
#######################################################
#                                                     #
#                        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   53 (  434),  selected   53 , name one
# Molecule2: number of CA atoms  166 ( 1331),  selected   53 , 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:    53      32_A - 84_A        4.42     4.42
  LCS_AVERAGE:     31.93

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      37_A - 62_A        1.96     6.93
  LCS_AVERAGE:     13.48

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      42_A - 61_A        0.91     6.32
  LONGEST_CONTINUOUS_SEGMENT:    20      43_A - 62_A        0.94     6.17
  LCS_AVERAGE:     10.15

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   53
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     H    32_A     H    32_A     13   19   53      2    3    4   14   15   18   25   25   32   35   38   41   43   46   48   49   51   53   53   53 
LCS_GDT     A    33_A     A    33_A     13   19   53      4   10   12   14   17   22   30   33   36   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     D    34_A     D    34_A     13   19   53      3   10   12   14   17   24   30   33   36   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     A    35_A     A    35_A     13   19   53      8   10   12   14   17   18   27   33   36   38   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     A    36_A     A    36_A     13   19   53      8   10   12   14   17   22   30   33   36   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     Y    37_A     Y    37_A     13   26   53      8   10   12   15   23   29   32   35   38   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     V    38_A     V    38_A     13   26   53      8   10   12   15   25   29   33   35   39   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    39_A     E    39_A     13   26   53      8   10   12   14   22   29   32   35   38   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     K    40_A     K    40_A     13   26   53      8   10   12   14   18   26   31   34   36   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     H    41_A     H    41_A     13   26   53      8   10   12   21   22   27   32   35   38   40   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     N    42_A     N    42_A     20   26   53      4   10   17   22   25   29   33   38   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     L    43_A     L    43_A     20   26   53      8   18   23   27   29   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     Q    44_A     Q    44_A     20   26   53     12   18   23   27   31   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     C    45_A     C    45_A     20   26   53     12   18   23   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     L    46_A     L    46_A     20   26   53      9   18   23   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     F    47_A     F    47_A     20   26   53     12   18   23   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     S    48_A     S    48_A     20   26   53     12   18   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    49_A     E    49_A     20   26   53     12   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     M    50_A     M    50_A     20   26   53     12   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     A    51_A     A    51_A     20   26   53     12   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    52_A     E    52_A     20   26   53     12   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     Q    53_A     Q    53_A     20   26   53     12   18   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     L    54_A     L    54_A     20   26   53     12   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     S    55_A     S    55_A     20   26   53     12   18   23   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    56_A     E    56_A     20   26   53     12   18   23   27   29   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     K    57_A     K    57_A     20   26   53     10   18   23   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     D    58_A     D    58_A     20   26   53     10   18   23   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     P    59_A     P    59_A     20   26   53     10   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     K    60_A     K    60_A     20   26   53      9   18   20   28   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     T    61_A     T    61_A     20   26   53      4   13   19   21   27   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    62_A     E    62_A     20   26   53      4    4    4    9   16   22   28   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     Q    63_A     Q    63_A      4   24   53      4    4    6   12   20   29   33   38   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    64_A     E    64_A      5   24   53      4    4    5    5    8   28   34   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     A    65_A     A    65_A      5    6   53      4    4    5    5    6    8   10   10   14   21   26   34   42   46   48   49   52   53   53   53 
LCS_GDT     E    66_A     E    66_A      5   19   53      4    4    5    5    6    8   11   16   26   30   38   39   44   46   48   49   52   53   53   53 
LCS_GDT     R    67_A     R    67_A     18   19   53      4    4   15   22   28   29   35   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     I    68_A     I    68_A     18   19   53      6   14   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     L    69_A     L    69_A     18   19   53      6   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     L    70_A     L    70_A     18   19   53      8   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    71_A     E    71_A     18   19   53      7   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     F    72_A     F    72_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     L    73_A     L    73_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     T    74_A     T    74_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     H    75_A     H    75_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     R    76_A     R    76_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     K    77_A     K    77_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     A    78_A     A    78_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     E    79_A     E    79_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     R    80_A     R    80_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   44   46   48   49   50   52   53   53   53 
LCS_GDT     D    81_A     D    81_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   43   46   48   49   50   52   53   53   53 
LCS_GDT     R    82_A     R    82_A     18   19   53     13   20   25   29   32   34   36   39   40   41   42   43   46   48   49   50   52   53   53   53 
LCS_GDT     A    83_A     A    83_A     18   19   53     13   20   25   28   32   34   36   39   40   41   42   43   45   47   49   50   52   53   53   53 
LCS_GDT     A    84_A     A    84_A     18   19   53     13   20   25   28   32   34   36   39   40   41   42   42   45   46   49   50   52   53   53   53 
LCS_AVERAGE  LCS_A:  18.52  (  10.15   13.48   31.93 )

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     20     25     29     32     34     36     39     40     41     42     44     46     48     49     50     52     53     53     53 
GDT PERCENT_AT   7.83  12.05  15.06  17.47  19.28  20.48  21.69  23.49  24.10  24.70  25.30  26.51  27.71  28.92  29.52  30.12  31.33  31.93  31.93  31.93
GDT RMS_LOCAL    0.27   0.64   0.85   1.21   1.32   1.47   1.69   2.02   2.11   2.27   2.48   3.32   3.50   3.75   3.84   3.98   4.27   4.42   4.42   4.42
GDT RMS_ALL_AT   7.55   6.94   6.64   5.94   6.12   6.00   5.88   5.87   5.80   5.64   5.42   4.68   4.48   4.45   4.49   4.45   4.43   4.42   4.42   4.42

# Checking swapping
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  E    49_A      E    49_A
#   possible swapping detected:  E    52_A      E    52_A
#   possible swapping detected:  E    56_A      E    56_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  E    64_A      E    64_A
#   possible swapping detected:  E    71_A      E    71_A
#   possible swapping detected:  F    72_A      F    72_A
#   possible swapping detected:  D    81_A      D    81_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    H    32_A      H    32_A    15.811     0    0.367   1.404    17.245    0.000    0.000
LGA    A    33_A      A    33_A    14.780     0    0.177   0.171    16.093    0.000    0.000
LGA    D    34_A      D    34_A    11.956     0    0.215   0.202    12.907    0.000    0.000
LGA    A    35_A      A    35_A    12.326     0    0.175   0.194    13.921    0.000    0.000
LGA    A    36_A      A    36_A    13.580     0    0.082   0.081    15.093    0.000    0.000
LGA    Y    37_A      Y    37_A    10.833     0    0.107   0.141    11.798    0.714    2.262
LGA    V    38_A      V    38_A     7.611     0    0.028   0.155     8.796    6.786    9.116
LGA    E    39_A      E    39_A     9.502     0    0.035   0.640    15.313    0.595    0.265
LGA    K    40_A      K    40_A    12.246     0    0.138   0.581    17.632    0.000    0.000
LGA    H    41_A      H    41_A     9.389     0    0.034   0.216    12.014    3.452    1.667
LGA    N    42_A      N    42_A     6.061     0    0.025   1.014     8.405   23.929   16.726
LGA    L    43_A      L    43_A     3.377     0    0.174   1.394     5.153   50.357   52.024
LGA    Q    44_A      Q    44_A     2.673     0    0.101   0.999     5.493   62.976   49.524
LGA    C    45_A      C    45_A     1.749     0    0.060   0.776     2.178   70.833   70.159
LGA    L    46_A      L    46_A     2.108     0    0.071   1.383     5.876   68.810   55.119
LGA    F    47_A      F    47_A     1.753     0    0.027   0.973     4.182   77.143   63.636
LGA    S    48_A      S    48_A     0.791     0    0.033   0.517     2.473   88.214   84.683
LGA    E    49_A      E    49_A     1.137     0    0.046   1.185     6.206   83.690   59.365
LGA    M    50_A      M    50_A     1.013     0    0.070   0.760     2.522   85.952   82.917
LGA    A    51_A      A    51_A     0.410     0    0.082   0.091     1.425   90.595   92.476
LGA    E    52_A      E    52_A     1.304     0    0.054   0.781     3.941   79.286   65.608
LGA    Q    53_A      Q    53_A     1.736     0    0.035   1.446     4.447   77.143   69.312
LGA    L    54_A      L    54_A     0.915     0    0.068   0.179     1.415   85.952   88.274
LGA    S    55_A      S    55_A     2.202     0    0.094   0.668     3.174   61.190   63.889
LGA    E    56_A      E    56_A     3.112     0    0.082   0.798     4.765   50.119   48.042
LGA    K    57_A      K    57_A     2.411     0    0.084   0.598     2.619   64.762   63.069
LGA    D    58_A      D    58_A     1.873     0    0.052   0.842     3.460   75.000   65.179
LGA    P    59_A      P    59_A     0.265     0    0.027   0.169     1.779   86.190   84.218
LGA    K    60_A      K    60_A     1.823     0    0.045   0.270     3.717   67.619   63.810
LGA    T    61_A      T    61_A     3.549     0    0.622   0.846     4.161   48.452   44.490
LGA    E    62_A      E    62_A     4.012     0    0.234   1.227     5.938   41.786   36.984
LGA    Q    63_A      Q    63_A     4.368     0    0.326   1.054     8.814   41.786   25.344
LGA    E    64_A      E    64_A     4.498     0    0.568   1.256     8.602   34.524   23.439
LGA    A    65_A      A    65_A     9.012     0    0.172   0.181    11.327    4.048    3.238
LGA    E    66_A      E    66_A     8.717     0    0.106   1.042    12.702    5.595    2.540
LGA    R    67_A      R    67_A     4.200     0    0.346   0.549     5.119   39.405   47.532
LGA    I    68_A      I    68_A     1.064     0    0.413   0.773     4.271   81.548   65.952
LGA    L    69_A      L    69_A     0.606     0    0.051   0.142     1.113   90.476   89.345
LGA    L    70_A      L    70_A     0.554     0    0.094   1.393     3.697   92.857   79.583
LGA    E    71_A      E    71_A     0.697     0    0.060   0.529     1.906   90.476   86.508
LGA    F    72_A      F    72_A     1.043     0    0.044   0.236     1.560   83.690   81.472
LGA    L    73_A      L    73_A     0.901     0    0.029   0.125     0.997   90.476   92.857
LGA    T    74_A      T    74_A     1.056     0    0.035   0.056     1.528   88.214   84.082
LGA    H    75_A      H    75_A     0.682     0    0.139   1.027     4.808   88.214   72.238
LGA    R    76_A      R    76_A     1.012     0    0.049   0.895     5.582   83.690   65.238
LGA    K    77_A      K    77_A     0.987     0    0.058   0.400     2.617   90.476   79.947
LGA    A    78_A      A    78_A     0.581     0    0.031   0.037     0.939   90.476   92.381
LGA    E    79_A      E    79_A     1.193     0    0.051   1.255     4.790   81.548   64.921
LGA    R    80_A      R    80_A     1.672     0    0.045   1.302     7.356   75.000   55.065
LGA    D    81_A      D    81_A     1.409     0    0.102   0.344     2.010   81.429   77.202
LGA    R    82_A      R    82_A     1.611     0    0.097   1.034     6.507   75.000   57.662
LGA    A    83_A      A    83_A     2.262     0    0.169   0.176     3.277   59.167   60.286
LGA    A    84_A      A    84_A     2.475     0    0.598   0.594     2.627   62.857   63.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       53     212    212  100.00     434    434  100.00               166
SUMMARY(RMSD_GDC):     4.418          4.339                  4.795           17.967   16.282

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53  166    4.0     39    2.02    20.783    19.463     1.836

LGA_LOCAL      RMSD:   2.024  Number of atoms:   39  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.867  Number of assigned atoms:   53 
Std_ASGN_ATOMS RMSD:   4.418  Standard rmsd on all 53 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.999713 * X  +   0.010365 * Y  +  -0.021583 * Z  +  16.156044
  Y_new =  -0.023022 * X  +   0.663711 * Y  +  -0.747635 * Z  +  41.552570
  Z_new =   0.006575 * X  +   0.747918 * Y  +   0.663759 * Z  + -43.364880 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.023024 -0.006575  0.844944   [DEG:   -1.3192   -0.3767   48.4117 ]
ZXZ: -0.028860  0.844963  0.008791   [DEG:   -1.6535   48.4128    0.5037 ]
 
# END of job
