0    0.220   0.220     4.678   38.810   38.810

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     9.602          9.497                 10.301           32.842   28.646

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     28    2.71    42.213    39.990     0.998

LGA_LOCAL      RMSD:   2.707  Number of atoms:   28  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.865  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   9.602  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.732823 * X  +   0.630188 * Y  +  -0.256582 * Z  +   3.649137
  Y_new =  -0.586627 * X  +   0.394110 * Y  +  -0.707493 * Z  +  28.670647
  Z_new =  -0.344731 * X  +   0.668985 * Y  +   0.658498 * Z  +  -9.108435 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.675048  0.351953  0.793298   [DEG:  -38.6774   20.1654   45.4526 ]
ZXZ: -0.347912  0.851975 -0.475817   [DEG:  -19.9339   48.8146  -27.2623 ]
 
# END of job
