
#######################################################
#                                                     #
#                        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        2.04     2.04
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    62       1_A - 62_A        2.00     2.04
  LCS_AVERAGE:     98.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    32       5_A - 36_A        0.97     3.46
  LCS_AVERAGE:     36.43

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     11   62   63      3   16   30   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     2_A     S     2_A     12   62   63      3   16   28   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     3_A     S     3_A     12   62   63      3   13   25   43   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     F     4_A     F     4_A     12   62   63      3   13   31   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     5_A     C     5_A     32   62   63      4   21   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D     6_A     D     6_A     32   62   63      6   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S     7_A     S     7_A     32   62   63      4   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K     8_A     K     8_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C     9_A     C     9_A     32   62   63      4   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    10_A     G    10_A     32   62   63      8   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    11_A     V    11_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    12_A     R    12_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    13_A     C    13_A     32   62   63      9   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    14_A     S    14_A     32   62   63      5   21   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    15_A     K    15_A     32   62   63      4   11   30   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     A    16_A     A    16_A     32   62   63      4   15   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    17_A     G    17_A     32   62   63      4   21   30   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    18_A     Y    18_A     32   62   63     10   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Q    19_A     Q    19_A     32   62   63      4   16   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    20_A     E    20_A     32   62   63      6   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    21_A     R    21_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    22_A     C    22_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    23_A     L    23_A     32   62   63      6   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    24_A     K    24_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    26_A     C    26_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    27_A     G    27_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     I    28_A     I    28_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    29_A     C    29_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    30_A     C    30_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    31_A     E    31_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    32_A     K    32_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    33_A     C    33_A     32   62   63     11   23   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     H    34_A     H    34_A     32   62   63     11   22   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    35_A     C    35_A     32   62   63     11   21   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     V    36_A     V    36_A     32   62   63     10   21   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   62   63     10   21   31   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    38_A     S    38_A     25   62   63     11   21   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    39_A     G    39_A     25   62   63     10   20   32   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     T    40_A     T    40_A     24   62   63      4   19   32   39   52   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    41_A     Y    41_A     16   62   63      3   11   26   34   52   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   62   63      3    8   18   37   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    43_A     N    43_A     12   62   63      5   19   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    44_A     K    44_A     12   62   63      3   17   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    45_A     D    45_A     12   62   63      3    8   23   38   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     E    46_A     E    46_A     12   62   63      4   16   29   42   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    47_A     C    47_A     12   62   63      4   17   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    48_A     P    48_A     12   62   63      5    7   20   34   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    49_A     C    49_A     12   62   63      5   11   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     12   62   63      5   11   30   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     R    51_A     R    51_A     12   62   63      5    8   30   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     D    52_A     D    52_A     12   62   63      5   17   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     L    53_A     L    53_A     12   62   63      4   17   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    54_A     K    54_A     12   62   63      4   16   25   42   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    55_A     N    55_A     12   62   63      3   11   24   35   50   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     S    56_A     S    56_A     12   62   63      3   11   23   35   42   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    57_A     K    57_A     12   62   63      3   12   23   35   43   55   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     G    58_A     G    58_A     12   62   63      4   10   24   38   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     N    59_A     N    59_A     11   62   63      8   17   29   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    60_A     P    60_A     11   62   63     11   21   31   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     K    61_A     K    61_A     11   62   63      4   10   30   44   53   59   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     C    62_A     C    62_A     11   62   63      5   16   31   38   48   56   61   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_GDT     P    63_A     P    63_A     11   56   63      3   15   30   38   45   52   59   63   63   63   63   63   63   63   63   63   63   63   63   63 
LCS_AVERAGE  LCS_A:  78.23  (  36.43   98.26  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     11     23     32     44     53     59     61     63     63     63     63     63     63     63     63     63     63     63     63     63 
GDT PERCENT_AT  17.46  36.51  50.79  69.84  84.13  93.65  96.83 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.32   0.61   0.92   1.40   1.61   1.82   1.95   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04
GDT RMS_ALL_AT   2.46   3.74   3.36   2.36   2.13   2.06   2.05   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04   2.04

# Checking swapping
#   possible swapping detected:  D     6_A      D     6_A
#   possible swapping detected:  E    20_A      E    20_A
#   possible swapping detected:  Y    25_A      Y    25_A
#   possible swapping detected:  E    31_A      E    31_A
#   possible swapping detected:  Y    41_A      Y    41_A
#   possible swapping detected:  D    45_A      D    45_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     2.146     0    0.167   0.167     2.755   71.190   71.190
LGA    S     2_A      S     2_A     2.296     0    0.160   0.812     3.542   68.810   61.429
LGA    S     3_A      S     3_A     2.481     0    0.149   0.365     4.725   64.762   56.746
LGA    F     4_A      F     4_A     1.669     0    0.055   0.301     3.347   72.857   64.372
LGA    C     5_A      C     5_A     1.945     0    0.081   0.799     2.765   72.857   68.889
LGA    D     6_A      D     6_A     1.955     0    0.075   0.818     4.017   70.833   59.821
LGA    S     7_A      S     7_A     2.463     0    0.126   0.246     2.822   62.857   63.492
LGA    K     8_A      K     8_A     1.634     0    0.109   0.671     3.653   72.857   67.407
LGA    C     9_A      C     9_A     1.711     0    0.053   0.216     1.779   72.857   72.857
LGA    G    10_A      G    10_A     1.634     0    0.084   0.084     1.676   75.000   75.000
LGA    V    11_A      V    11_A     2.188     0    0.028   0.192     2.652   64.762   63.673
LGA    R    12_A      R    12_A     1.965     0    0.034   1.349     7.703   72.857   55.584
LGA    C    13_A      C    13_A     1.063     0    0.653   0.744     2.578   77.619   77.460
LGA    S    14_A      S    14_A     1.219     0    0.050   0.118     1.578   79.286   80.000
LGA    K    15_A      K    15_A     1.563     0    0.195   1.156    10.070   79.286   49.101
LGA    A    16_A      A    16_A     1.470     0    0.126   0.121     2.310   75.119   76.381
LGA    G    17_A      G    17_A     2.355     0    0.182   0.182     2.857   65.119   65.119
LGA    Y    18_A      Y    18_A     2.469     0    0.350   1.167     7.933   64.881   51.508
LGA    Q    19_A      Q    19_A     1.430     0    0.067   0.894     4.015   81.429   64.127
LGA    E    20_A      E    20_A     2.427     0    0.027   0.972     7.554   62.857   41.587
LGA    R    21_A      R    21_A     2.706     0    0.054   1.359     9.260   62.857   31.905
LGA    C    22_A      C    22_A     1.584     0    0.079   0.174     1.806   75.000   75.714
LGA    L    23_A      L    23_A     1.347     0    0.045   0.964     4.560   81.429   68.036
LGA    K    24_A      K    24_A     1.942     0    0.044   1.240    10.886   72.857   44.709
LGA    Y    25_A      Y    25_A     2.133     0    0.111   0.264     2.436   68.810   68.810
LGA    C    26_A      C    26_A     1.199     0    0.051   0.678     2.578   81.429   77.381
LGA    G    27_A      G    27_A     0.989     0    0.025   0.025     1.290   85.952   85.952
LGA    I    28_A      I    28_A     1.568     0    0.019   1.358     6.342   79.286   61.667
LGA    C    29_A      C    29_A     1.378     0    0.109   0.657     4.113   85.952   75.635
LGA    C    30_A      C    30_A     0.892     0    0.095   0.089     1.154   88.214   90.556
LGA    E    31_A      E    31_A     0.904     0    0.064   0.958     4.053   85.952   76.720
LGA    K    32_A      K    32_A     1.219     0    0.056   1.528     5.688   81.429   67.037
LGA    C    33_A      C    33_A     1.247     0    0.130   0.165     1.975   79.286   81.508
LGA    H    34_A      H    34_A     1.481     0    0.132   1.170     3.011   79.286   75.048
LGA    C    35_A      C    35_A     1.365     0    0.018   0.184     1.883   81.429   78.571
LGA    V    36_A      V    36_A     1.313     0    0.083   0.338     2.553   81.429   75.510
LGA    P    37_A      P    37_A     0.922     0    0.042   0.177     1.185   88.214   86.599
LGA    S    38_A      S    38_A     1.323     0    0.272   0.688     5.050   81.548   69.524
LGA    G    39_A      G    39_A     1.668     0    0.038   0.038     2.467   68.810   68.810
LGA    T    40_A      T    40_A     2.946     0    0.544   0.442     4.136   52.262   55.578
LGA    Y    41_A      Y    41_A     3.050     0    0.222   1.316     9.913   57.381   34.365
LGA    G    42_A      G    42_A     2.571     0    0.678   0.678     4.534   50.714   50.714
LGA    N    43_A      N    43_A     1.394     0    0.199   1.098     5.010   81.429   62.440
LGA    K    44_A      K    44_A     1.334     0    0.021   0.905     7.261   77.143   57.725
LGA    D    45_A      D    45_A     2.377     0    0.110   0.947     4.477   66.786   59.524
LGA    E    46_A      E    46_A     1.946     0    0.080   0.435     3.415   72.976   66.825
LGA    C    47_A      C    47_A     1.220     0    0.041   0.648     2.706   72.976   71.746
LGA    P    48_A      P    48_A     2.286     0    0.154   0.281     2.659   70.833   69.524
LGA    C    49_A      C    49_A     1.679     0    0.096   0.221     1.937   77.143   78.651
LGA    Y    50_A      Y    50_A     1.781     0    0.125   0.845     5.217   72.857   55.159
LGA    R    51_A      R    51_A     1.219     0    0.049   1.544     7.187   83.690   62.857
LGA    D    52_A      D    52_A     0.238     0    0.042   0.649     2.380   97.619   89.762
LGA    L    53_A      L    53_A     0.981     0    0.095   0.963     4.780   85.952   73.214
LGA    K    54_A      K    54_A     1.565     0    0.043   1.056     4.535   70.952   67.460
LGA    N    55_A      N    55_A     2.909     0    0.080   0.088     3.309   55.476   56.310
LGA    S    56_A      S    56_A     4.247     0    0.030   0.502     6.128   37.262   32.937
LGA    K    57_A      K    57_A     4.051     0    0.222   0.844     6.732   40.238   30.899
LGA    G    58_A      G    58_A     2.751     0    0.046   0.046     3.101   59.167   59.167
LGA    N    59_A      N    59_A     0.665     0    0.045   1.475     4.564   90.833   73.631
LGA    P    60_A      P    60_A     1.524     0    0.099   0.393     3.358   75.000   68.503
LGA    K    61_A      K    61_A     2.620     0    0.066   1.077     3.615   53.810   59.312
LGA    C    62_A      C    62_A     3.621     0    0.122   0.562     4.578   43.452   41.429
LGA    P    63_A      P    63_A     3.909     0    0.534   0.536     4.179   41.786   45.374

# 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):     2.042          2.048                  3.051           71.825   64.580

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     63    2.04    76.587    87.152     2.941

LGA_LOCAL      RMSD:   2.042  Number of atoms:   63  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.042  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.042  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.872300 * X  +  -0.344829 * Y  +  -0.346677 * Z  +   2.953256
  Y_new =  -0.269861 * X  +  -0.251735 * Y  +   0.929411 * Z  +  -0.724309
  Z_new =  -0.407759 * X  +   0.904280 * Y  +   0.126533 * Z  +  -1.137951 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.841565  0.419998  1.431772   [DEG: -162.8097   24.0641   82.0345 ]
ZXZ: -2.784570  1.443923 -0.423620   [DEG: -159.5441   82.7307  -24.2716 ]
 
# END of job
