
#######################################################
#                                                     #
#                        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   73 (  604),  selected   65 , name one
# Molecule2: number of CA atoms   72 (  603),  selected   65 , 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:    65       8_A - 80_A        4.76     4.76
  LCS_AVERAGE:     90.28

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      33_A - 80_A        0.56     9.70
  LCS_AVERAGE:     55.41

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    48      33_A - 80_A        0.56     9.70
  LCS_AVERAGE:     55.41

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   65
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     L     8_A     L     8_A     17   17   65     13   16   17   17   17   17   17   18   24   31   38   47   51   57   61   63   64   65   65   65 
LCS_GDT     I     9_A     I     9_A     17   17   65     13   16   17   17   17   17   29   42   47   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    10_A     R    10_A     17   17   65     13   16   17   17   17   17   17   22   31   38   48   54   58   60   62   63   64   65   65   65 
LCS_GDT     R    11_A     R    11_A     17   17   65     13   16   17   17   17   17   17   18   28   32   42   47   51   57   59   63   64   65   65   65 
LCS_GDT     S    12_A     S    12_A     17   17   65     13   16   17   17   17   17   17   19   28   40   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     E    13_A     E    13_A     17   17   65     13   16   17   17   17   17   23   37   46   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     E    14_A     E    14_A     17   17   65     13   16   17   17   17   17   17   21   28   34   43   50   55   59   62   63   64   65   65   65 
LCS_GDT     Q    15_A     Q    15_A     17   17   65     13   16   17   17   17   17   17   18   28   32   43   50   55   60   62   63   64   65   65   65 
LCS_GDT     Q    16_A     Q    16_A     17   17   65     13   16   17   17   17   22   36   45   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    17_A     R    17_A     17   17   65     13   16   17   17   17   17   17   22   31   43   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    18_A     R    18_A     17   17   65     13   16   17   17   17   17   17   21   28   32   43   51   55   60   62   63   64   65   65   65 
LCS_GDT     N    19_A     N    19_A     17   17   65     13   16   17   17   17   17   17   17   28   40   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     E    20_A     E    20_A     17   17   65     13   16   17   17   17   20   39   45   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     E    21_A     E    21_A     17   17   65     13   16   17   17   17   17   17   21   28   37   50   57   58   60   62   63   64   65   65   65 
LCS_GDT     A    22_A     A    22_A     17   17   65     13   16   17   17   17   17   17   21   30   44   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    23_A     L    23_A     17   17   65      7   16   17   17   17   36   42   45   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    24_A     R    24_A     17   17   65      7   15   17   17   17   17   17   19   28   37   51   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    33_A     Q    33_A     48   48   65     17   37   48   48   48   48   48   48   48   50   52   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    34_A     L    34_A     48   48   65     36   46   48   48   48   48   48   48   48   49   51   53   56   60   62   63   64   65   65   65 
LCS_GDT     L    35_A     L    35_A     48   48   65     18   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     S    36_A     S    36_A     48   48   65     17   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     G    37_A     G    37_A     48   48   65     31   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     I    38_A     I    38_A     48   48   65     36   46   48   48   48   48   48   48   48   50   52   57   58   60   62   63   64   65   65   65 
LCS_GDT     V    39_A     V    39_A     48   48   65     31   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    40_A     Q    40_A     48   48   65     31   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    41_A     Q    41_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    42_A     Q    42_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     N    43_A     N    43_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     N    44_A     N    44_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    45_A     L    45_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    46_A     L    46_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    47_A     R    47_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     A    48_A     A    48_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     I    49_A     I    49_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     E    50_A     E    50_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     A    51_A     A    51_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    52_A     Q    52_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    53_A     Q    53_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     H    54_A     H    54_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    55_A     L    55_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    56_A     L    56_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    57_A     Q    57_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    58_A     L    58_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     T    59_A     T    59_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     V    60_A     V    60_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     W    61_A     W    61_A     48   48   65     13   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     G    62_A     G    62_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     I    63_A     I    63_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     K    64_A     K    64_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    65_A     Q    65_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    66_A     L    66_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    67_A     Q    67_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     A    68_A     A    68_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    69_A     R    69_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     I    70_A     I    70_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    71_A     L    71_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     A    72_A     A    72_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     V    73_A     V    73_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     E    74_A     E    74_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    75_A     R    75_A     48   48   65     36   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Y    76_A     Y    76_A     48   48   65     31   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     L    77_A     L    77_A     48   48   65     35   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     R    78_A     R    78_A     48   48   65     26   46   48   48   48   48   48   48   48   50   51   53   57   58   62   63   64   65   65   65 
LCS_GDT     D    79_A     D    79_A     48   48   65     18   46   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_GDT     Q    80_A     Q    80_A     48   48   65     18   31   48   48   48   48   48   48   48   50   53   57   58   60   62   63   64   65   65   65 
LCS_AVERAGE  LCS_A:  67.03  (  55.41   55.41   90.28 )

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     36     46     48     48     48     48     48     48     48     50     53     57     58     60     62     63     64     65     65     65 
GDT PERCENT_AT  50.00  63.89  66.67  66.67  66.67  66.67  66.67  66.67  66.67  69.44  73.61  79.17  80.56  83.33  86.11  87.50  88.89  90.28  90.28  90.28
GDT RMS_LOCAL    0.31   0.50   0.56   0.56   0.56   0.56   0.56   0.56   0.56   2.76   3.67   3.98   4.10   4.32   4.44   4.54   4.65   4.76   4.76   4.76
GDT RMS_ALL_AT   9.62   9.68   9.70   9.70   9.70   9.70   9.70   9.70   9.70   6.72   5.10   4.96   4.89   4.80   4.82   4.78   4.76   4.76   4.76   4.76

# Checking swapping
#   possible swapping detected:  E    13_A      E    13_A
#   possible swapping detected:  E    14_A      E    14_A
#   possible swapping detected:  E    20_A      E    20_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L     8_A      L     8_A    19.531     0    0.099   0.090    22.916    0.000    0.000
LGA    I     9_A      I     9_A    14.530     0    0.035   0.076    16.163    0.000    0.060
LGA    R    10_A      R    10_A    19.327     0    0.028   1.081    25.794    0.000    0.000
LGA    R    11_A      R    11_A    21.720     0    0.035   0.716    29.195    0.000    0.000
LGA    S    12_A      S    12_A    16.266     0    0.055   0.073    18.038    0.000    0.000
LGA    E    13_A      E    13_A    16.272     0    0.038   0.630    18.227    0.000    0.000
LGA    E    14_A      E    14_A    21.908     0    0.025   1.313    27.743    0.000    0.000
LGA    Q    15_A      Q    15_A    20.018     0    0.060   1.248    23.377    0.000    0.000
LGA    Q    16_A      Q    16_A    15.013     0    0.031   1.457    16.614    0.000    0.635
LGA    R    17_A      R    17_A    19.783     0    0.030   1.506    28.111    0.000    0.000
LGA    R    18_A      R    18_A    22.313     0    0.028   1.005    30.173    0.000    0.000
LGA    N    19_A      N    19_A    17.104     0    0.050   0.051    18.755    0.000    0.000
LGA    E    20_A      E    20_A    16.004     0    0.020   1.042    17.968    0.000    0.000
LGA    E    21_A      E    21_A    21.907     0    0.051   1.080    27.812    0.000    0.000
LGA    A    22_A      A    22_A    20.958     0    0.067   0.072    21.075    0.000    0.000
LGA    L    23_A      L    23_A    16.117     0    0.049   0.716    17.556    0.000    0.000
LGA    R    24_A      R    24_A    20.112     0    0.275   1.189    21.849    0.000    0.000
LGA    Q    33_A      Q    33_A     1.244     0    0.024   1.105     5.072   85.952   67.196
LGA    L    34_A      L    34_A     0.417     0    0.025   0.165     1.552  100.000   91.905
LGA    L    35_A      L    35_A     0.952     0    0.044   1.427     5.040   90.476   66.964
LGA    S    36_A      S    36_A     1.071     0    0.047   0.690     3.594   88.214   79.603
LGA    G    37_A      G    37_A     0.550     0    0.039   0.039     0.608   95.238   95.238
LGA    I    38_A      I    38_A     0.149     0    0.047   0.161     0.682  100.000   97.619
LGA    V    39_A      V    39_A     0.510     0    0.018   0.065     1.074   97.619   93.265
LGA    Q    40_A      Q    40_A     0.571     0    0.021   0.968     3.307   95.238   81.534
LGA    Q    41_A      Q    41_A     0.416     0    0.071   0.174     0.510  100.000   98.942
LGA    Q    42_A      Q    42_A     0.361     0    0.061   1.212     3.366  100.000   80.794
LGA    N    43_A      N    43_A     0.146     0    0.019   0.104     0.541  100.000   98.810
LGA    N    44_A      N    44_A     0.288     0    0.035   0.047     0.576  100.000   98.810
LGA    L    45_A      L    45_A     0.350     0    0.056   0.097     0.385  100.000  100.000
LGA    L    46_A      L    46_A     0.393     0    0.017   0.127     0.690  100.000   98.810
LGA    R    47_A      R    47_A     0.387     0    0.014   0.899     3.766  100.000   86.537
LGA    A    48_A      A    48_A     0.198     0    0.026   0.033     0.287  100.000  100.000
LGA    I    49_A      I    49_A     0.339     0    0.046   0.088     0.582  100.000   97.619
LGA    E    50_A      E    50_A     0.601     0    0.050   0.986     4.893   90.476   71.111
LGA    A    51_A      A    51_A     0.488     0    0.016   0.015     0.491  100.000  100.000
LGA    Q    52_A      Q    52_A     0.471     0    0.023   0.062     0.536   95.238   97.884
LGA    Q    53_A      Q    53_A     0.563     0    0.028   0.366     1.580   90.476   86.508
LGA    H    54_A      H    54_A     0.528     0    0.017   1.184     6.141   95.238   68.095
LGA    L    55_A      L    55_A     0.573     0    0.037   1.306     3.677   95.238   82.560
LGA    L    56_A      L    56_A     0.376     0    0.025   0.088     0.532  100.000   98.810
LGA    Q    57_A      Q    57_A     0.274     0    0.027   1.533     5.591  100.000   74.339
LGA    L    58_A      L    58_A     0.229     0    0.030   0.206     0.953  100.000   97.619
LGA    T    59_A      T    59_A     0.411     0    0.052   1.113     2.478  100.000   89.728
LGA    V    60_A      V    60_A     0.148     0    0.022   0.075     0.428  100.000  100.000
LGA    W    61_A      W    61_A     0.656     0    0.058   1.352     9.307   97.619   48.571
LGA    G    62_A      G    62_A     0.362     0    0.046   0.046     0.420  100.000  100.000
LGA    I    63_A      I    63_A     0.402     0    0.023   1.280     4.245  100.000   83.155
LGA    K    64_A      K    64_A     0.454     0    0.040   1.107     6.546  100.000   73.862
LGA    Q    65_A      Q    65_A     0.528     0    0.060   1.352     4.954   95.238   78.360
LGA    L    66_A      L    66_A     0.533     0    0.022   0.170     1.379   95.238   91.726
LGA    Q    67_A      Q    67_A     0.355     0    0.014   0.062     0.472  100.000  100.000
LGA    A    68_A      A    68_A     0.357     0    0.016   0.020     0.614   95.238   96.190
LGA    R    69_A      R    69_A     0.783     0    0.013   0.467     2.099   90.476   81.775
LGA    I    70_A      I    70_A     0.739     0    0.012   0.250     1.625   90.476   87.143
LGA    L    71_A      L    71_A     0.359     0    0.015   0.083     0.482  100.000  100.000
LGA    A    72_A      A    72_A     0.490     0    0.041   0.048     0.511   97.619   96.190
LGA    V    73_A      V    73_A     0.440     0    0.030   0.044     0.637   97.619   94.558
LGA    E    74_A      E    74_A     0.256     0    0.032   0.118     0.744  100.000   96.825
LGA    R    75_A      R    75_A     0.224     0    0.031   0.095     0.570  100.000   99.134
LGA    Y    76_A      Y    76_A     0.478     0    0.015   0.147     1.262   97.619   92.143
LGA    L    77_A      L    77_A     0.356     0    0.057   0.211     1.011   92.976   95.298
LGA    R    78_A      R    78_A     0.694     0    0.086   1.423     6.804   90.595   67.532
LGA    D    79_A      D    79_A     1.045     0    0.029   0.772     3.812   83.690   71.726
LGA    Q    80_A      Q    80_A     1.309     0    0.653   1.225     4.783   71.429   67.090

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       65     260    260  100.00     547    547  100.00                72
SUMMARY(RMSD_GDC):     4.755          4.308                  7.113           64.101   58.643

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   73   72    4.0     48    0.56    71.181    66.727     7.262

LGA_LOCAL      RMSD:   0.561  Number of atoms:   48  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.695  Number of assigned atoms:   65 
Std_ASGN_ATOMS RMSD:   4.755  Standard rmsd on all 65 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.176652 * X  +   0.950025 * Y  +  -0.257385 * Z  + -31.150621
  Y_new =   0.977840 * X  +  -0.199239 * Y  +  -0.064280 * Z  + -15.128099
  Z_new =  -0.112349 * X  +  -0.240326 * Y  +  -0.964169 * Z  + 127.462112 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.392069  0.112586 -2.897313   [DEG:   79.7597    6.4507 -166.0038 ]
ZXZ: -1.326060  2.873088 -2.704295   [DEG:  -75.9777  164.6158 -154.9447 ]
 
# END of job
