
#######################################################
#                                                     #
#                        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   72 (  487),  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        4.51     4.51
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      61_A - 85_A        1.98     5.44
  LCS_AVERAGE:     29.27

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      69_A - 85_A        0.79     5.23
  LCS_AVERAGE:     17.70

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    4    7   11   18   25   34   40   49   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     D    23_A     D    23_A      3    4   64      3    3    5   10   15   18   25   34   39   49   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    24_A     G    24_A      3   20   64      3    3   10   29   36   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     D    25_A     D    25_A     16   20   64      3    3    9   24   35   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    26_A     G    26_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     Q    27_A     Q    27_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    28_A     G    28_A     16   20   64     12   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    29_A     L    29_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     Y    30_A     Y    30_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    31_A     A    31_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    32_A     A    32_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     N    33_A     N    33_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     C    34_A     C    34_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    35_A     A    35_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    36_A     A    36_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     C    37_A     C    37_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     H    38_A     H    38_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    39_A     G    39_A     16   20   64     13   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    40_A     A    40_A     16   20   64     10   21   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    41_A     L    41_A      5   20   64      3    4    5   12   21   32   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    42_A     A    42_A      3   20   64      3    4   10   17   21   27   34   43   47   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     T    43_A     T    43_A      4   20   64      3    4    9   30   34   40   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     S    44_A     S    44_A      4   19   64      3    3    6    9   14   29   36   46   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     E    45_A     E    45_A      4    7   64      3    3    6    9   13   22   29   44   51   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     K    46_A     K    46_A      4    7   64      3    4    6    7   10   12   15   20   22   27   36   48   58   59   62   64   64   64   64   64 
LCS_GDT     K    47_A     K    47_A      3    7   64      3    4    5    6   10   12   15   20   20   26   32   42   55   59   61   64   64   64   64   64 
LCS_GDT     G    48_A     G    48_A      4    7   64      3    4    4    5    7   12   13   20   20   23   30   32   41   50   60   64   64   64   64   64 
LCS_GDT     T    49_A     T    49_A      4    5   64      3    4    5    7    9   13   20   25   33   43   45   54   58   59   62   64   64   64   64   64 
LCS_GDT     T    50_A     T    50_A      4    5   64      3    4    4    5    7    9   12   20   22   27   32   46   50   59   62   64   64   64   64   64 
LCS_GDT     L    51_A     L    51_A      4    5   64      3    4    4    5    7   10   13   20   22   27   38   46   50   58   62   64   64   64   64   64 
LCS_GDT     A    52_A     A    52_A      3    4   64      3    3    4    5    6    7   13   20   25   33   43   49   58   59   62   64   64   64   64   64 
LCS_GDT     R    53_A     R    53_A      3   10   64      3    3    4    8   23   35   45   50   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    54_A     L    54_A      9   13   64      7    8    8   10   36   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     Q    55_A     Q    55_A      9   13   64      7    8    8   12   32   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     S    56_A     S    56_A      9   13   64      7    8   18   26   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    57_A     A    57_A      9   13   64      7    8   18   32   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     V    58_A     V    58_A      9   13   64      7    8    8   12   20   39   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     S    59_A     S    59_A      9   13   64      7    8    8   12   20   31   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    60_A     A    60_A      9   13   64      7    8    8   12   20   31   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     N    61_A     N    61_A      9   25   64      3    8   11   26   35   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    62_A     A    62_A      9   25   64      5   11   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    63_A     G    63_A      5   25   64      3    4   10   28   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    64_A     G    64_A      5   25   64      3    6    9   22   35   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     M    65_A     M    65_A      5   25   64      3    4    9   15   35   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     G    66_A     G    66_A      5   25   64      3    4    8   10   35   39   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     F    67_A     F    67_A      6   25   64      4    5    7   12   17   20   44   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    68_A     L    68_A     15   25   64      4    5    9   16   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     S    69_A     S    69_A     17   25   64      8   17   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     S    70_A     S    70_A     17   25   64      4   21   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    71_A     L    71_A     17   25   64     10   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     T    72_A     T    72_A     17   25   64     10   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     S    73_A     S    73_A     17   25   64      7   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    74_A     A    74_A     17   25   64      9   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     Q    75_A     Q    75_A     17   25   64      9   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    76_A     L    76_A     17   25   64      9   20   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     Q    77_A     Q    77_A     17   25   64      9   17   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    78_A     A    78_A     17   25   64      9   17   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     I    79_A     I    79_A     17   25   64      9   17   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     V    80_A     V    80_A     17   25   64      9   17   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     D    81_A     D    81_A     17   25   64      9   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     V    82_A     V    82_A     17   25   64      6   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     L    83_A     L    83_A     17   25   64      6   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     A    84_A     A    84_A     17   25   64     12   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_GDT     V    85_A     V    85_A     17   25   64     12   24   33   33   37   41   46   51   52   54   55   57   58   59   62   64   64   64   64   64 
LCS_AVERAGE  LCS_A:  48.99  (  17.70   29.27  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     13     24     33     33     37     41     46     51     52     54     55     57     58     59     62     64     64     64     64     64 
GDT PERCENT_AT  20.31  37.50  51.56  51.56  57.81  64.06  71.88  79.69  81.25  84.38  85.94  89.06  90.62  92.19  96.88 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.36   0.73   0.97   0.97   1.42   1.72   2.03   2.34   2.41   2.59   2.76   3.11   3.33   3.53   4.14   4.51   4.51   4.51   4.51   4.51
GDT RMS_ALL_AT   5.26   5.14   5.13   5.13   5.15   5.24   5.25   5.15   5.12   5.04   4.93   4.82   4.72   4.67   4.54   4.51   4.51   4.51   4.51   4.51

# Checking swapping
#   possible swapping detected:  D    25_A      D    25_A
#   possible swapping detected:  Y    30_A      Y    30_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     9.348     0    0.071   0.100    11.445    3.452    2.762
LGA    D    23_A      D    23_A     8.572     0    0.173   0.224    12.848   10.119    5.119
LGA    G    24_A      G    24_A     3.605     0    0.515   0.515     5.564   41.667   41.667
LGA    D    25_A      D    25_A     3.356     0    0.309   1.127     7.601   52.976   33.571
LGA    G    26_A      G    26_A     1.278     0    0.075   0.075     1.427   81.429   81.429
LGA    Q    27_A      Q    27_A     0.818     0    0.033   1.453     5.307   90.476   73.175
LGA    G    28_A      G    28_A     0.974     0    0.026   0.026     1.069   88.214   88.214
LGA    L    29_A      L    29_A     0.849     0    0.022   0.164     1.636   88.214   83.750
LGA    Y    30_A      Y    30_A     1.007     0    0.045   0.115     1.220   83.690   82.183
LGA    A    31_A      A    31_A     1.176     0    0.084   0.091     1.976   77.143   79.810
LGA    A    32_A      A    32_A     1.352     0    0.042   0.053     1.691   79.286   79.714
LGA    N    33_A      N    33_A     1.600     0    0.029   0.195     1.940   75.000   73.929
LGA    C    34_A      C    34_A     1.247     0    0.015   0.035     1.292   81.429   81.429
LGA    A    35_A      A    35_A     1.310     0    0.027   0.028     1.369   81.429   81.429
LGA    A    36_A      A    36_A     1.302     0    0.036   0.039     1.426   81.429   81.429
LGA    C    37_A      C    37_A     1.364     0    0.049   0.052     1.425   81.429   81.429
LGA    H    38_A      H    38_A     1.359     0    0.098   0.460     2.392   81.429   73.857
LGA    G    39_A      G    39_A     1.400     0    0.032   0.032     1.400   81.429   81.429
LGA    A    40_A      A    40_A     1.148     0    0.634   0.609     2.313   75.119   76.381
LGA    L    41_A      L    41_A     4.140     0    0.241   1.364    10.537   46.786   26.012
LGA    A    42_A      A    42_A     5.702     0    0.258   0.256     6.903   25.476   23.048
LGA    T    43_A      T    43_A     4.098     0    0.178   0.169     4.426   37.143   40.748
LGA    S    44_A      S    44_A     5.725     0    0.054   0.084     7.922   17.024   13.730
LGA    E    45_A      E    45_A     8.144     0    0.533   1.028     9.968    5.714    4.921
LGA    K    46_A      K    46_A    12.166     0    0.209   0.859    15.896    0.000    0.000
LGA    K    47_A      K    47_A    12.522     0    0.601   1.420    15.567    0.000    0.000
LGA    G    48_A      G    48_A    15.375     0    0.134   0.134    15.375    0.000    0.000
LGA    T    49_A      T    49_A    11.049     0    0.712   1.357    12.082    0.000    0.748
LGA    T    50_A      T    50_A    13.109     0    0.497   1.371    15.611    0.000    0.000
LGA    L    51_A      L    51_A    12.264     0    0.268   1.393    17.066    0.000    0.000
LGA    A    52_A      A    52_A    10.841     0    0.583   0.557    12.058    1.071    0.857
LGA    R    53_A      R    53_A     4.840     0    0.646   1.639     7.300   32.500   25.411
LGA    L    54_A      L    54_A     2.853     0    0.635   1.413     8.768   61.071   36.667
LGA    Q    55_A      Q    55_A     3.210     0    0.025   0.294     5.373   53.571   46.772
LGA    S    56_A      S    56_A     2.204     0    0.041   0.080     2.636   62.857   64.841
LGA    A    57_A      A    57_A     1.917     0    0.065   0.101     2.757   65.000   66.571
LGA    V    58_A      V    58_A     3.895     0    0.066   0.136     5.488   41.905   37.483
LGA    S    59_A      S    59_A     4.329     0    0.139   0.196     5.097   35.952   35.397
LGA    A    60_A      A    60_A     3.751     0    0.081   0.075     3.751   45.000   44.667
LGA    N    61_A      N    61_A     2.838     0    0.564   1.212     4.302   54.048   54.762
LGA    A    62_A      A    62_A     0.902     0    0.356   0.486     3.811   72.262   74.095
LGA    G    63_A      G    63_A     2.738     0    0.571   0.571     3.081   61.190   61.190
LGA    G    64_A      G    64_A     3.370     0    0.211   0.211     4.389   48.810   48.810
LGA    M    65_A      M    65_A     3.071     0    0.650   0.942     4.379   46.786   60.000
LGA    G    66_A      G    66_A     3.593     0    0.659   0.659     4.816   43.690   43.690
LGA    F    67_A      F    67_A     3.987     0    0.672   1.145    11.942   53.810   22.684
LGA    L    68_A      L    68_A     2.563     0    0.103   1.345     6.663   61.190   45.595
LGA    S    69_A      S    69_A     1.860     0    0.097   0.098     2.458   72.976   71.587
LGA    S    70_A      S    70_A     1.764     0    0.129   0.141     2.280   72.976   70.238
LGA    L    71_A      L    71_A     0.956     0    0.028   0.115     1.353   85.952   83.690
LGA    T    72_A      T    72_A     1.148     0    0.033   0.071     1.292   83.690   85.306
LGA    S    73_A      S    73_A     1.981     0    0.024   0.051     2.469   70.833   68.810
LGA    A    74_A      A    74_A     1.728     0    0.047   0.066     1.850   72.857   72.857
LGA    Q    75_A      Q    75_A     0.991     0    0.018   0.148     1.143   83.690   87.460
LGA    L    76_A      L    76_A     1.276     0    0.027   1.236     4.441   79.286   73.750
LGA    Q    77_A      Q    77_A     1.836     0    0.075   1.327     7.169   70.833   51.217
LGA    A    78_A      A    78_A     1.747     0    0.050   0.058     2.048   70.833   71.238
LGA    I    79_A      I    79_A     1.593     0    0.036   0.059     1.859   72.857   75.000
LGA    V    80_A      V    80_A     1.941     0    0.039   0.118     2.299   68.810   68.231
LGA    D    81_A      D    81_A     2.175     0    0.058   0.101     2.395   64.762   64.762
LGA    V    82_A      V    82_A     2.199     0    0.139   0.838     3.879   64.762   65.374
LGA    L    83_A      L    83_A     1.784     0    0.092   0.182     2.148   68.810   70.833
LGA    A    84_A      A    84_A     1.921     0    0.099   0.092     2.104   72.857   71.238
LGA    V    85_A      V    85_A     1.888     0    0.621   0.585     3.774   65.476   68.639

# 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):     4.506          4.454                  5.183           55.476   52.838

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   72   64    4.0     51    2.34    67.188    59.628     2.090

LGA_LOCAL      RMSD:   2.341  Number of atoms:   51  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.151  Number of assigned atoms:   64 
Std_ASGN_ATOMS RMSD:   4.506  Standard rmsd on all 64 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.729664 * X  +   0.325443 * Y  +   0.601397 * Z  +  47.818657
  Y_new =  -0.621344 * X  +   0.051679 * Y  +  -0.781832 * Z  +  27.774967
  Z_new =  -0.285521 * X  +  -0.944148 * Y  +   0.164503 * Z  +  14.979001 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.436200  0.289550 -1.398293   [DEG: -139.5840   16.5900  -80.1163 ]
ZXZ:  0.655686  1.405542 -2.847925   [DEG:   37.5680   80.5316 -163.1741 ]
 
# END of job
