
#######################################################
#                                                     #
#                        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   42 (  348),  selected   41 , name one
# Molecule2: number of CA atoms   41 (  336),  selected   41 , 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:    35       2_B - 36_B        4.75     9.31
  LONGEST_CONTINUOUS_SEGMENT:    35       3_B - 37_B        4.96     9.04
  LCS_AVERAGE:     81.20

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    23       7_B - 29_B        1.97    11.06
  LCS_AVERAGE:     48.96

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17       8_B - 24_B        0.79    10.68
  LCS_AVERAGE:     33.49

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   41
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     A     2_B     A     2_B      5    5   35      4    4    5    5    5    8   10   11   13   14   15   20   28   30   31   33   33   34   35   35 
LCS_GDT     S     3_B     S     3_B      5    5   35      4    4    5    5    7   11   21   21   22   24   25   28   30   31   32   34   34   34   35   36 
LCS_GDT     Q     4_B     Q     4_B      5   21   35      4    4    5    5    5   19   21   21   23   26   27   28   30   31   32   34   34   34   35   36 
LCS_GDT     R     5_B     R     5_B     11   21   35      5    8   13   15   20   20   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     L     6_B     L     6_B     11   21   35      5    9   13   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     F     7_B     F     7_B     11   23   35      5    9   13   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     V     8_B     V     8_B     17   23   35      5   13   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     L     9_B     L     9_B     17   23   35      7   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     D    10_B     D    10_B     17   23   35      4   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     N    11_B     N    11_B     17   23   35      5   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     E    12_B     E    12_B     17   23   35      4   14   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     R    13_B     R    13_B     17   23   35      5   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     Y    14_B     Y    14_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     D    15_B     D    15_B     17   23   35      5   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     S    16_B     S    16_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     F    17_B     F    17_B     17   23   35      7   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     I    18_B     I    18_B     17   23   35      7   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     T    19_B     T    19_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     Q    20_B     Q    20_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     L    21_B     L    21_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     E    22_B     E    22_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     A    23_B     A    23_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     P    24_B     P    24_B     17   23   35      8   16   18   19   20   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     V    25_B     V    25_B     15   23   35      3    4   10   17   19   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     Q    26_B     Q    26_B     14   23   35      3   12   13   16   18   20   21   21   23   26   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     N    27_B     N    27_B     14   23   35      4    7   15   18   19   20   21   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     A    28_B     A    28_B     14   23   35      4   16   18   18   19   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     E    29_B     E    29_B     14   23   35      9   12   13   14   19   22   22   23   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     G    30_B     G    30_B     14   17   35      9   12   13   14   15   16   16   17   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     R    31_B     R    31_B     14   17   35      9   12   13   14   15   16   16   17   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     E    32_B     E    32_B     14   17   35      9   12   13   14   15   16   16   22   26   27   28   28   30   32   32   34   34   34   35   36 
LCS_GDT     R    33_B     R    33_B     14   17   35      9   12   13   14   15   16   16   17   17   17   24   28   30   32   32   34   34   34   35   36 
LCS_GDT     L    34_B     L    34_B     14   17   35      9   12   13   14   15   16   16   17   17   17   18   18   26   32   32   34   34   34   35   36 
LCS_GDT     M    35_B     M    35_B     14   17   35      9   12   13   14   15   16   16   17   17   17   23   28   30   32   32   34   34   34   35   36 
LCS_GDT     A    36_B     A    36_B     14   17   35      9   12   13   14   15   16   16   17   17   17   18   20   29   32   32   34   34   34   35   36 
LCS_GDT     V    37_B     V    37_B     14   17   35      9   12   13   14   15   16   16   17   17   17   18   18   18   21   22   30   33   34   35   36 
LCS_GDT     K    38_B     K    38_B     14   17   21      9   12   13   14   15   16   16   17   17   17   18   18   18   19   22   25   30   34   34   36 
LCS_GDT     P    39_B     P    39_B     14   17   21      4   12   13   14   15   16   16   17   17   17   18   18   18   19   22   23   24   28   34   35 
LCS_GDT     E    40_B     E    40_B      5   17   21      3    5    5   13   15   16   16   17   17   17   18   18   18   18   19   19   19   20   21   22 
LCS_GDT     W    41_B     W    41_B      5   17   21      3    5    5    6   12   16   16   17   17   17   18   18   18   18   19   19   19   20   21   22 
LCS_GDT     K    42_B     K    42_B      5   17   21      3    5    5    5    7   11   15   17   17   17   18   18   18   18   19   19   19   20   20   20 
LCS_AVERAGE  LCS_A:  54.55  (  33.49   48.96   81.20 )

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      9     16     18     19     20     22     22     23     26     27     28     28     30     32     32     34     34     34     35     36 
GDT PERCENT_AT  21.95  39.02  43.90  46.34  48.78  53.66  53.66  56.10  63.41  65.85  68.29  68.29  73.17  78.05  78.05  82.93  82.93  82.93  85.37  87.80
GDT RMS_LOCAL    0.24   0.65   0.83   1.18   1.35   1.70   1.70   1.94   2.71   2.82   2.95   2.95   3.57   4.27   4.05   4.57   4.57   4.49   4.75   5.41
GDT RMS_ALL_AT  19.09  11.39  10.93   9.99   9.89  10.26  10.26  10.46   9.86   9.97  10.06  10.06   9.67   9.38   9.43   9.19   9.19   9.46   9.31   8.87

# Checking swapping
#   possible swapping detected:  F     7_B      F     7_B
#   possible swapping detected:  Y    14_B      Y    14_B
#   possible swapping detected:  F    17_B      F    17_B
#   possible swapping detected:  E    22_B      E    22_B
#   possible swapping detected:  E    29_B      E    29_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     2_B      A     2_B    14.447     0    0.654   0.644    17.138    0.000    0.000
LGA    S     3_B      S     3_B    11.953     0    0.180   0.701    12.625    1.190    0.794
LGA    Q     4_B      Q     4_B     9.921     0    0.128   1.307    14.361    0.833    0.370
LGA    R     5_B      R     5_B     5.654     0    0.656   1.142     7.446   25.357   26.537
LGA    L     6_B      L     6_B     3.943     0    0.132   1.375     5.890   43.690   40.952
LGA    F     7_B      F     7_B     3.068     0    0.137   0.188     5.161   55.476   43.030
LGA    V     8_B      V     8_B     1.159     0    0.049   1.183     4.363   86.190   74.218
LGA    L     9_B      L     9_B     0.794     0    0.667   0.590     3.801   78.810   80.179
LGA    D    10_B      D    10_B     0.525     0    0.024   0.811     3.432   95.238   79.524
LGA    N    11_B      N    11_B     0.649     0    0.027   0.961     2.717   92.857   84.167
LGA    E    12_B      E    12_B     1.146     0    0.193   1.031     4.016   81.548   68.836
LGA    R    13_B      R    13_B     0.624     0    0.036   1.184     4.849   90.476   73.636
LGA    Y    14_B      Y    14_B     0.802     0    0.078   1.356     6.651   79.643   62.183
LGA    D    15_B      D    15_B     1.179     0    0.156   0.874     4.079   79.524   66.786
LGA    S    16_B      S    16_B     1.015     0    0.285   0.725     2.122   83.810   81.746
LGA    F    17_B      F    17_B     1.484     0    0.052   0.229     2.749   81.429   68.745
LGA    I    18_B      I    18_B     1.754     0    0.025   0.725     2.430   77.143   71.964
LGA    T    19_B      T    19_B     1.123     0    0.016   0.239     1.367   81.429   81.429
LGA    Q    20_B      Q    20_B     0.839     0    0.012   1.138     4.610   90.476   76.508
LGA    L    21_B      L    21_B     1.340     0    0.024   1.331     4.067   81.429   71.667
LGA    E    22_B      E    22_B     1.154     0    0.124   0.770     3.380   79.286   66.508
LGA    A    23_B      A    23_B     1.107     0    0.073   0.106     1.107   85.952   85.048
LGA    P    24_B      P    24_B     1.209     0    0.675   0.604     3.004   73.571   74.490
LGA    V    25_B      V    25_B     3.024     0    0.021   1.252     5.732   59.405   48.639
LGA    Q    26_B      Q    26_B     5.316     0    0.692   0.705     8.729   22.976   14.603
LGA    N    27_B      N    27_B     4.424     0    0.390   0.370     6.780   41.905   31.250
LGA    A    28_B      A    28_B     0.636     0    0.058   0.061     3.139   71.548   73.524
LGA    E    29_B      E    29_B     3.408     0    0.594   1.058     7.031   41.071   37.831
LGA    G    30_B      G    30_B     6.212     0    0.195   0.195     7.720   18.690   18.690
LGA    R    31_B      R    31_B     6.050     0    0.065   1.398     8.846   16.429   20.130
LGA    E    32_B      E    32_B     6.500     0    0.016   0.808     9.036   11.190   24.709
LGA    R    33_B      R    33_B     9.646     0    0.071   0.606    11.784    1.310    3.247
LGA    L    34_B      L    34_B    10.985     0    0.011   1.407    13.978    0.000    0.000
LGA    M    35_B      M    35_B     9.928     0    0.048   1.320    11.573    0.238    4.940
LGA    A    36_B      A    36_B    12.110     0    0.045   0.047    14.535    0.000    0.000
LGA    V    37_B      V    37_B    15.157     0    0.012   0.080    16.839    0.000    0.000
LGA    K    38_B      K    38_B    17.314     4    0.596   0.603    20.512    0.000    0.000
LGA    P    39_B      P    39_B    19.598     0    0.076   0.357    23.000    0.000    0.000
LGA    E    40_B      E    40_B    25.966     0    0.078   0.300    30.928    0.000    0.000
LGA    W    41_B      W    41_B    26.260     0    0.066   1.253    30.324    0.000    0.000
LGA    K    42_B      K    42_B    32.167     0    0.604   1.338    39.314    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       41     164    164  100.00     336    336  100.00                41
SUMMARY(RMSD_GDC):     8.500          8.619                  9.416           44.637   40.412

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   42   41    4.0     23    1.94    56.098    55.062     1.130

LGA_LOCAL      RMSD:   1.936  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.459  Number of assigned atoms:   41 
Std_ASGN_ATOMS RMSD:   8.500  Standard rmsd on all 41 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.257744 * X  +   0.950278 * Y  +  -0.174758 * Z  +   4.831239
  Y_new =  -0.074750 * X  +   0.199939 * Y  +   0.976953 * Z  + -22.587582
  Z_new =   0.963317 * X  +  -0.238741 * Y  +   0.122566 * Z  +  44.153969 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.282273 -1.299101 -1.096497   [DEG:  -16.1730  -74.4330  -62.8246 ]
ZXZ: -2.964584  1.447921  1.813733   [DEG: -169.8581   82.9598  103.9193 ]
 
# END of job
