
#######################################################
#                                                     #
#                        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        4.70    13.90
  LONGEST_CONTINUOUS_SEGMENT:    28       8_F - 35_F        4.62    13.88
  LCS_AVERAGE:     52.44

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      10_F - 26_F        1.75    15.70
  LONGEST_CONTINUOUS_SEGMENT:    17      11_F - 27_F        1.59    15.35
  LCS_AVERAGE:     21.82

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      11_F - 25_F        0.92    16.37
  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    4   10      0    3    3    3    4    4    5    5    7    7    7    8   10   14   17   19   19   21   24   25 
LCS_GDT     G     2_F     G     2_F      3    4   11      0    3    3    4    4    6    6    6    7    9   12   12   14   15   17   19   20   22   24   25 
LCS_GDT     K     3_F     K     3_F      3    4   12      3    3    3    4    4    6    7    8    8   10   12   12   14   15   17   19   20   22   24   25 
LCS_GDT     I     4_F     I     4_F      3    4   12      3    3    3    4    5    6    7    8    8   10   12   12   14   15   17   19   20   22   24   27 
LCS_GDT     K     5_F     K     5_F      3    4   12      3    3    3    4    4    6    6    8    8   10   12   12   14   16   18   21   24   24   26   29 
LCS_GDT     R     6_F     R     6_F      3    3   12      2    3    3    3    3    4    6    6    7    8   10   11   13   15   18   20   24   25   27   29 
LCS_GDT     F     7_F     F     7_F      3    3   28      0    3    3    3    4    4    6    6    8    9   10   15   19   23   25   28   29   31   33   35 
LCS_GDT     F     8_F     F     8_F      3    3   28      1    3    3    6    8    9   10   14   17   22   24   24   26   28   30   34   35   36   37   38 
LCS_GDT     A     9_F     A     9_F      4    4   28      3    3    4    5    6    7   14   16   20   22   24   25   26   28   30   34   35   36   37   38 
LCS_GDT     K    10_F     K    10_F      4   17   28      3    3    5    8   13   16   18   21   22   22   24   25   26   28   30   34   34   35   37   38 
LCS_GDT     D    11_F     D    11_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     M    12_F     M    12_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     R    13_F     R    13_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     A    14_F     A    14_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     A    15_F     A    15_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     L    16_F     L    16_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     A    17_F     A    17_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     Q    18_F     Q    18_F     15   17   28      7   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     V    19_F     V    19_F     15   17   28      6   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     K    20_F     K    20_F     15   17   28      7   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     D    21_F     D    21_F     15   17   28      8   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     T    22_F     T    22_F     15   17   28      7   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     L    23_F     L    23_F     15   17   28      7   13   14   16   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     G    24_F     G    24_F     15   17   28      3    3   14   15   18   18   19   21   22   22   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     S    25_F     S    25_F     15   17   28      3    9   12   15   15   16   19   21   22   24   24   25   26   27   28   29   32   36   38   39 
LCS_GDT     D    26_F     D    26_F      6   17   28      4   11   14   16   18   18   19   21   22   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   16   18   18   19   21   22   24   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     V    28_F     V    28_F      6   10   28      4    5    6   10   12   16   18   20   22   24   24   25   26   29   31   34   35   36   38   39 
LCS_GDT     I    29_F     I    29_F      6   10   28      3    4    6   14   18   18   19   21   22   24   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     M    30_F     M    30_F      6   10   28      3    5    6   10   12   16   18   20   22   24   24   24   26   29   31   34   35   36   38   39 
LCS_GDT     S    31_F     S    31_F      6    9   28      4    5    6   16   18   18   19   21   22   24   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     N    32_F     N    32_F      5    9   28      3    4    5   10   12   16   19   21   22   24   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     K    33_F     K    33_F      5    9   28      3    5    6   10   12   16   18   20   22   24   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     K    34_F     K    34_F      5    9   28      3    4    5    6   12   16   18   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     V    35_F     V    35_F      4    7   28      2    4    4    5    6    7   12   18   22   24   24   24   25   30   31   34   35   36   38   39 
LCS_GDT     N    36_F     N    36_F      3    8   27      1    3    5    7   11   16   18   20   22   24   24   24   25   29   31   34   35   36   38   39 
LCS_GDT     G    37_F     G    37_F      5    8   27      4    5    5    6    7    9   17   20   22   24   24   24   25   26   29   30   33   36   38   39 
LCS_GDT     G    38_F     G    38_F      5    8   27      4    5    5    6   12   16   18   20   22   24   24   24   25   26   27   29   30   34   37   39 
LCS_GDT     I    39_F     I    39_F      5    8   27      4    5    5    6   12   16   18   20   22   24   24   24   25   29   31   34   35   36   38   39 
LCS_GDT     E    40_F     E    40_F      5    8   27      4    5    6   10   12   16   18   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     I    41_F     I    41_F      5    8   27      4    5    6   10   12   16   18   20   22   24   24   25   26   30   31   34   35   36   38   39 
LCS_GDT     V    42_F     V    42_F      5    8   27      5    5    6   10   12   16   18   20   22   24   24   24   25   28   31   34   35   36   38   39 
LCS_GDT     A    43_F     A    43_F      5    8   27      5    5    6    7   11   14   18   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     A    44_F     A    44_F      5    8   27      5    5    6   10   12   16   18   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     V    45_F     V    45_F      5    8   27      5    5    6   10   12   16   18   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     L    46_F     L    46_F      5    8   27      5    5    5    6    9   13   17   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     E    47_F     E    47_F      3    8   27      3    4    6    6   11   16   18   20   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     H    48_F     H    48_F      3    8   27      3    4    6    6    9   13   17   19   22   24   24   24   26   30   31   34   35   36   38   39 
LCS_GDT     H    49_F     H    49_F      3    8   27      3    4    5    6    8    9   10   10   13   17   21   24   26   30   31   34   35   36   38   39 
LCS_AVERAGE  LCS_A:  29.95  (  15.58   21.82   52.44 )

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     16     18     18     19     21     22     24     24     25     26     30     31     34     35     36     38     39 
GDT PERCENT_AT  16.33  26.53  28.57  32.65  36.73  36.73  38.78  42.86  44.90  48.98  48.98  51.02  53.06  61.22  63.27  69.39  71.43  73.47  77.55  79.59
GDT RMS_LOCAL    0.19   0.60   0.74   1.48   1.62   1.62   1.89   2.33   2.66   3.21   3.21   3.49   3.64   5.35   5.27   5.86   5.97   6.05   6.39   6.59
GDT RMS_ALL_AT  15.55  16.09  16.04  14.64  14.57  14.57  14.65  14.55  14.46  14.78  14.78  14.08  14.08  13.00  13.16  12.94  12.99  12.98  13.10  13.17

# Checking swapping
#   possible swapping detected:  F     8_F      F     8_F
#   possible swapping detected:  D    11_F      D    11_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    42.149     0    0.353   0.941    48.340    0.000    0.000
LGA    G     2_F      G     2_F    38.038     0    0.639   0.639    39.951    0.000    0.000
LGA    K     3_F      K     3_F    32.457     0    0.556   1.178    35.700    0.000    0.000
LGA    I     4_F      I     4_F    27.039     0    0.589   0.916    29.558    0.000    0.000
LGA    K     5_F      K     5_F    23.483     0    0.619   1.314    26.608    0.000    0.000
LGA    R     6_F      R     6_F    20.527     0    0.574   0.946    25.465    0.000    0.000
LGA    F     7_F      F     7_F    14.570     0    0.589   0.687    21.784    0.000    0.000
LGA    F     8_F      F     8_F     9.424     0    0.600   1.149    11.594    1.786    3.030
LGA    A     9_F      A     9_F     8.346     0    0.601   0.584     9.546   11.548    9.333
LGA    K    10_F      K    10_F     4.883     0    0.086   1.341     6.877   36.786   30.423
LGA    D    11_F      D    11_F     2.245     0    0.609   1.296     7.859   73.214   45.714
LGA    M    12_F      M    12_F     2.270     0    0.054   1.336     8.448   66.786   49.643
LGA    R    13_F      R    13_F     1.679     0    0.062   0.829     3.825   77.143   68.225
LGA    A    14_F      A    14_F     0.936     0    0.029   0.041     1.215   88.214   86.857
LGA    A    15_F      A    15_F     1.201     0    0.062   0.060     1.452   81.429   81.429
LGA    L    16_F      L    16_F     1.210     0    0.060   1.217     3.852   85.952   77.857
LGA    A    17_F      A    17_F     0.984     0    0.050   0.051     1.403   88.214   86.857
LGA    Q    18_F      Q    18_F     1.447     0    0.065   0.692     3.068   81.548   70.635
LGA    V    19_F      V    19_F     1.679     0    0.027   1.112     4.598   79.286   70.680
LGA    K    20_F      K    20_F     1.211     0    0.039   0.929     3.630   85.952   74.762
LGA    D    21_F      D    21_F     1.600     0    0.059   0.880     5.173   79.405   59.643
LGA    T    22_F      T    22_F     1.623     0    0.060   1.148     3.568   75.000   69.864
LGA    L    23_F      L    23_F     1.615     0    0.030   0.120     2.031   72.976   72.917
LGA    G    24_F      G    24_F     1.864     0    0.620   0.620     4.526   58.571   58.571
LGA    S    25_F      S    25_F     3.724     0    0.622   0.796     7.068   57.500   42.857
LGA    D    26_F      D    26_F     0.946     0    0.611   0.806     5.005   63.810   65.714
LGA    A    27_F      A    27_F     3.134     0    0.092   0.161     4.050   59.286   54.857
LGA    V    28_F      V    28_F     5.207     0    0.089   0.111     8.864   27.976   17.823
LGA    I    29_F      I    29_F     3.004     0    0.162   0.694     4.997   42.143   59.702
LGA    M    30_F      M    30_F     6.495     0    0.637   0.765    12.195   20.476   10.595
LGA    S    31_F      S    31_F     2.309     0    0.110   0.716     5.504   59.167   50.238
LGA    N    32_F      N    32_F     4.023     0    0.458   1.076     5.940   38.690   36.012
LGA    K    33_F      K    33_F     6.523     0    0.061   0.813    11.743   12.262    7.937
LGA    K    34_F      K    34_F    11.083     0    0.279   1.272    12.324    0.119    0.053
LGA    V    35_F      V    35_F    14.682     0    0.585   0.884    18.583    0.000    0.000
LGA    N    36_F      N    36_F    19.804     0    0.634   0.539    22.509    0.000    0.000
LGA    G    37_F      G    37_F    21.887     0    0.604   0.604    22.708    0.000    0.000
LGA    G    38_F      G    38_F    20.382     0    0.202   0.202    20.725    0.000    0.000
LGA    I    39_F      I    39_F    14.039     0    0.038   0.183    16.825    0.000    0.000
LGA    E    40_F      E    40_F    12.293     0    0.167   1.104    17.415    1.190    0.529
LGA    I    41_F      I    41_F     9.100     0    0.158   1.144    12.359    0.357    1.845
LGA    V    42_F      V    42_F    11.445     0    0.629   0.630    11.975    0.119    0.068
LGA    A    43_F      A    43_F    11.236     0    0.054   0.073    11.539    0.000    0.000
LGA    A    44_F      A    44_F    12.407     0    0.031   0.043    13.042    0.000    0.000
LGA    V    45_F      V    45_F    12.927     0    0.041   0.981    13.850    0.000    0.000
LGA    L    46_F      L    46_F    14.716     0    0.599   1.378    18.688    0.000    0.000
LGA    E    47_F      E    47_F    14.794     0    0.620   0.642    17.927    0.000    0.000
LGA    H    48_F      H    48_F    19.445     0    0.079   0.218    25.884    0.000    0.000
LGA    H    49_F      H    49_F    18.780     0    0.447   1.207    24.642    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):    12.108         11.997                 12.653           31.161   27.850

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53   49    4.0     21    2.33    42.857    36.919     0.863

LGA_LOCAL      RMSD:   2.334  Number of atoms:   21  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  14.554  Number of assigned atoms:   49 
Std_ASGN_ATOMS RMSD:  12.108  Standard rmsd on all 49 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.735493 * X  +   0.582075 * Y  +  -0.346756 * Z  +  59.708420
  Y_new =  -0.078543 * X  +  -0.581591 * Y  +  -0.809681 * Z  + -23.665150
  Z_new =  -0.672965 * X  +  -0.568279 * Y  +   0.473474 * Z  +  16.368839 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -3.035207  0.738210 -0.876154   [DEG: -173.9045   42.2963  -50.1999 ]
ZXZ: -0.404631  1.077566 -2.272054   [DEG:  -23.1837   61.7400 -130.1791 ]
 
# END of job
