
#######################################################
#                                                     #
#                        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   97 (  681),  selected   64 , name one
# Molecule2: number of CA atoms   64 (  433),  selected   64 , 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:    64      22_A - 85_A        3.14     3.14
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      43_A - 68_A        1.99     5.49
  LONGEST_CONTINUOUS_SEGMENT:    26      44_A - 69_A        1.89     5.61
  LONGEST_CONTINUOUS_SEGMENT:    26      60_A - 85_A        1.99     3.68
  LCS_AVERAGE:     36.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19      45_A - 63_A        0.95     6.16
  LONGEST_CONTINUOUS_SEGMENT:    19      46_A - 64_A        1.00     6.22
  LCS_AVERAGE:     24.95

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   64
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    22_A     A    22_A      3    3   64      3    3    6    8   14   19   30   42   53   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    3   11   16   23   31   38   43   54   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   20   64      3    4   10   25   35   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     15   20   64      3    4   11   30   38   42   49   53   59   60   61   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     15   20   64      5   10   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     15   20   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     15   20   64      5   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     15   20   64      5   20   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     15   20   64      4   19   27   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A      6   20   64      4    7   23   29   34   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      6   23   64      4    5    8   23   31   36   42   52   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      6   26   64      4    7   21   29   33   41   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A     15   26   64      3    3    7   15   20   23   29   40   57   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A     19   26   64      4   14   19   22   23   35   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A     19   26   64      6   13   19   22   31   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A     19   26   64      6   14   19   22   23   31   46   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A     19   26   64      4   14   19   22   28   41   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A     19   26   64      6   14   19   22   32   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A     19   26   64      9   14   19   22   30   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A     19   26   64      9   14   19   22   30   42   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A     19   26   64      9   14   19   22   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A     19   26   64      9   14   19   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A     19   26   64      9   14   19   22   30   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A     19   26   64      9   14   19   22   30   44   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A     19   26   64      9   14   19   28   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A     19   26   64      9   14   19   31   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A     19   26   64      9   13   19   22   25   38   50   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A     19   26   64      9   14   19   22   23   36   46   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A     19   26   64      7   13   19   22   25   36   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A     19   26   64      7   13   18   22   25   38   50   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A     19   26   64      9   14   19   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A     19   26   64      5   14   27   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A     19   26   64      4   12   27   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A     18   26   64      4    7   18   27   34   42   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      7   26   64      3    5    6   10   18   21   35   44   51   58   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A     11   26   64      3    8   18   29   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     18   26   64      4    5   17   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     18   26   64      4   12   27   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     18   26   64      4   19   28   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     18   26   64     25   26   29   32   39   44   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     18   26   64     25   26   29   32   39   45   53   57   59   61   62   63   64   64   64   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     18   26   64      5   25   29   31   38   42   50   56   59   60   62   63   64   64   64   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  53.92  (  24.95   36.82  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     25     26     29     32     39     45     53     57     59     61     62     63     64     64     64     64     64     64     64     64 
GDT PERCENT_AT  39.06  40.62  45.31  50.00  60.94  70.31  82.81  89.06  92.19  95.31  96.88  98.44 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.40   0.60   1.13   1.51   2.03   2.41   2.60   2.65   3.00   3.02   3.01   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14
GDT RMS_ALL_AT   3.85   3.86   3.90   3.61   3.52   3.29   3.20   3.17   3.20   3.15   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14   3.14

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    22_A      A    22_A     8.176     0    0.380   0.366     8.555    5.476    5.333
LGA    D    23_A      D    23_A     7.397     0    0.232   1.110    11.346   18.214    9.702
LGA    G    24_A      G    24_A     3.103     0    0.524   0.524     4.851   47.857   47.857
LGA    D    25_A      D    25_A     3.951     0    0.277   1.090     7.938   44.762   27.560
LGA    G    26_A      G    26_A     1.861     0    0.099   0.099     2.021   70.833   70.833
LGA    Q    27_A      Q    27_A     1.400     0    0.023   0.786     3.246   79.286   72.328
LGA    G    28_A      G    28_A     1.297     0    0.071   0.071     1.297   83.690   83.690
LGA    L    29_A      L    29_A     1.307     0    0.009   0.100     1.805   81.429   78.214
LGA    Y    30_A      Y    30_A     1.191     0    0.079   0.125     1.385   81.429   81.429
LGA    A    31_A      A    31_A     1.165     0    0.008   0.013     1.323   81.429   81.429
LGA    A    32_A      A    32_A     1.226     0    0.034   0.036     1.308   81.429   81.429
LGA    N    33_A      N    33_A     1.353     0    0.025   0.077     1.760   81.429   77.143
LGA    C    34_A      C    34_A     1.260     0    0.052   0.090     1.372   81.429   81.429
LGA    A    35_A      A    35_A     1.489     0    0.027   0.029     2.082   75.119   74.667
LGA    A    36_A      A    36_A     2.395     0    0.012   0.011     2.735   64.881   63.333
LGA    C    37_A      C    37_A     1.955     0    0.072   0.745     2.614   70.833   68.889
LGA    H    38_A      H    38_A     2.113     0    0.123   0.107     2.683   64.881   67.238
LGA    G    39_A      G    39_A     2.451     0    0.253   0.253     2.451   73.095   73.095
LGA    A    40_A      A    40_A     1.527     0    0.064   0.091     2.856   77.619   73.524
LGA    L    41_A      L    41_A     3.054     0    0.080   0.881     4.457   47.262   55.536
LGA    A    42_A      A    42_A     5.238     0    0.157   0.165     5.660   30.238   28.476
LGA    T    43_A      T    43_A     4.084     0    0.602   1.356     6.578   38.690   33.810
LGA    S    44_A      S    44_A     6.189     0    0.271   0.368     7.673   22.738   18.016
LGA    E    45_A      E    45_A     4.411     0    0.168   0.763     6.974   38.810   28.413
LGA    K    46_A      K    46_A     3.068     0    0.112   0.112     3.849   45.000   63.492
LGA    K    47_A      K    47_A     4.932     0    0.094   0.839     9.496   34.286   20.370
LGA    G    48_A      G    48_A     4.110     0    0.102   0.102     4.521   43.929   43.929
LGA    T    49_A      T    49_A     2.915     0    0.184   0.977     4.248   57.262   52.381
LGA    T    50_A      T    50_A     3.250     0    0.033   0.062     3.250   50.000   51.020
LGA    L    51_A      L    51_A     3.507     0    0.019   1.360     7.024   48.333   35.119
LGA    A    52_A      A    52_A     2.512     0    0.017   0.017     2.848   60.952   61.714
LGA    R    53_A      R    53_A     1.967     0    0.020   0.585     3.505   66.786   61.472
LGA    L    54_A      L    54_A     3.121     0    0.037   1.389     7.321   51.786   38.750
LGA    Q    55_A      Q    55_A     3.328     0    0.014   1.221     4.230   50.000   53.651
LGA    S    56_A      S    56_A     2.310     0    0.056   0.062     2.575   60.952   64.921
LGA    A    57_A      A    57_A     2.260     0    0.007   0.016     2.994   60.952   61.714
LGA    V    58_A      V    58_A     4.113     0    0.033   0.130     5.505   38.929   34.286
LGA    S    59_A      S    59_A     4.363     0    0.018   0.754     6.463   35.714   32.857
LGA    A    60_A      A    60_A     3.788     0    0.027   0.031     3.919   43.333   44.667
LGA    N    61_A      N    61_A     4.046     0    0.077   0.913     6.611   45.357   33.631
LGA    A    62_A      A    62_A     1.835     0    0.052   0.062     2.663   68.929   69.714
LGA    G    63_A      G    63_A     1.597     0    0.065   0.065     2.125   72.976   72.976
LGA    G    64_A      G    64_A     1.821     0    0.050   0.050     3.262   63.214   63.214
LGA    M    65_A      M    65_A     3.467     0    0.323   0.717     4.183   46.905   55.119
LGA    G    66_A      G    66_A     6.514     0    0.592   0.592     6.514   24.286   24.286
LGA    F    67_A      F    67_A     2.212     0    0.354   1.317     4.801   63.452   59.870
LGA    L    68_A      L    68_A     1.347     0    0.183   0.209     2.161   83.810   78.393
LGA    S    69_A      S    69_A     0.644     0    0.028   0.052     1.670   83.810   81.587
LGA    S    70_A      S    70_A     2.166     0    0.043   0.091     2.974   67.024   65.000
LGA    L    71_A      L    71_A     2.002     0    0.079   0.117     2.272   66.786   69.821
LGA    T    72_A      T    72_A     2.470     0    0.026   0.040     2.510   62.857   63.673
LGA    S    73_A      S    73_A     2.756     0    0.029   0.633     4.162   57.143   53.810
LGA    A    74_A      A    74_A     2.215     0    0.034   0.038     2.395   66.786   66.381
LGA    Q    75_A      Q    75_A     1.873     0    0.016   0.087     2.039   70.833   71.058
LGA    L    76_A      L    76_A     2.128     0    0.019   0.112     2.755   64.762   64.821
LGA    Q    77_A      Q    77_A     2.316     0    0.057   0.180     3.180   64.762   60.582
LGA    A    78_A      A    78_A     1.879     0    0.025   0.033     2.016   70.833   71.238
LGA    I    79_A      I    79_A     1.833     0    0.023   0.041     1.890   72.857   72.857
LGA    V    80_A      V    80_A     2.156     0    0.016   0.058     2.705   64.762   63.673
LGA    D    81_A      D    81_A     2.324     0    0.061   0.062     2.692   64.762   63.810
LGA    V    82_A      V    82_A     1.983     0    0.089   0.863     3.557   68.810   68.844
LGA    L    83_A      L    83_A     1.976     0    0.135   0.201     2.271   70.833   68.810
LGA    A    84_A      A    84_A     2.543     0    0.130   0.138     2.793   60.952   60.190
LGA    V    85_A      V    85_A     3.540     0    0.304   1.342     6.270   46.667   44.830

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       64     256    256  100.00     433    433  100.00                64
SUMMARY(RMSD_GDC):     3.136          3.069                  3.423           59.144   57.374

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   97   64    4.0     57    2.60    69.922    65.221     2.108

LGA_LOCAL      RMSD:   2.604  Number of atoms:   57  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.173  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   3.136  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.748559 * X  +   0.180234 * Y  +  -0.638103 * Z  +  20.290548
  Y_new =   0.630829 * X  +  -0.490006 * Y  +   0.601622 * Z  + -19.156063
  Z_new =  -0.204241 * X  +  -0.852883 * Y  +  -0.480495 * Z  + -16.946224 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.700255  0.205689 -2.083852   [DEG:   40.1217   11.7851 -119.3959 ]
ZXZ: -2.326776  2.072016 -2.906547   [DEG: -133.3145  118.7178 -166.5329 ]
 
# END of job
