
#######################################################
#                                                     #
#                        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 (  471),  selected   63 , name one
# Molecule2: number of CA atoms   63 (  471),  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        2.65     2.65
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    60       4_A - 63_A        1.93     2.76
  LCS_AVERAGE:     93.15

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      14_A - 38_A        0.99     3.12
  LCS_AVERAGE:     29.58

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     A     1_A     A     1_A      3    4   63      3    3    4    4    4    4    6    7    8   17   26   31   35   37   42   48   61   63   63   63 
LCS_GDT     H     2_A     H     2_A      3   40   63      3    3    4    6   14   32   42   54   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I     3_A     I     3_A      3   53   63      3    3   15   16   24   29   42   47   59   60   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     4_A     D     4_A     20   60   63      8   18   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     5_A     C     5_A     20   60   63      8   14   33   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D     6_A     D     6_A     20   60   63      8   11   31   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K     7_A     K     7_A     20   60   63      8   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E     8_A     E     8_A     20   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C     9_A     C     9_A     20   60   63      8   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    10_A     N    10_A     20   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    11_A     R    11_A     20   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    12_A     R    12_A     20   60   63      5   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    13_A     C    13_A     20   60   63      8   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    14_A     S    14_A     25   60   63      6   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    15_A     K    15_A     25   60   63      3   11   21   43   53   56   57   58   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    16_A     A    16_A     25   60   63      4   20   38   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    17_A     S    17_A     25   60   63      5   20   34   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    18_A     A    18_A     25   60   63      3   16   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    19_A     H    19_A     25   60   63      4   19   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    20_A     D    20_A     25   60   63      7   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     R    21_A     R    21_A     25   60   63      7   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    22_A     C    22_A     25   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    23_A     L    23_A     25   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    24_A     K    24_A     25   60   63      5   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    25_A     Y    25_A     25   60   63      6   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    26_A     C    26_A     25   60   63      5   19   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    27_A     G    27_A     25   60   63      4   17   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     I    28_A     I    28_A     25   60   63      6   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    29_A     C    29_A     25   60   63      7   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    30_A     C    30_A     25   60   63      5   17   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    31_A     E    31_A     25   60   63      4   12   33   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    32_A     K    32_A     25   60   63      4   19   34   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    33_A     C    33_A     25   60   63      6   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    34_A     N    34_A     25   60   63      4   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    35_A     C    35_A     25   60   63      6   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     V    36_A     V    36_A     25   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    37_A     P    37_A     25   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    38_A     P    38_A     25   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    39_A     G    39_A     24   60   63      6   21   38   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     T    40_A     T    40_A      8   60   63      3    6   13   29   42   50   56   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    41_A     Y    41_A      8   60   63      3    6   17   25   38   48   54   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    42_A     G    42_A     13   60   63      3    4   17   25   38   48   56   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    43_A     N    43_A     13   60   63      5   18   38   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     E    44_A     E    44_A     13   60   63      6   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     D    45_A     D    45_A     13   60   63      5   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    46_A     S    46_A     13   60   63      5   17   38   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    47_A     C    47_A     13   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    48_A     P    48_A     13   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    49_A     C    49_A     13   60   63     10   21   36   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     Y    50_A     Y    50_A     14   60   63      4   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     A    51_A     A    51_A     14   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    52_A     N    52_A     14   60   63     11   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     L    53_A     L    53_A     14   60   63      6   21   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    54_A     K    54_A     14   60   63      4   12   33   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     N    55_A     N    55_A     14   60   63      6   15   31   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     S    56_A     S    56_A     14   60   63      6   10   21   36   48   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    57_A     K    57_A     14   60   63      6   12   28   39   51   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    58_A     G    58_A     14   60   63      6   12   28   39   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     G    59_A     G    59_A     14   60   63      6   12   31   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     H    60_A     H    60_A     14   60   63      6   16   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     K    61_A     K    61_A     14   60   63      5   12   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     C    62_A     C    62_A     14   60   63      7   20   38   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_GDT     P    63_A     P    63_A     14   60   63      7   20   39   50   54   56   57   59   61   61   62   62   62   62   62   62   62   63   63   63 
LCS_AVERAGE  LCS_A:  74.24  (  29.58   93.15  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     21     39     50     54     56     57     59     61     61     62     62     62     62     62     62     62     63     63     63 
GDT PERCENT_AT  17.46  33.33  61.90  79.37  85.71  88.89  90.48  93.65  96.83  96.83  98.41  98.41  98.41  98.41  98.41  98.41  98.41 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.64   1.11   1.31   1.48   1.58   1.65   1.90   2.07   2.07   2.20   2.20   2.20   2.20   2.20   2.20   2.20   2.65   2.65   2.65
GDT RMS_ALL_AT   3.05   3.04   2.87   2.82   2.77   2.77   2.78   2.76   2.71   2.71   2.68   2.68   2.68   2.68   2.68   2.68   2.68   2.65   2.65   2.65

# Checking swapping
#   possible swapping detected:  D     4_A      D     4_A
#   possible swapping detected:  D     6_A      D     6_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:  Y    50_A      Y    50_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A    13.071     0    0.115   0.146    15.596    0.000    0.000
LGA    H     2_A      H     2_A     6.389     0    0.108   0.607     8.448   12.262   22.000
LGA    I     3_A      I     3_A     6.701     0    0.600   1.570    12.632   23.810   12.500
LGA    D     4_A      D     4_A     1.076     0    0.553   1.202     4.279   75.357   62.917
LGA    C     5_A      C     5_A     1.924     0    0.096   0.196     2.456   72.857   70.159
LGA    D     6_A      D     6_A     1.525     0    0.020   0.661     3.340   79.405   72.262
LGA    K     7_A      K     7_A     0.537     0    0.064   1.025     4.511   90.476   75.503
LGA    E     8_A      E     8_A     1.032     0    0.045   0.639     2.053   83.690   80.582
LGA    C     9_A      C     9_A     1.272     0    0.037   0.172     1.794   83.690   80.079
LGA    N    10_A      N    10_A     0.383     0    0.131   1.148     2.807   90.595   85.357
LGA    R    11_A      R    11_A     0.998     0    0.021   1.068     4.899   85.952   75.498
LGA    R    12_A      R    12_A     1.288     0    0.040   1.376     6.063   81.429   68.571
LGA    C    13_A      C    13_A     1.116     0    0.264   0.261     3.180   79.286   74.762
LGA    S    14_A      S    14_A     1.324     0    0.052   0.680     3.781   73.452   69.762
LGA    K    15_A      K    15_A     3.494     0    0.274   1.006     4.695   55.357   47.513
LGA    A    16_A      A    16_A     2.250     0    0.055   0.063     2.633   62.857   64.857
LGA    S    17_A      S    17_A     2.907     0    0.110   0.267     3.343   57.143   54.762
LGA    A    18_A      A    18_A     2.312     0    0.232   0.230     2.455   64.762   64.762
LGA    H    19_A      H    19_A     2.111     0    0.153   1.180     3.202   62.857   61.000
LGA    D    20_A      D    20_A     1.903     0    0.153   0.368     2.826   72.857   67.857
LGA    R    21_A      R    21_A     1.888     0    0.066   1.242     9.825   77.143   44.156
LGA    C    22_A      C    22_A     1.251     0    0.101   0.226     1.547   79.286   83.016
LGA    L    23_A      L    23_A     1.055     0    0.104   1.045     2.880   83.690   77.440
LGA    K    24_A      K    24_A     2.125     0    0.049   0.925     6.548   70.833   51.058
LGA    Y    25_A      Y    25_A     2.137     0    0.028   0.415     2.519   66.786   64.802
LGA    C    26_A      C    26_A     1.865     0    0.021   0.566     2.376   72.857   71.508
LGA    G    27_A      G    27_A     1.920     0    0.130   0.130     2.597   66.905   66.905
LGA    I    28_A      I    28_A     1.631     0    0.052   1.761     6.992   77.143   62.381
LGA    C    29_A      C    29_A     1.611     0    0.042   0.647     1.782   77.143   78.651
LGA    C    30_A      C    30_A     1.577     0    0.032   0.085     1.912   72.857   72.857
LGA    E    31_A      E    31_A     1.785     0    0.049   0.548     4.142   70.833   61.270
LGA    K    32_A      K    32_A     1.620     0    0.047   0.651     3.885   72.976   69.630
LGA    C    33_A      C    33_A     0.929     0    0.631   0.544     3.600   74.286   71.190
LGA    N    34_A      N    34_A     1.018     0    0.245   0.356     3.402   88.333   72.917
LGA    C    35_A      C    35_A     1.184     0    0.116   0.903     1.707   85.952   81.587
LGA    V    36_A      V    36_A     0.470     0    0.151   0.168     1.371   97.619   93.265
LGA    P    37_A      P    37_A     0.390     0    0.032   0.325     0.941   95.238   94.558
LGA    P    38_A      P    38_A     1.308     0    0.059   0.360     2.471   83.690   77.891
LGA    G    39_A      G    39_A     1.924     0    0.205   0.205     2.448   68.810   68.810
LGA    T    40_A      T    40_A     4.369     0    0.611   0.993     5.242   37.619   36.599
LGA    Y    41_A      Y    41_A     4.531     0    0.097   1.359     5.113   34.286   38.452
LGA    G    42_A      G    42_A     4.319     0    0.630   0.630     5.497   34.524   34.524
LGA    N    43_A      N    43_A     1.324     0    0.272   0.490     1.922   77.143   79.345
LGA    E    44_A      E    44_A     0.606     0    0.097   1.234     5.355   90.476   70.000
LGA    D    45_A      D    45_A     0.966     0    0.115   0.263     1.435   90.476   85.952
LGA    S    46_A      S    46_A     1.167     0    0.049   0.442     1.594   85.952   83.016
LGA    C    47_A      C    47_A     0.581     0    0.102   0.451     2.822   90.476   83.413
LGA    P    48_A      P    48_A     0.631     0    0.066   0.365     1.301   90.595   91.905
LGA    C    49_A      C    49_A     1.708     0    0.035   0.256     3.155   72.976   67.778
LGA    Y    50_A      Y    50_A     0.994     0    0.096   0.302     2.573   88.214   77.460
LGA    A    51_A      A    51_A     0.933     0    0.097   0.128     1.304   85.952   85.048
LGA    N    52_A      N    52_A     0.967     0    0.056   0.902     2.551   85.952   78.571
LGA    L    53_A      L    53_A     1.076     0    0.149   0.866     3.632   83.690   77.798
LGA    K    54_A      K    54_A     1.252     0    0.081   1.277     5.040   81.429   68.360
LGA    N    55_A      N    55_A     1.909     0    0.031   0.481     2.713   67.143   65.000
LGA    S    56_A      S    56_A     3.823     0    0.045   0.354     4.686   43.452   40.397
LGA    K    57_A      K    57_A     3.359     0    0.058   0.723     5.881   48.333   43.968
LGA    G    58_A      G    58_A     2.936     0    0.103   0.103     2.936   57.143   57.143
LGA    G    59_A      G    59_A     1.588     0    0.081   0.081     2.062   77.381   77.381
LGA    H    60_A      H    60_A     1.111     0    0.125   1.392     6.741   85.952   56.048
LGA    K    61_A      K    61_A     1.507     0    0.046   0.862     2.056   75.238   76.878
LGA    C    62_A      C    62_A     2.163     0    0.095   0.182     2.533   66.786   64.841
LGA    P    63_A      P    63_A     1.871     0    0.504   0.549     2.554   66.786   64.830

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       63     252    252  100.00     471    471  100.00                63
SUMMARY(RMSD_GDC):     2.653          2.663                  3.061           71.563   66.338

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   63   63    4.0     59    1.90    76.190    85.651     2.955

LGA_LOCAL      RMSD:   1.897  Number of atoms:   59  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.763  Number of assigned atoms:   63 
Std_ASGN_ATOMS RMSD:   2.653  Standard rmsd on all 63 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.961722 * X  +  -0.236433 * Y  +  -0.138526 * Z  +   5.714911
  Y_new =  -0.253416 * X  +   0.959719 * Y  +   0.121325 * Z  +  -1.740253
  Z_new =   0.104261 * X  +   0.151785 * Y  +  -0.982899 * Z  +  -3.468576 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.883947 -0.104451  2.988377   [DEG: -165.2380   -5.9846  171.2214 ]
ZXZ: -2.290092  2.956391  0.601879   [DEG: -131.2126  169.3887   34.4851 ]
 
# END of job
