
#######################################################
#                                                     #
#                        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   56 (  447),  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        3.76     3.76
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    37       5_B - 41_B        1.94     4.54
  LCS_AVERAGE:     80.80

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25       8_B - 32_B        0.99     5.07
  LCS_AVERAGE:     45.70

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     22   37   43     13   16   21   26   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     L     6_B     L     6_B     22   37   43     13   16   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     E     7_B     E     7_B     23   37   43     13   16   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     T     8_B     T     8_B     25   37   43     13   16   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     K     9_B     K     9_B     25   37   43     13   16   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     K    10_B     K    10_B     25   37   43     13   17   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     A    11_B     A    11_B     25   37   43     13   17   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     25   37   43     13   17   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     A    13_B     A    13_B     25   37   43     13   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     A    14_B     A    14_B     25   37   43     13   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     R    15_B     R    15_B     25   37   43     13   16   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     T    16_B     T    16_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     R    17_B     R    17_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     R    18_B     R    18_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     S    19_B     S    19_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     N    20_B     N    20_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     A    22_B     A    22_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     A    23_B     A    23_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     S    24_B     S    24_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     L    25_B     L    25_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     R    26_B     R    26_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     L    27_B     L    27_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     E    28_B     E    28_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     G    29_B     G    29_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     F    30_B     F    30_B     25   37   43     15   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     K    31_B     K    31_B     25   37   43     14   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     V    32_B     V    32_B     25   37   43     10   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     T    33_B     T    33_B     22   37   43      5   11   20   27   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     F    34_B     F    34_B     15   37   43      6   11   18   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     A    35_B     A    35_B     12   37   43      6   11   21   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     D    36_B     D    36_B     12   37   43      6   14   21   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     G    37_B     G    37_B     12   37   43      6   18   24   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     E    38_B     E    38_B     12   37   43      6   16   22   28   33   34   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     R    39_B     R    39_B     12   37   43      6   10   21   27   29   33   35   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     K    40_B     K    40_B     12   37   43      4    9   21   26   27   31   34   35   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     M    41_B     M    41_B     10   37   43      4    9   21   26   29   33   34   36   37   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     P    42_B     P    42_B      7   35   43      4    6   13   24   26   31   32   35   36   38   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     T    43_B     T    43_B      7   33   43      4    6   12   20   25   27   32   35   36   37   39   40   40   40   41   41   42   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   31   43      4    6   11   17   23   26   29   33   35   37   38   40   40   40   41   41   42   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   14   43      3    5    7   13   17   23   27   29   31   33   35   37   38   40   41   41   42   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    4    9   10   12   13   22   28   32   36   37   40   40   41   42   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4    7   29   32   34   36   37   40   40   41   42   43   43   43 
LCS_AVERAGE  LCS_A:  75.50  (  45.70   80.80  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     15     18     24     28     33     34     35     36     37     38     39     40     40     40     41     41     42     43     43     43 
GDT PERCENT_AT  34.88  41.86  55.81  65.12  76.74  79.07  81.40  83.72  86.05  88.37  90.70  93.02  93.02  93.02  95.35  95.35  97.67 100.00 100.00 100.00
GDT RMS_LOCAL    0.30   0.43   0.89   1.15   1.52   1.57   1.67   1.79   1.94   2.16   2.44   2.69   2.69   2.69   3.11   3.11   3.48   3.76   3.76   3.76
GDT RMS_ALL_AT   5.02   4.67   4.95   5.21   4.80   4.77   4.73   4.63   4.54   4.39   4.20   4.05   4.05   4.05   3.88   3.88   3.79   3.76   3.76   3.76

# Checking swapping
#   possible swapping detected:  E     7_B      E     7_B
#   possible swapping detected:  E    38_B      E    38_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.649     0    0.027   0.177     3.624   59.048   54.921
LGA    L     6_B      L     6_B     2.869     0    0.036   0.878     3.366   59.048   57.202
LGA    E     7_B      E     7_B     2.533     0    0.036   1.104     7.224   65.000   48.307
LGA    T     8_B      T     8_B     1.146     0    0.064   1.226     3.280   83.810   77.211
LGA    K     9_B      K     9_B     1.108     0    0.018   0.811     5.094   85.952   64.603
LGA    K    10_B      K    10_B     1.259     0    0.015   0.953     5.353   81.429   66.296
LGA    A    11_B      A    11_B     1.445     0    0.022   0.023     1.732   81.429   79.714
LGA    Y    12_B      Y    12_B     0.756     0    0.039   0.091     3.163   88.214   75.595
LGA    A    13_B      A    13_B     0.516     0    0.011   0.015     1.020   90.595   92.476
LGA    A    14_B      A    14_B     1.350     0    0.057   0.063     2.295   77.381   76.476
LGA    R    15_B      R    15_B     2.220     0    0.047   1.243     5.133   64.881   62.035
LGA    T    16_B      T    16_B     2.403     0    0.099   0.112     2.923   64.762   62.585
LGA    R    17_B      R    17_B     1.050     0    0.052   1.059     5.917   81.548   61.818
LGA    R    18_B      R    18_B     1.656     0    0.012   0.869     5.905   75.000   56.277
LGA    S    19_B      S    19_B     2.391     0    0.040   0.704     3.044   66.786   63.651
LGA    N    20_B      N    20_B     1.808     0    0.032   0.351     2.321   77.143   73.988
LGA    Y    21_B      Y    21_B     0.412     0    0.088   0.189     5.110   95.238   67.381
LGA    A    22_B      A    22_B     1.066     0    0.006   0.014     1.614   88.214   85.143
LGA    A    23_B      A    23_B     1.343     0    0.021   0.022     1.785   81.429   79.714
LGA    S    24_B      S    24_B     1.208     0    0.067   0.723     1.340   81.429   82.937
LGA    L    25_B      L    25_B     0.705     0    0.026   0.060     0.975   90.476   90.476
LGA    R    26_B      R    26_B     0.610     0    0.045   1.031     4.813   90.476   70.087
LGA    L    27_B      L    27_B     1.074     0    0.026   0.208     1.903   83.690   81.488
LGA    E    28_B      E    28_B     1.163     0    0.030   1.099     5.319   81.429   69.101
LGA    G    29_B      G    29_B     0.973     0    0.084   0.084     0.973   90.476   90.476
LGA    F    30_B      F    30_B     1.083     0    0.032   0.059     1.673   88.214   82.338
LGA    K    31_B      K    31_B     1.167     0    0.065   0.620     3.911   81.429   69.259
LGA    V    32_B      V    32_B     0.658     0    0.050   0.221     2.254   83.810   81.701
LGA    T    33_B      T    33_B     2.220     0    0.057   1.103     5.282   75.119   61.973
LGA    F    34_B      F    34_B     1.919     0    0.013   1.109     8.411   77.381   42.121
LGA    A    35_B      A    35_B     2.029     0    0.034   0.036     2.917   68.810   66.476
LGA    D    36_B      D    36_B     1.915     0    0.114   0.126     3.041   68.929   67.024
LGA    G    37_B      G    37_B     1.716     0    0.098   0.098     2.360   72.976   72.976
LGA    E    38_B      E    38_B     1.433     0    0.055   0.857     4.315   71.190   66.032
LGA    R    39_B      R    39_B     3.292     0    0.144   1.352     6.038   48.452   37.965
LGA    K    40_B      K    40_B     4.976     0    0.632   1.304    11.351   24.286   15.079
LGA    M    41_B      M    41_B     4.212     0    0.010   0.259     5.469   33.214   39.940
LGA    P    42_B      P    42_B     6.661     0    0.041   0.059     7.133   14.524   14.694
LGA    T    43_B      T    43_B     8.415     0    0.076   1.119    11.044    4.048    2.721
LGA    R    44_B      R    44_B     9.305     0    0.599   0.920     9.926    2.381    1.645
LGA    E    45_B      E    45_B    13.083     0    0.441   1.123    18.060    0.000    0.000
LGA    E    46_B      E    46_B    14.342     0    0.613   1.427    16.603    0.000    0.000
LGA    V    47_B      V    47_B    14.207     0    0.470   1.381    15.686    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):     3.758          3.700                  4.490           65.108   58.416

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     36    1.79    71.512    77.728     1.900

LGA_LOCAL      RMSD:   1.794  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.628  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.758  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.396371 * X  +  -0.764298 * Y  +   0.508663 * Z  +  18.985004
  Y_new =   0.701079 * X  +  -0.105746 * Y  +  -0.705199 * Z  + -58.077858
  Z_new =   0.592771 * X  +   0.636134 * Y  +   0.493919 * Z  +  10.923285 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.056227 -0.634495  0.910588   [DEG:   60.5174  -36.3539   52.1729 ]
ZXZ:  0.624882  1.054205  0.750127   [DEG:   35.8031   60.4015   42.9791 ]
 
# END of job
