
#######################################################
#                                                     #
#                        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   63 (  472),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  472),  selected   63 , 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:    63       1_A - 63_A        4.12     4.12
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       3_A - 37_A        1.95     4.97
  LONGEST_CONTINUOUS_SEGMENT:    35       5_A - 39_A        1.99     4.93
  LCS_AVERAGE:     46.51

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24       8_A - 31_A        0.97     6.14
  LONGEST_CONTINUOUS_SEGMENT:    24       9_A - 32_A        0.93     6.23
  LCS_AVERAGE:     28.97

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   63
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     G     1_A     G     1_A      3   26   63      3    3    5   12   27   28   36   42   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     S     2_A     S     2_A     10   28   63      5    8   12   15   20   25   33   36   38   47   51   58   60   61   62   62   62   63   63   63 
LCS_GDT     S     3_A     S     3_A     10   35   63      5    8   12   16   27   33   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     F     4_A     F     4_A     10   35   63      5    8   12   19   27   33   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C     5_A     C     5_A     10   35   63      5    9   17   22   30   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     D     6_A     D     6_A     10   35   63      5    9   17   24   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     S     7_A     S     7_A     10   35   63      4   13   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K     8_A     K     8_A     24   35   63      4   13   23   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C     9_A     C     9_A     24   35   63      8   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     G    10_A     G    10_A     24   35   63      8   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     V    11_A     V    11_A     24   35   63      8   19   24   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     R    12_A     R    12_A     24   35   63      4   17   23   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    13_A     C    13_A     24   35   63      8   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     S    14_A     S    14_A     24   35   63      5   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    15_A     K    15_A     24   35   63      5   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     A    16_A     A    16_A     24   35   63      6   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     G    17_A     G    17_A     24   35   63      6   13   22   28   31   36   40   45   49   53   55   58   60   61   62   62   62   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     24   35   63      6   18   25   29   31   36   40   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     24   35   63      3   13   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     E    20_A     E    20_A     24   35   63      4   19   25   29   31   36   40   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     R    21_A     R    21_A     24   35   63      9   19   25   29   31   36   40   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    22_A     C    22_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     L    23_A     L    23_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    24_A     K    24_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    26_A     C    26_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     G    27_A     G    27_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     I    28_A     I    28_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    29_A     C    29_A     24   35   63      8   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    30_A     C    30_A     24   35   63      9   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     E    31_A     E    31_A     24   35   63      8   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    32_A     K    32_A     24   35   63      6   15   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    33_A     C    33_A     22   35   63      6   15   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     H    34_A     H    34_A     22   35   63      6   19   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    35_A     C    35_A     18   35   63      6   11   24   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     V    36_A     V    36_A     17   35   63      3   15   25   29   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     P    37_A     P    37_A      6   35   63      3    5    6   22   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     S    38_A     S    38_A      6   35   63      3    5    6    6   12   33   40   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     G    39_A     G    39_A      6   35   63      4   10   16   21   29   35   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     T    40_A     T    40_A      5    7   63      4    4    8   16   22   25   31   37   44   48   54   58   60   61   62   62   62   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      5    6   63      4    4    5    5    6    7   10   15   17   23   29   33   38   45   50   54   56   63   63   63 
LCS_GDT     G    42_A     G    42_A      5   22   63      4    4    5    5    6    8   14   21   27   31   40   49   54   59   62   62   62   63   63   63 
LCS_GDT     N    43_A     N    43_A     17   22   63      4   12   17   21   26   34   38   44   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    44_A     K    44_A     17   22   63      4    7   17   21   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     D    45_A     D    45_A     17   22   63      4    7   16   21   24   33   40   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     E    46_A     E    46_A     18   22   63      4   11   17   21   24   29   36   44   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    47_A     C    47_A     18   22   63      3   12   17   21   24   35   40   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     P    48_A     P    48_A     18   22   63      4    7   17   21   24   29   37   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    49_A     C    49_A     18   22   63      4   12   17   21   24   29   39   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     18   22   63      4   12   17   24   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     R    51_A     R    51_A     18   22   63      4   11   17   24   31   36   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     D    52_A     D    52_A     18   22   63      4   12   17   21   28   34   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     L    53_A     L    53_A     18   22   63      4   12   17   21   27   34   41   45   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    54_A     K    54_A     18   22   63      4   12   17   21   24   29   41   43   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     N    55_A     N    55_A     18   22   63      4   12   17   21   24   29   36   41   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     S    56_A     S    56_A     18   22   63      6   12   17   21   24   29   36   41   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    57_A     K    57_A     18   22   63      6   12   17   21   24   29   36   42   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     G    58_A     G    58_A     18   22   63      6   12   17   21   24   29   41   43   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     N    59_A     N    59_A     18   22   63      6   12   17   21   25   29   41   43   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     P    60_A     P    60_A     18   22   63      6   12   17   21   27   32   41   44   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     K    61_A     K    61_A     18   22   63      6    9   17   21   24   29   36   42   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     C    62_A     C    62_A     18   22   63      4   12   17   21   24   29   36   42   49   54   56   58   60   61   62   62   62   63   63   63 
LCS_GDT     P    63_A     P    63_A     18   22   63      3    9   17   21   24   29   36   39   45   51   56   58   60   61   62   62   62   63   63   63 
LCS_AVERAGE  LCS_A:  58.50  (  28.97   46.51  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      9     19     25     29     31     36     41     45     49     54     56     58     60     61     62     62     62     63     63     63 
GDT PERCENT_AT  14.29  30.16  39.68  46.03  49.21  57.14  65.08  71.43  77.78  85.71  88.89  92.06  95.24  96.83  98.41  98.41  98.41 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.64   1.00   1.17   1.48   1.81   2.46   2.53   2.73   3.17   3.31   3.43   3.57   3.68   3.87   3.87   3.87   4.12   4.12   4.12
GDT RMS_ALL_AT   6.26   5.98   5.53   5.42   5.06   4.90   4.41   4.74   4.71   4.24   4.19   4.19   4.19   4.16   4.13   4.13   4.13   4.12   4.12   4.12

# Checking swapping
#   possible swapping detected:  Y    18_A      Y    18_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  Y    50_A      Y    50_A
#   possible swapping detected:  D    52_A      D    52_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    G     1_A      G     1_A     4.625     0    0.026   0.026     6.794   23.095   23.095
LGA    S     2_A      S     2_A     6.475     0    0.301   0.964     8.164   25.238   19.286
LGA    S     3_A      S     3_A     4.085     0    0.141   0.324     6.289   48.333   40.317
LGA    F     4_A      F     4_A     3.093     0    0.032   0.255     7.346   57.381   33.420
LGA    C     5_A      C     5_A     2.338     0    0.127   0.144     2.900   71.310   67.857
LGA    D     6_A      D     6_A     2.165     0    0.079   1.078     7.331   68.810   45.714
LGA    S     7_A      S     7_A     2.068     0    0.082   0.241     3.386   65.238   65.079
LGA    K     8_A      K     8_A     2.799     0    0.153   0.878    10.578   61.071   39.788
LGA    C     9_A      C     9_A     1.808     0    0.017   0.035     2.311   68.810   73.016
LGA    G    10_A      G    10_A     2.377     0    0.086   0.086     2.887   60.952   60.952
LGA    V    11_A      V    11_A     4.028     0    0.029   1.340     6.605   40.357   36.463
LGA    R    12_A      R    12_A     3.825     0    0.019   1.318    10.385   45.000   28.095
LGA    C    13_A      C    13_A     2.165     0    0.638   0.713     3.485   59.167   63.810
LGA    S    14_A      S    14_A     2.885     0    0.067   0.577     3.561   57.143   57.460
LGA    K    15_A      K    15_A     2.566     0    0.129   0.686     5.342   60.952   50.952
LGA    A    16_A      A    16_A     1.339     0    0.644   0.585     2.486   77.381   78.190
LGA    G    17_A      G    17_A     2.710     0    0.028   0.028     3.443   59.286   59.286
LGA    Y    18_A      Y    18_A     2.617     0    0.326   1.355     6.781   62.976   48.532
LGA    Q    19_A      Q    19_A     1.507     0    0.049   0.996     2.838   79.405   72.222
LGA    E    20_A      E    20_A     2.895     0    0.042   0.908     4.424   57.262   49.577
LGA    R    21_A      R    21_A     3.131     0    0.065   1.163    11.169   55.357   27.749
LGA    C    22_A      C    22_A     1.739     0    0.083   0.124     2.053   68.810   71.587
LGA    L    23_A      L    23_A     1.308     0    0.019   1.177     4.047   77.143   70.536
LGA    K    24_A      K    24_A     2.677     0    0.060   1.196    11.964   59.048   35.026
LGA    Y    25_A      Y    25_A     2.930     0    0.136   0.563     3.851   55.357   51.865
LGA    C    26_A      C    26_A     1.756     0    0.017   0.063     1.949   75.000   75.714
LGA    G    27_A      G    27_A     1.040     0    0.040   0.040     1.263   81.429   81.429
LGA    I    28_A      I    28_A     2.028     0    0.012   0.753     5.232   70.833   57.619
LGA    C    29_A      C    29_A     2.431     0    0.124   0.730     6.110   66.786   55.714
LGA    C    30_A      C    30_A     1.468     0    0.136   0.140     1.730   81.548   80.079
LGA    E    31_A      E    31_A     0.870     0    0.038   0.863     4.066   88.214   75.979
LGA    K    32_A      K    32_A     1.015     0    0.018   0.945     1.873   83.690   79.577
LGA    C    33_A      C    33_A     1.303     0    0.206   0.244     1.649   79.286   80.000
LGA    H    34_A      H    34_A     1.315     0    0.169   0.904     2.530   81.429   79.238
LGA    C    35_A      C    35_A     0.870     0    0.077   0.154     3.533   70.000   69.762
LGA    V    36_A      V    36_A     2.835     0    0.013   1.266     7.021   73.214   50.204
LGA    P    37_A      P    37_A     2.081     0    0.029   0.310     5.144   73.214   56.190
LGA    S    38_A      S    38_A     3.506     0    0.184   0.688     7.533   59.524   43.730
LGA    G    39_A      G    39_A     2.996     0    0.708   0.708     6.398   39.405   39.405
LGA    T    40_A      T    40_A     9.463     0    0.484   0.607    12.176    3.690    2.517
LGA    Y    41_A      Y    41_A    13.678     0    0.051   1.416    23.999    0.000    0.000
LGA    G    42_A      G    42_A    11.312     0    0.592   0.592    12.202    3.690    3.690
LGA    N    43_A      N    43_A     4.551     0    0.674   1.204     9.259   33.690   21.548
LGA    K    44_A      K    44_A     1.513     0    0.028   0.698     2.605   64.881   74.127
LGA    D    45_A      D    45_A     3.870     0    0.172   0.875     5.558   43.690   35.655
LGA    E    46_A      E    46_A     4.577     0    0.250   0.279     7.097   37.262   28.836
LGA    C    47_A      C    47_A     2.997     0    0.049   0.663     4.492   53.571   52.698
LGA    P    48_A      P    48_A     4.088     0    0.201   0.405     5.534   46.905   38.095
LGA    C    49_A      C    49_A     3.595     0    0.097   0.177     5.286   50.238   44.048
LGA    Y    50_A      Y    50_A     1.464     0    0.123   0.606     4.403   75.119   62.103
LGA    R    51_A      R    51_A     1.504     0    0.018   1.371     8.475   72.976   49.913
LGA    D    52_A      D    52_A     3.050     0    0.114   0.767     3.957   52.024   51.012
LGA    L    53_A      L    53_A     3.750     0    0.032   0.939     4.436   41.905   47.857
LGA    K    54_A      K    54_A     6.192     0    0.016   1.090    10.682   15.833   10.847
LGA    N    55_A      N    55_A     8.819     0    0.058   0.181    10.067    3.571    2.321
LGA    S    56_A      S    56_A    10.089     0    0.129   0.521    12.196    0.238    0.159
LGA    K    57_A      K    57_A     9.435     0    0.039   0.756    11.134    2.381    1.111
LGA    G    58_A      G    58_A     7.657     0    0.058   0.058     8.353    8.810    8.810
LGA    N    59_A      N    59_A     7.193     0    0.034   0.316     9.138   10.833    8.036
LGA    P    60_A      P    60_A     5.953     0    0.126   0.351     6.564   17.262   18.435
LGA    K    61_A      K    61_A     7.012     0    0.066   1.378     7.220   11.667   14.868
LGA    C    62_A      C    62_A     6.492     0    0.126   0.559     6.850   14.286   16.111
LGA    P    63_A      P    63_A     7.684     0    0.430   0.545     8.394    9.286    8.435

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     472    472  100.00                63
SUMMARY(RMSD_GDC):     4.117          4.014                  5.211           50.195   44.377

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     45    2.53    61.508    60.632     1.711

LGA_LOCAL      RMSD:   2.531  Number of atoms:   45  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.743  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   4.117  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.273872 * X  +  -0.482779 * Y  +  -0.831817 * Z  +  -7.993976
  Y_new =  -0.042386 * X  +  -0.870103 * Y  +   0.491044 * Z  +   2.099005
  Z_new =  -0.960832 * X  +  -0.099226 * Y  +  -0.258760 * Z  +  -6.688970 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.153546  1.289988 -2.775418   [DEG:   -8.7976   73.9109 -159.0197 ]
ZXZ: -2.104074  1.832534 -1.673703   [DEG: -120.5545  104.9965  -95.8961 ]
 
# END of job
