
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.38     1.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    61       1_B - 61_B        1.38     1.38
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41      15_B - 55_B        0.99     1.51
  LONGEST_CONTINUOUS_SEGMENT:    41      16_B - 56_B        0.99     1.52
  LONGEST_CONTINUOUS_SEGMENT:    41      17_B - 57_B        0.99     1.53
  LCS_AVERAGE:     56.46

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     D     1_B     D     1_B     14   61   61      4   10   43   54   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Y     2_B     Y     2_B     14   61   61     10   12   21   53   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I     3_B     I     3_B     14   61   61      7   12   16   36   58   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     4_B     R     4_B     14   61   61     10   12   43   54   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E     5_B     E     5_B     14   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L     6_B     L     6_B     14   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R     7_B     R     7_B     14   61   61     10   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     8_B     A     8_B     14   61   61     16   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A     9_B     A     9_B     14   61   61     10   23   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    10_B     L    10_B     14   61   61     17   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     I    11_B     I    11_B     14   61   61     10   22   36   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    12_B     L    12_B     14   61   61     10   12   32   52   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    13_B     L    13_B     14   61   61      8   22   36   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    14_B     A    14_B     23   61   61      8   12   43   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    15_B     L    15_B     41   61   61      8   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    16_B     K    16_B     41   61   61      8   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    17_B     K    17_B     41   61   61     12   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    18_B     Q    18_B     41   61   61     12   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    19_B     H    19_B     41   61   61      8    9   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    20_B     A    20_B     41   61   61      6   10   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    21_B     E    21_B     41   61   61      5   24   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    22_B     D    22_B     41   61   61     11   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     P    23_B     P    23_B     41   61   61     13   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    24_B     D    24_B     41   61   61      6   28   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    25_B     A    25_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     Q    26_B     Q    26_B     41   61   61      7   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    27_B     R    27_B     41   61   61      7   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    28_B     V    28_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    29_B     A    29_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    30_B     D    30_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    31_B     E    31_B     41   61   61     12   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    32_B     L    32_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     M    33_B     M    33_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    34_B     K    34_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    35_B     K    35_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     L    36_B     L    36_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     F    37_B     F    37_B     41   61   61     12   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    38_B     D    38_B     41   61   61     12   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    39_B     A    39_B     41   61   61     12   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    40_B     A    40_B     41   61   61     12   27   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     H    41_B     H    41_B     41   61   61      8   20   32   54   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     R    42_B     R    42_B     41   61   61      5   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     N    43_B     N    43_B     41   61   61      5   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    44_B     D    44_B     41   61   61     16   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    45_B     K    45_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     D    46_B     D    46_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    47_B     K    47_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    48_B     V    48_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    49_B     K    49_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    50_B     K    50_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    51_B     V    51_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    52_B     V    52_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    53_B     E    53_B     41   61   61     17   30   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     E    54_B     E    54_B     41   61   61     17   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     A    55_B     A    55_B     41   61   61     17   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    56_B     K    56_B     41   61   61     17   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     K    57_B     K    57_B     41   61   61     17   27   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    58_B     V    58_B     37   61   61     12   27   43   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     V    59_B     V    59_B     32   61   61     10   27   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     S    60_B     S    60_B     32   61   61     17   29   49   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_GDT     T    61_B     T    61_B     32   61   61     17   27   43   55   59   61   61   61   61   61   61   61   61   61   61   61   61   61   61   61 
LCS_AVERAGE  LCS_A:  85.49  (  56.46  100.00  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     17     30     49     55     59     61     61     61     61     61     61     61     61     61     61     61     61     61     61     61 
GDT PERCENT_AT  27.87  49.18  80.33  90.16  96.72 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.27   0.61   1.01   1.16   1.29   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38
GDT RMS_ALL_AT   1.89   1.81   1.41   1.39   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38   1.38

# Checking swapping
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  E    53_B      E    53_B
#   possible swapping detected:  E    54_B      E    54_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     2.104     0    0.074   1.009     5.041   69.048   52.619
LGA    Y     2_B      Y     2_B     2.412     0    0.076   1.496    11.668   64.762   31.865
LGA    I     3_B      I     3_B     3.096     0    0.037   1.538     6.331   59.167   52.381
LGA    R     4_B      R     4_B     2.012     0    0.060   1.233     4.685   73.095   60.043
LGA    E     5_B      E     5_B     0.502     0    0.051   0.689     1.966   90.476   87.513
LGA    L     6_B      L     6_B     1.099     0    0.047   0.940     4.800   88.214   71.607
LGA    R     7_B      R     7_B     1.045     0    0.031   1.304     4.027   88.214   68.312
LGA    A     8_B      A     8_B     1.123     0    0.065   0.062     1.819   81.548   83.333
LGA    A     9_B      A     9_B     1.396     0    0.035   0.038     2.027   79.524   78.190
LGA    L    10_B      L    10_B     0.849     0    0.043   0.149     1.450   85.952   85.952
LGA    I    11_B      I    11_B     2.195     0    0.033   1.317     4.712   62.976   63.869
LGA    L    12_B      L    12_B     2.797     0    0.156   0.882     5.348   60.952   54.345
LGA    L    13_B      L    13_B     2.335     0    0.041   1.031     5.010   66.905   57.262
LGA    A    14_B      A    14_B     1.711     0    0.036   0.045     2.167   79.405   76.476
LGA    L    15_B      L    15_B     0.723     0    0.045   0.963     2.684   92.976   86.429
LGA    K    16_B      K    16_B     0.967     0    0.030   0.668     4.158   90.476   72.063
LGA    K    17_B      K    17_B     0.488     0    0.034   0.585     1.653   95.238   85.714
LGA    Q    18_B      Q    18_B     0.915     0    0.034   1.317     4.675   86.190   69.206
LGA    H    19_B      H    19_B     1.649     0    0.169   0.711     4.037   75.000   65.619
LGA    A    20_B      A    20_B     1.650     0    0.187   0.237     2.287   70.833   71.238
LGA    E    21_B      E    21_B     1.142     0    0.071   0.572     2.009   83.690   77.725
LGA    D    22_B      D    22_B     0.718     0    0.059   0.962     4.285   90.476   72.083
LGA    P    23_B      P    23_B     1.413     0    0.084   0.359     1.730   79.286   78.980
LGA    D    24_B      D    24_B     1.547     0    0.076   0.328     2.730   79.286   72.083
LGA    A    25_B      A    25_B     1.055     0    0.046   0.050     1.481   81.429   83.238
LGA    Q    26_B      Q    26_B     1.556     0    0.038   1.038     3.925   75.000   70.582
LGA    R    27_B      R    27_B     1.728     0    0.019   1.265     5.933   72.857   60.519
LGA    V    28_B      V    28_B     1.351     0    0.020   0.994     2.634   81.429   77.959
LGA    A    29_B      A    29_B     1.324     0    0.028   0.050     1.339   81.429   81.429
LGA    D    30_B      D    30_B     1.021     0    0.022   1.158     5.507   85.952   69.464
LGA    E    31_B      E    31_B     0.775     0    0.038   1.288     5.762   92.857   67.302
LGA    L    32_B      L    32_B     0.955     0    0.033   1.376     3.669   90.476   80.119
LGA    M    33_B      M    33_B     1.020     0    0.030   0.929     5.279   88.214   73.750
LGA    K    34_B      K    34_B     0.501     0    0.038   1.083     3.986   90.476   75.397
LGA    K    35_B      K    35_B     0.361     0    0.057   0.790     4.834   97.619   79.630
LGA    L    36_B      L    36_B     0.751     0    0.034   1.061     2.963   90.476   83.095
LGA    F    37_B      F    37_B     1.243     0    0.059   1.227     4.701   81.548   70.173
LGA    D    38_B      D    38_B     1.347     0    0.049   0.265     1.944   77.143   79.286
LGA    A    39_B      A    39_B     1.327     0    0.024   0.035     1.676   77.143   78.000
LGA    A    40_B      A    40_B     1.931     0    0.109   0.106     2.285   68.810   69.619
LGA    H    41_B      H    41_B     2.689     0    0.082   0.997     7.326   59.048   38.048
LGA    R    42_B      R    42_B     1.829     0    0.174   1.249     4.256   70.833   65.931
LGA    N    43_B      N    43_B     1.198     0    0.070   0.769     3.479   85.952   76.607
LGA    D    44_B      D    44_B     0.409     0    0.096   0.946     3.848   97.619   81.071
LGA    K    45_B      K    45_B     0.354     0    0.063   0.743     4.301  100.000   76.138
LGA    D    46_B      D    46_B     0.359     0    0.044   0.617     2.024  100.000   92.024
LGA    K    47_B      K    47_B     0.312     0    0.032   1.170     7.087  100.000   71.111
LGA    V    48_B      V    48_B     0.069     0    0.079   1.273     2.974  100.000   88.844
LGA    K    49_B      K    49_B     0.557     0    0.085   0.772     5.152   92.857   69.418
LGA    K    50_B      K    50_B     0.623     0    0.041   0.923     5.766   90.476   67.249
LGA    V    51_B      V    51_B     0.496     0    0.031   1.100     2.521   95.238   86.122
LGA    V    52_B      V    52_B     0.400     0    0.038   0.124     0.691   95.238   95.918
LGA    E    53_B      E    53_B     0.690     0    0.030   1.367     6.400   88.214   63.915
LGA    E    54_B      E    54_B     0.969     0    0.045   0.746     2.897   90.476   76.349
LGA    A    55_B      A    55_B     0.942     0    0.043   0.058     1.167   88.214   88.667
LGA    K    56_B      K    56_B     0.870     0    0.046   0.862     3.885   85.952   76.667
LGA    K    57_B      K    57_B     1.175     0    0.029   0.965     7.346   81.429   55.820
LGA    V    58_B      V    58_B     1.676     0    0.082   0.093     2.461   75.000   70.612
LGA    V    59_B      V    59_B     1.380     0    0.068   0.261     1.651   81.429   80.204
LGA    S    60_B      S    60_B     1.048     0    0.208   0.210     2.103   77.262   80.159
LGA    T    61_B      T    61_B     1.626     0    0.031   0.075     2.340   72.976   71.769

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     491    491  100.00                61
SUMMARY(RMSD_GDC):     1.377          1.353                  2.480           82.865   72.904

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     61    1.38    84.836    93.615     4.131

LGA_LOCAL      RMSD:   1.377  Number of atoms:   61  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   1.377  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   1.377  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.978324 * X  +  -0.207073 * Y  +   0.001770 * Z  +  -7.965794
  Y_new =  -0.201006 * X  +  -0.947531 * Y  +   0.248559 * Z  + -15.257221
  Z_new =  -0.049793 * X  +  -0.243527 * Y  +  -0.968615 * Z  +  37.422314 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.202639  0.049813 -2.895280   [DEG:  -11.6104    2.8541 -165.8873 ]
ZXZ:  3.134471  2.890393 -2.939908   [DEG:  179.5919  165.6073 -168.4443 ]
 
# END of job
