
#######################################################
#                                                     #
#                        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   62 (  507),  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        2.19     2.19
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    41       5_B - 45_B        1.85     2.24
  LCS_AVERAGE:     91.89

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        0.74     3.68
  LCS_AVERAGE:     52.73

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     28   41   43      5   17   26   28   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     28   41   43     17   25   27   28   34   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     28   41   43     17   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     28   41   43     16   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     28   41   43     12   25   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     28   41   43      7   22   27   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     27   41   43      7   10   22   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     14   41   43      7   10   18   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     14   41   43      7   10   18   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     14   41   43      7   10   22   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     14   41   43      7   10   18   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     14   41   43      7   10   16   27   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     14   41   43      7   10   18   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     14   41   43      6   10   21   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     14   41   43      4   10   22   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     14   41   43      4   10   22   29   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     12   41   43      4    8   15   27   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B     12   41   43      4    8   12   22   35   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      8   41   43      4    8   11   19   32   39   41   41   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   15   43      3    3    3    3    5    5   10   31   42   43   43   43   43   43   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4   34   41   43   43   43   43   43   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  81.54  (  52.73   91.89  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     25     27     29     35     39     41     41     42     43     43     43     43     43     43     43     43     43     43     43 
GDT PERCENT_AT  39.53  58.14  62.79  67.44  81.40  90.70  95.35  95.35  97.67 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.33   0.53   0.66   1.24   1.53   1.71   1.85   1.85   2.06   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19
GDT RMS_ALL_AT   4.16   4.08   3.64   2.37   2.32   2.38   2.24   2.24   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19   2.19

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.677     0    0.616   0.696     6.809   71.310   55.000
LGA    L     6_B      L     6_B     1.923     0    0.061   0.854     2.490   75.119   70.952
LGA    E     7_B      E     7_B     0.932     0    0.069   0.940     5.151   92.976   70.635
LGA    T     8_B      T     8_B     0.602     0    0.049   1.162     2.322   92.857   83.197
LGA    K     9_B      K     9_B     0.950     0    0.018   0.108     2.765   90.476   77.249
LGA    K    10_B      K    10_B     0.567     0    0.049   0.864     3.766   95.238   81.429
LGA    A    11_B      A    11_B     0.923     0    0.030   0.044     1.348   85.952   85.048
LGA    Y    12_B      Y    12_B     1.333     0    0.019   0.050     3.238   81.548   69.206
LGA    A    13_B      A    13_B     0.780     0    0.019   0.027     1.005   88.214   88.667
LGA    A    14_B      A    14_B     1.277     0    0.088   0.101     2.065   77.381   76.476
LGA    R    15_B      R    15_B     2.239     0    0.030   0.897     4.005   64.881   58.182
LGA    T    16_B      T    16_B     2.373     0    0.062   0.069     3.128   68.810   63.878
LGA    R    17_B      R    17_B     0.856     0    0.061   0.795     2.009   83.690   80.823
LGA    R    18_B      R    18_B     2.421     0    0.031   0.957     8.062   62.976   42.944
LGA    S    19_B      S    19_B     3.059     0    0.040   0.731     3.536   55.357   54.921
LGA    N    20_B      N    20_B     1.940     0    0.077   0.452     2.265   75.119   72.976
LGA    Y    21_B      Y    21_B     0.800     0    0.060   0.201     3.918   83.690   68.929
LGA    A    22_B      A    22_B     2.063     0    0.045   0.043     2.541   66.786   64.857
LGA    A    23_B      A    23_B     2.180     0    0.059   0.065     2.437   68.810   68.000
LGA    S    24_B      S    24_B     1.239     0    0.081   0.719     1.598   83.810   83.016
LGA    L    25_B      L    25_B     0.939     0    0.020   0.076     1.527   88.214   83.750
LGA    R    26_B      R    26_B     1.464     0    0.016   1.029     3.991   81.429   69.957
LGA    L    27_B      L    27_B     1.306     0    0.071   0.198     2.769   81.429   76.250
LGA    E    28_B      E    28_B     0.435     0    0.041   0.576     2.208   95.238   89.788
LGA    G    29_B      G    29_B     0.748     0    0.045   0.045     0.949   90.476   90.476
LGA    F    30_B      F    30_B     1.064     0    0.060   0.120     1.594   83.690   84.762
LGA    K    31_B      K    31_B     1.715     0    0.101   0.633     5.702   75.000   56.931
LGA    V    32_B      V    32_B     1.341     0    0.069   0.265     2.780   79.286   74.354
LGA    T    33_B      T    33_B     1.555     0    0.078   1.069     4.029   77.262   69.116
LGA    F    34_B      F    34_B     2.406     0    0.018   1.393     4.522   64.762   57.749
LGA    A    35_B      A    35_B     2.512     0    0.026   0.032     2.548   62.857   61.714
LGA    D    36_B      D    36_B     1.458     0    0.009   0.219     1.813   75.000   81.726
LGA    G    37_B      G    37_B     2.037     0    0.013   0.013     2.658   64.881   64.881
LGA    E    38_B      E    38_B     3.059     0    0.020   0.137     4.890   51.786   44.392
LGA    R    39_B      R    39_B     2.723     0    0.116   1.123     5.512   60.952   51.342
LGA    K    40_B      K    40_B     1.918     0    0.068   1.227     5.731   68.810   61.376
LGA    M    41_B      M    41_B     1.362     0    0.048   0.281     3.043   81.429   71.310
LGA    P    42_B      P    42_B     1.265     0    0.055   0.061     1.732   79.286   77.755
LGA    T    43_B      T    43_B     1.828     0    0.007   0.049     2.036   72.976   72.925
LGA    R    44_B      R    44_B     2.716     0    0.606   0.958     6.850   67.024   44.199
LGA    E    45_B      E    45_B     3.767     0    0.483   1.091     8.615   41.786   27.249
LGA    E    46_B      E    46_B     6.573     0    0.595   1.402    12.063   21.786   10.000
LGA    V    47_B      V    47_B     5.716     0    0.405   1.358     8.585   23.929   17.415

# 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):     2.186          2.066                  2.931           73.355   66.414

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     41    1.85    80.233    87.191     2.100

LGA_LOCAL      RMSD:   1.852  Number of atoms:   41  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.244  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   2.186  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.580793 * X  +  -0.692441 * Y  +   0.428025 * Z  +  25.457708
  Y_new =  -0.772718 * X  +  -0.303529 * Y  +   0.557475 * Z  + -32.315609
  Z_new =  -0.256100 * X  +  -0.654520 * Y  +  -0.711348 * Z  +  20.986399 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.926257  0.258986 -2.397777   [DEG:  -53.0706   14.8388 -137.3825 ]
ZXZ:  2.486801  2.362211 -2.768626   [DEG:  142.4832  135.3447 -158.6306 ]
 
# END of job
