
#######################################################
#                                                     #
#                        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 (  410),  selected   49 , name one
# Molecule2: number of CA atoms   49 (  370),  selected   49 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:F  -ch2:F  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       7_F - 34_F        4.75    13.99
  LONGEST_CONTINUOUS_SEGMENT:    28       8_F - 35_F        4.71    13.96
  LCS_AVERAGE:     52.39

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      10_F - 26_F        1.72    15.85
  LONGEST_CONTINUOUS_SEGMENT:    17      11_F - 27_F        1.63    15.50
  LCS_AVERAGE:     22.16

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      11_F - 25_F        0.93    16.50
  LCS_AVERAGE:     15.58

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   49
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     M     1_F     M     1_F      3    3    9      0    3    3    3    3    4    4    5    6    7   11   11   13   15   15   19   20   21   24   27 
LCS_GDT     G     2_F     G     2_F      3    4   11      1    3    3    4    4    4    6    6    7   10   11   12   13   16   19   19   20   23   24   27 
LCS_GDT     K     3_F     K     3_F      3    4   12      3    3    3    4    4    4    6    6    8   10   11   12   13   16   19   19   20   23   24   27 
LCS_GDT     I     4_F     I     4_F      3    4   12      3    3    3    4    4    4    6    6    8   10   11   12   13   16   19   19   20   23   24   27 
LCS_GDT     K     5_F     K     5_F      3    4   12      3    3    3    4    4    4    6    6    8   10   11   12   14   16   20   20   23   25   26   28 
LCS_GDT     R     6_F     R     6_F      3    3   12      1    3    3    3    3    4    6    6    8    9   10   12   13   15   17   21   23   25   28   28 
LCS_GDT     F     7_F     F     7_F      3    3   28      0    3    5    5    5    5    6    6    8    9   10   16   19   24   25   28   28   29   32   33 
LCS_GDT     F     8_F     F     8_F      3    3   28      1    3    5    7    9    9    9   11   18   22   23   24   26   27   31   33   34   36   37   38 
LCS_GDT     A     9_F     A     9_F      4    4   28      3    3    5    5    5    5    9   13   20   22   24   25   26   28   31   33   34   36   37   38 
LCS_GDT     K    10_F     K    10_F      4   17   28      4    6    7   11   13   16   18   20   22   22   24   25   26   28   31   33   34   35   37   38 
LCS_GDT     D    11_F     D    11_F     15   17   28      7   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     M    12_F     M    12_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     R    13_F     R    13_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     A    14_F     A    14_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     A    15_F     A    15_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     L    16_F     L    16_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     A    17_F     A    17_F     15   17   28      7   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     Q    18_F     Q    18_F     15   17   28      6   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     V    19_F     V    19_F     15   17   28      6   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     K    20_F     K    20_F     15   17   28      6   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     D    21_F     D    21_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     T    22_F     T    22_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     L    23_F     L    23_F     15   17   28      8   13   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     G    24_F     G    24_F     15   17   28      4    6   14   15   18   18   19   20   22   22   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     S    25_F     S    25_F     15   17   28      5   10   13   15   15   16   19   20   23   24   24   25   26   27   28   30   31   36   38   39 
LCS_GDT     D    26_F     D    26_F      6   17   28      4   10   14   15   18   18   19   20   23   24   24   25   26   28   31   34   35   36   38   39 
LCS_GDT     A    27_F     A    27_F      6   17   28      4    5    7   15   18   18   19   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     V    28_F     V    28_F      6   13   28      4    5    7   10   12   16   18   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     I    29_F     I    29_F      6   13   28      4    5    7   13   18   18   19   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     M    30_F     M    30_F      6   13   28      3    5    7   10   12   16   18   20   23   24   24   24   26   29   31   33   34   36   38   39 
LCS_GDT     S    31_F     S    31_F      6    9   28      4    5    7   13   18   18   19   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     N    32_F     N    32_F      5    9   28      3    4    5    7   11   16   19   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     K    33_F     K    33_F      5    9   28      3    4    7   10   12   16   18   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     K    34_F     K    34_F      5    9   28      3    4    5    6   10   16   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     V    35_F     V    35_F      4    7   28      3    4    4    6    6    7   12   18   22   24   24   24   25   29   31   34   35   36   38   39 
LCS_GDT     N    36_F     N    36_F      3    8   27      1    3    4    7   10   15   18   20   23   24   24   24   25   29   30   34   35   36   38   39 
LCS_GDT     G    37_F     G    37_F      5    8   27      3    5    5    6    7    9   16   20   23   24   24   24   25   26   28   30   33   36   38   39 
LCS_GDT     G    38_F     G    38_F      5    8   27      4    5    5    7   11   15   18   20   23   24   24   24   25   26   28   28   29   34   37   39 
LCS_GDT     I    39_F     I    39_F      5    8   27      4    5    5    7   11   16   18   20   23   24   24   24   25   29   31   34   35   36   38   39 
LCS_GDT     E    40_F     E    40_F      5    8   27      4    5    5   10   12   16   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     I    41_F     I    41_F      5    8   27      4    5    6    8   12   16   18   20   23   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     V    42_F     V    42_F      5    8   27      4    5    6    9   12   16   18   20   23   24   24   24   25   29   31   33   35   36   38   39 
LCS_GDT     A    43_F     A    43_F      5    8   27      4    5    6    7   10   14   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     A    44_F     A    44_F      5    8   27      4    5    7   10   12   16   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     V    45_F     V    45_F      5    8   27      4    5    7   10   12   16   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     L    46_F     L    46_F      5    8   27      4    5    5    7   10   13   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     E    47_F     E    47_F      3    8   27      3    4    6    7    9   16   18   20   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     H    48_F     H    48_F      3    8   27      3    4    6    6   10   13   15   19   23   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     H    49_F     H    49_F      3    8   27      3    3    5    7    9    9    9   12   13   17   21   23   26   29   31   34   35   36   38   39 
LCS_AVERAGE  LCS_A:  30.04  (  15.58   22.16   52.39 )

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      8     13     14     15     18     18     19     20     23     24     24     25     26     29     31     34     35     36     38     39 
GDT PERCENT_AT  16.33  26.53  28.57  30.61  36.73  36.73  38.78  40.82  46.94  48.98  48.98  51.02  53.06  59.18  63.27  69.39  71.43  73.47  77.55  79.59
GDT RMS_LOCAL    0.33   0.63   0.76   0.91   1.69   1.69   1.95   2.12   3.17   3.26   3.26   3.49   3.69   4.96   5.55   5.94   6.00   6.09   6.43   6.63
GDT RMS_ALL_AT  15.93  16.22  16.18  15.77  14.70  14.70  14.78  14.73  14.86  14.84  14.84  14.19  14.19  13.49  13.10  13.17  13.09  13.08  13.20  13.26

# Checking swapping
#   possible swapping detected:  F     8_F      F     8_F
#   possible swapping detected:  D    11_F      D    11_F
#   possible swapping detected:  D    26_F      D    26_F
#   possible swapping detected:  E    40_F      E    40_F

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    M     1_F      M     1_F    42.118     0    0.316   1.033    48.785    0.000    0.000
LGA    G     2_F      G     2_F    39.028     0    0.609   0.609    40.534    0.000    0.000
LGA    K     3_F      K     3_F    33.376     0    0.575   1.289    35.237    0.000    0.000
LGA    I     4_F      I     4_F    28.382     0    0.590   0.894    30.761    0.000    0.000
LGA    K     5_F      K     5_F    24.332     0    0.632   1.316    29.059    0.000    0.000
LGA    R     6_F      R     6_F    21.276     0    0.588   0.761    25.723    0.000    0.000
LGA    F     7_F      F     7_F    15.291     0    0.596   0.634    22.167    0.000    0.000
LGA    F     8_F      F     8_F    10.820     0    0.567   1.530    12.770    0.238    0.260
LGA    A     9_F      A     9_F     9.224     0    0.607   0.579    10.215    6.310    5.048
LGA    K    10_F      K    10_F     5.900     0    0.080   1.531     9.033   27.381   20.212
LGA    D    11_F      D    11_F     1.467     0    0.596   1.198     4.751   79.286   57.500
LGA    M    12_F      M    12_F     1.570     0    0.065   1.396     7.038   77.143   60.000
LGA    R    13_F      R    13_F     1.337     0    0.042   1.177     6.457   81.429   55.758
LGA    A    14_F      A    14_F     0.693     0    0.042   0.047     0.834   90.476   90.476
LGA    A    15_F      A    15_F     0.692     0    0.087   0.086     0.936   90.476   90.476
LGA    L    16_F      L    16_F     1.184     0    0.027   1.252     5.294   88.214   73.690
LGA    A    17_F      A    17_F     1.597     0    0.069   0.068     2.207   77.143   74.667
LGA    Q    18_F      Q    18_F     2.224     0    0.032   1.444     7.713   68.810   45.238
LGA    V    19_F      V    19_F     1.646     0    0.036   1.091     4.638   79.286   70.680
LGA    K    20_F      K    20_F     1.080     0    0.059   0.956     2.782   85.952   75.185
LGA    D    21_F      D    21_F     1.519     0    0.064   0.439     4.316   79.405   68.690
LGA    T    22_F      T    22_F     1.634     0    0.062   1.145     3.488   75.000   70.816
LGA    L    23_F      L    23_F     1.605     0    0.042   1.125     3.637   70.833   68.155
LGA    G    24_F      G    24_F     2.017     0    0.615   0.615     4.800   56.548   56.548
LGA    S    25_F      S    25_F     4.197     0    0.626   0.781     6.903   52.143   39.841
LGA    D    26_F      D    26_F     0.304     0    0.585   1.374     4.409   68.690   71.964
LGA    A    27_F      A    27_F     2.840     0    0.075   0.139     3.864   63.214   59.238
LGA    V    28_F      V    28_F     4.989     0    0.112   0.157     8.517   29.286   18.844
LGA    I    29_F      I    29_F     2.886     0    0.157   0.724     4.925   43.929   61.667
LGA    M    30_F      M    30_F     6.581     0    0.640   1.087    10.837   19.524    9.940
LGA    S    31_F      S    31_F     2.696     0    0.064   0.734     5.647   53.571   46.508
LGA    N    32_F      N    32_F     4.063     0    0.471   1.251     5.850   36.786   37.083
LGA    K    33_F      K    33_F     6.426     0    0.067   1.247    11.552   13.214    9.577
LGA    K    34_F      K    34_F    11.362     0    0.286   0.844    12.998    0.119    0.053
LGA    V    35_F      V    35_F    14.896     0    0.553   0.876    18.935    0.000    0.000
LGA    N    36_F      N    36_F    20.219     0    0.621   1.052    25.431    0.000    0.000
LGA    G    37_F      G    37_F    21.777     0    0.617   0.617    22.733    0.000    0.000
LGA    G    38_F      G    38_F    20.312     0    0.262   0.262    20.592    0.000    0.000
LGA    I    39_F      I    39_F    14.056     0    0.040   0.184    16.812    0.000    0.000
LGA    E    40_F      E    40_F    12.531     0    0.174   1.104    15.037    1.190    0.529
LGA    I    41_F      I    41_F     9.269     0    0.171   1.108    12.584    0.357    1.131
LGA    V    42_F      V    42_F    11.836     0    0.637   0.667    12.610    0.119    0.068
LGA    A    43_F      A    43_F    11.130     0    0.044   0.080    11.500    0.000    0.000
LGA    A    44_F      A    44_F    12.344     0    0.049   0.081    13.247    0.000    0.000
LGA    V    45_F      V    45_F    12.551     0    0.053   0.950    13.698    0.000    0.000
LGA    L    46_F      L    46_F    14.117     0    0.589   1.502    17.472    0.000    0.000
LGA    E    47_F      E    47_F    13.756     0    0.608   1.074    17.081    0.000    0.000
LGA    H    48_F      H    48_F    18.487     0    0.081   1.098    24.522    0.000    0.000
LGA    H    49_F      H    49_F    17.695     0    0.505   1.204    23.357    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       49     196    196  100.00     370    370  100.00                49
SUMMARY(RMSD_GDC):    12.048         11.931                 12.630           30.940   27.344

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     20    2.12    41.837    36.796     0.902

LGA_LOCAL      RMSD:   2.117  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.733  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:  12.048  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.636428 * X  +   0.642609 * Y  +  -0.426630 * Z  +  58.015598
  Y_new =  -0.085845 * X  +  -0.608678 * Y  +  -0.788760 * Z  + -23.001719
  Z_new =  -0.766544 * X  +  -0.465365 * Y  +   0.442544 * Z  +  15.810723 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.007517  0.873443 -0.810528   [DEG: -172.3180   50.0446  -46.4398 ]
ZXZ: -0.495820  1.112363 -2.116416   [DEG:  -28.4084   63.7337 -121.2617 ]
 
# END of job
