
#######################################################
#                                                     #
#                        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   56 (  447),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    43       5_B - 47_B        3.84     3.84
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       5_B - 41_B        1.95     4.64
  LCS_AVERAGE:     80.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       5_B - 27_B        0.84     5.78
  LCS_AVERAGE:     40.94

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   41   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     23   37   43     16   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     23   37   43     15   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     23   37   43     13   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     23   37   43     13   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     23   37   43     10   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     23   37   43     11   21   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     23   37   43      9   19   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     23   37   43      6   16   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     19   37   43      3   10   23   26   31   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     18   37   43      3    3   14   27   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     18   37   43      3   16   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     18   37   43      7   16   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     18   37   43      7   16   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     11   37   43      5   11   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     11   37   43      5   11   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     11   37   43      5   12   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     11   37   43      5   11   23   28   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     11   37   43      5   16   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     11   37   43      5   16   23   29   33   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     11   37   43      6   13   23   26   31   34   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     11   37   43      6   10   23   26   28   33   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     10   37   43      6    7   16   24   27   30   34   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      9   33   43      6    7   12   19   25   28   31   34   36   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      8   31   43      6    7   11   17   23   26   30   33   36   37   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   30   43      6    7   11   16   21   25   28   33   35   37   38   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      8   14   43      3    6    8   13   19   22   25   27   31   32   34   35   38   40   41   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    5    5    5    8   10   13   24   27   29   35   37   40   40   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4   24   30   32   32   35   36   40   40   42   43   43   43   43 
LCS_AVERAGE  LCS_A:  73.82  (  40.94   80.53  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     16     21     23     29     33     34     35     36     37     38     39     40     40     40     41     42     43     43     43     43 
GDT PERCENT_AT  37.21  48.84  53.49  67.44  76.74  79.07  81.40  83.72  86.05  88.37  90.70  93.02  93.02  93.02  95.35  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.26   0.58   0.81   1.27   1.50   1.57   1.64   1.78   1.95   2.21   2.50   2.77   2.77   2.77   3.19   3.76   3.84   3.84   3.84   3.84
GDT RMS_ALL_AT   6.24   5.98   5.62   5.07   4.87   4.88   4.84   4.75   4.64   4.48   4.29   4.13   4.13   4.13   3.96   3.85   3.84   3.84   3.84   3.84

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.301     0    0.036   0.194     3.357   66.786   62.381
LGA    L     6_B      L     6_B     2.695     0    0.033   0.866     3.241   60.952   60.060
LGA    E     7_B      E     7_B     2.263     0    0.031   1.105     6.912   68.810   52.381
LGA    T     8_B      T     8_B     0.799     0    0.062   1.228     2.848   88.214   82.109
LGA    K     9_B      K     9_B     1.097     0    0.011   0.132     2.396   83.690   76.825
LGA    K    10_B      K    10_B     1.508     0    0.015   0.945     5.661   79.286   62.381
LGA    A    11_B      A    11_B     1.364     0    0.017   0.018     1.545   81.429   79.714
LGA    Y    12_B      Y    12_B     0.528     0    0.037   0.083     2.517   92.857   80.437
LGA    A    13_B      A    13_B     0.415     0    0.004   0.013     0.867   97.619   96.190
LGA    A    14_B      A    14_B     1.321     0    0.035   0.039     1.904   81.548   79.810
LGA    R    15_B      R    15_B     1.689     0    0.022   1.204     5.342   72.976   63.853
LGA    T    16_B      T    16_B     1.562     0    0.066   0.072     1.812   79.286   77.755
LGA    R    17_B      R    17_B     0.947     0    0.014   1.099     3.789   85.952   73.853
LGA    R    18_B      R    18_B     1.439     0    0.015   1.263     6.787   77.143   57.489
LGA    S    19_B      S    19_B     2.126     0    0.037   0.698     2.507   70.833   70.317
LGA    N    20_B      N    20_B     1.720     0    0.047   0.368     1.797   77.143   76.071
LGA    Y    21_B      Y    21_B     0.549     0    0.076   0.216     4.006   88.214   72.659
LGA    A    22_B      A    22_B     1.212     0    0.020   0.022     1.581   81.429   79.714
LGA    A    23_B      A    23_B     1.531     0    0.013   0.016     1.846   79.286   78.000
LGA    S    24_B      S    24_B     1.197     0    0.064   0.721     1.274   83.690   84.444
LGA    L    25_B      L    25_B     0.629     0    0.044   0.077     1.154   90.476   89.345
LGA    R    26_B      R    26_B     0.595     0    0.075   1.399     4.619   90.476   75.368
LGA    L    27_B      L    27_B     1.725     0    0.017   0.173     3.637   70.952   63.274
LGA    E    28_B      E    28_B     3.006     0    0.206   0.776     7.425   52.024   36.508
LGA    G    29_B      G    29_B     2.235     0    0.090   0.090     3.570   57.500   57.500
LGA    F    30_B      F    30_B     1.524     0    0.577   0.488     3.936   63.452   79.004
LGA    K    31_B      K    31_B     0.848     0    0.269   0.653     2.001   88.214   79.735
LGA    V    32_B      V    32_B     0.200     0    0.038   0.861     2.924   90.833   79.864
LGA    T    33_B      T    33_B     1.704     0    0.065   1.111     5.153   81.548   66.667
LGA    F    34_B      F    34_B     1.266     0    0.019   1.206     8.733   86.190   48.831
LGA    A    35_B      A    35_B     1.860     0    0.046   0.049     2.730   70.833   68.095
LGA    D    36_B      D    36_B     2.295     0    0.113   0.126     3.369   63.095   61.131
LGA    G    37_B      G    37_B     1.881     0    0.081   0.081     2.301   70.833   70.833
LGA    E    38_B      E    38_B     1.333     0    0.054   0.854     4.234   73.095   67.884
LGA    R    39_B      R    39_B     3.032     0    0.126   1.352     5.797   53.690   40.823
LGA    K    40_B      K    40_B     4.305     0    0.058   0.863    12.065   35.833   20.741
LGA    M    41_B      M    41_B     5.271     0    0.029   1.279     6.059   24.048   35.893
LGA    P    42_B      P    42_B     7.244     0    0.012   0.024     7.702    9.405    9.728
LGA    T    43_B      T    43_B     8.800     0    0.081   1.128    11.268    2.381    1.633
LGA    R    44_B      R    44_B     9.755     0    0.600   0.934    10.353    1.190    0.779
LGA    E    45_B      E    45_B    13.456     0    0.439   1.118    18.474    0.000    0.000
LGA    E    46_B      E    46_B    14.517     0    0.595   1.384    16.515    0.000    0.000
LGA    V    47_B      V    47_B    14.538     0    0.431   1.369    16.096    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     3.835          3.784                  4.506           64.493   58.606

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     36    1.78    74.419    78.272     1.913

LGA_LOCAL      RMSD:   1.782  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.750  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.835  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.074109 * X  +  -0.164648 * Y  +  -0.983564 * Z  +  17.500923
  Y_new =   0.747310 * X  +   0.643894 * Y  +  -0.164095 * Z  + -60.191891
  Z_new =   0.660329 * X  +  -0.747189 * Y  +   0.075325 * Z  +  15.452303 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.669641 -0.721257 -1.470325   [DEG:   95.6634  -41.3250  -84.2434 ]
ZXZ: -1.405482  1.495400  2.417827   [DEG:  -80.5282   85.6801  138.5313 ]
 
# END of job
