
#######################################################
#                                                     #
#                        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        4.81     4.81
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       9_B - 37_B        1.97     5.70
  LCS_AVERAGE:     55.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      13_B - 32_B        0.95     4.92
  LCS_AVERAGE:     30.94

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      3   28   43      0    3    3    3    3   23   24   29   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     L     6_B     L     6_B     10   28   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     E     7_B     E     7_B     10   28   43      5    9   16   21   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     T     8_B     T     8_B     12   28   43      5    9   13   17   25   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     K     9_B     K     9_B     12   29   43      5   10   16   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     K    10_B     K    10_B     14   29   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     A    11_B     A    11_B     15   29   43      5   10   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     Y    12_B     Y    12_B     19   29   43      4   10   17   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     A    13_B     A    13_B     20   29   43      4   10   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     A    14_B     A    14_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     R    15_B     R    15_B     20   29   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     T    16_B     T    16_B     20   29   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     R    17_B     R    17_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     R    18_B     R    18_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     S    19_B     S    19_B     20   29   43     10   16   20   23   25   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     N    20_B     N    20_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     Y    21_B     Y    21_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     A    22_B     A    22_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     A    23_B     A    23_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     S    24_B     S    24_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     L    25_B     L    25_B     20   29   43     10   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     R    26_B     R    26_B     20   29   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     L    27_B     L    27_B     20   29   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     E    28_B     E    28_B     20   29   43      9   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     G    29_B     G    29_B     20   29   43      4   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     F    30_B     F    30_B     20   29   43      7   17   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     K    31_B     K    31_B     20   29   43      4   16   20   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     V    32_B     V    32_B     20   29   43      4   10   18   23   26   28   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     T    33_B     T    33_B      7   29   43      4    5    8   11   20   25   29   31   32   32   33   34   37   39   39   39   42   42   42   42 
LCS_GDT     F    34_B     F    34_B      7   29   43      4    5    7   11   15   24   29   30   32   32   33   34   36   39   39   39   42   42   42   42 
LCS_GDT     A    35_B     A    35_B      7   29   43      4    5    8   18   24   27   30   31   32   32   33   34   37   39   39   39   42   42   42   42 
LCS_GDT     D    36_B     D    36_B      7   29   43      4    9   17   23   26   28   30   31   32   32   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     G    37_B     G    37_B      4   29   43      3    4    4    5    6   23   30   31   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     E    38_B     E    38_B      4    6   43      3    4    4    5    6    8   13   22   29   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     R    39_B     R    39_B      5    7   43      3    4    5    5    7   19   27   29   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     K    40_B     K    40_B      5    7   43      3    4    5    5    7   19   25   29   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     M    41_B     M    41_B      5    7   43      3    4    5    7   13   19   27   29   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     P    42_B     P    42_B      5    7   43      3    4    5    5   14   19   25   29   32   33   35   35   37   39   39   39   42   42   42   42 
LCS_GDT     T    43_B     T    43_B      5    7   43      3    4    5    5    7    7   13   14   22   26   31   35   36   39   39   39   42   42   42   42 
LCS_GDT     R    44_B     R    44_B      5    7   43      3    4    5    5    7    7    8   11   16   22   25   27   30   33   37   39   42   42   42   42 
LCS_GDT     E    45_B     E    45_B      5    7   43      3    4    5    5    7    7    8    8   13   19   24   27   29   33   35   39   42   42   42   42 
LCS_GDT     E    46_B     E    46_B      3    6   43      3    3    3    3    4    5    7    8    8   10   14   17   25   32   37   38   42   42   42   42 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    3    3    4    6    6    6    8    8    9    9   10   23   25   28   31   32 
LCS_AVERAGE  LCS_A:  61.98  (  30.94   55.00  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     10     17     20     23     26     28     30     31     32     33     35     35     37     39     39     39     42     42     42     42 
GDT PERCENT_AT  23.26  39.53  46.51  53.49  60.47  65.12  69.77  72.09  74.42  76.74  81.40  81.40  86.05  90.70  90.70  90.70  97.67  97.67  97.67  97.67
GDT RMS_LOCAL    0.33   0.59   0.73   1.10   1.43   1.57   1.83   1.97   2.11   2.49   2.76   2.76   3.20   3.55   3.55   3.55   4.32   4.32   4.32   4.32
GDT RMS_ALL_AT   5.15   4.89   4.87   4.89   5.16   5.13   5.40   5.56   5.69   5.07   4.99   4.99   4.94   4.93   4.93   4.93   4.82   4.82   4.82   4.82

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_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

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     6.535     0    0.144   0.695     7.911   18.333   20.952
LGA    L     6_B      L     6_B     0.959     0    0.596   1.132     6.024   79.881   60.238
LGA    E     7_B      E     7_B     2.836     0    0.066   1.119     5.414   60.952   45.926
LGA    T     8_B      T     8_B     3.127     0    0.065   1.192     6.105   57.262   48.503
LGA    K     9_B      K     9_B     1.948     0    0.060   0.998     2.866   75.000   67.672
LGA    K    10_B      K    10_B     0.697     0    0.048   1.125     4.366   90.476   72.593
LGA    A    11_B      A    11_B     0.899     0    0.050   0.053     1.428   90.476   88.667
LGA    Y    12_B      Y    12_B     1.518     0    0.043   1.502    12.517   77.143   37.778
LGA    A    13_B      A    13_B     1.697     0    0.057   0.068     1.986   75.000   74.571
LGA    A    14_B      A    14_B     1.625     0    0.063   0.061     2.212   70.833   71.238
LGA    R    15_B      R    15_B     2.074     0    0.091   1.425     5.016   66.786   61.558
LGA    T    16_B      T    16_B     2.395     0    0.085   1.083     4.006   64.762   59.728
LGA    R    17_B      R    17_B     1.351     0    0.037   1.036     4.420   75.000   71.255
LGA    R    18_B      R    18_B     2.483     0    0.033   0.969     7.307   60.952   36.580
LGA    S    19_B      S    19_B     3.190     0    0.042   0.553     4.814   55.357   49.365
LGA    N    20_B      N    20_B     1.875     0    0.044   0.349     2.796   75.119   70.000
LGA    Y    21_B      Y    21_B     0.381     0    0.047   1.065     7.060   92.857   60.040
LGA    A    22_B      A    22_B     1.817     0    0.032   0.040     2.668   75.000   71.429
LGA    A    23_B      A    23_B     1.921     0    0.039   0.044     2.565   77.143   73.143
LGA    S    24_B      S    24_B     1.024     0    0.037   0.046     1.659   85.952   83.016
LGA    L    25_B      L    25_B     0.489     0    0.038   1.032     3.663  100.000   84.881
LGA    R    26_B      R    26_B     0.908     0    0.066   1.177     3.883   90.476   73.074
LGA    L    27_B      L    27_B     1.215     0    0.084   0.069     2.630   83.690   74.286
LGA    E    28_B      E    28_B     1.057     0    0.157   0.960     5.894   88.214   66.349
LGA    G    29_B      G    29_B     0.625     0    0.088   0.088     0.655   90.476   90.476
LGA    F    30_B      F    30_B     0.399     0    0.062   0.469     2.317   95.238   86.667
LGA    K    31_B      K    31_B     1.104     0    0.295   0.938     7.668   81.548   56.508
LGA    V    32_B      V    32_B     1.270     0    0.050   1.269     4.115   69.405   68.299
LGA    T    33_B      T    33_B     4.240     0    0.076   1.076     7.149   46.905   35.714
LGA    F    34_B      F    34_B     4.843     0    0.091   1.501    12.260   39.048   16.797
LGA    A    35_B      A    35_B     3.198     0    0.058   0.057     4.046   59.881   55.333
LGA    D    36_B      D    36_B     1.433     0    0.337   0.288     4.779   77.381   60.774
LGA    G    37_B      G    37_B     3.387     0    0.088   0.088     5.476   43.095   43.095
LGA    E    38_B      E    38_B     6.332     0    0.714   0.874    10.214   20.714   13.069
LGA    R    39_B      R    39_B     8.985     0    0.052   0.791    16.279    4.405    1.602
LGA    K    40_B      K    40_B     9.687     0    0.382   1.415    18.548    1.310    0.582
LGA    M    41_B      M    41_B     8.376     0    0.059   0.497     9.400    2.976    4.524
LGA    P    42_B      P    42_B     9.159     0    0.463   0.652     9.638    1.548    2.993
LGA    T    43_B      T    43_B     9.873     0    0.083   0.067    10.717    0.238    0.476
LGA    R    44_B      R    44_B    11.446     0    0.576   1.454    13.871    0.000    0.043
LGA    E    45_B      E    45_B    11.109     0    0.447   1.172    11.247    0.000    0.582
LGA    E    46_B      E    46_B    12.228     0    0.583   1.246    16.585    0.000    0.000
LGA    V    47_B      V    47_B    16.491     0    0.460   1.322    18.062    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):     4.807          4.757                  5.854           56.298   47.916

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     31    1.97    63.953    64.046     1.497

LGA_LOCAL      RMSD:   1.970  Number of atoms:   31  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   5.558  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.807  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.859731 * X  +   0.181293 * Y  +   0.477489 * Z  +  12.553942
  Y_new =  -0.298510 * X  +  -0.936944 * Y  +  -0.181735 * Z  + -62.423756
  Z_new =   0.414434 * X  +  -0.298778 * Y  +   0.859637 * Z  +   4.633110 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.807403 -0.427320 -0.334502   [DEG: -160.8523  -24.4837  -19.1656 ]
ZXZ:  1.207120  0.536237  2.195433   [DEG:   69.1629   30.7241  125.7890 ]
 
# END of job
