
#######################################################
#                                                     #
#                        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        3.82     3.82
  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     4.63
  LCS_AVERAGE:     80.53

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    28       5_B - 32_B        1.00     5.53
  LCS_AVERAGE:     50.57

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   37   43     15   19   25   29   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     28   37   43     15   19   26   29   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     28   37   43     15   19   26   29   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     28   37   43     15   19   25   29   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     28   37   43     15   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     28   37   43     13   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     28   37   43      9   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     28   37   43      9   19   26   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     20   37   43      4   10   20   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     12   37   43      5   10   18   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     12   37   43      5   10   22   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     12   37   43      5   14   22   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     12   37   43      5   10   22   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     12   37   43      5   16   22   30   34   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     12   37   43      6   11   22   26   32   35   35   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     12   37   43      6    9   20   26   28   32   34   36   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      9   37   43      6    7   12   24   27   31   34   35   37   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      8   34   43      6    7   11   21   25   28   31   35   36   38   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      8   31   43      6    7   11   16   23   26   30   33   36   37   39   40   40   40   41   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   30   43      6    7   11   16   20   26   28   33   34   37   38   40   40   40   41   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      8   13   43      3    6    7   12   18   22   24   28   31   32   35   36   40   40   41   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    5    5    5    8   10   14   24   27   30   36   40   40   40   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      0    3    3    3    3    3    4   24   31   32   34   36   40   40   40   42   43   43   43   43 
LCS_AVERAGE  LCS_A:  77.03  (  50.57   80.53  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     19     26     30     34     35     35     36     37     38     39     40     40     40     41     42     43     43     43     43 
GDT PERCENT_AT  34.88  44.19  60.47  69.77  79.07  81.40  81.40  83.72  86.05  88.37  90.70  93.02  93.02  93.02  95.35  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.28   0.54   0.93   1.35   1.51   1.61   1.61   1.76   1.94   2.20   2.50   2.76   2.76   2.76   3.18   3.54   3.82   3.82   3.82   3.82
GDT RMS_ALL_AT   6.42   6.09   5.46   4.70   4.89   4.84   4.84   4.74   4.63   4.46   4.27   4.10   4.10   4.10   3.93   3.84   3.82   3.82   3.82   3.82

# 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     2.320     0    0.026   0.164     3.150   64.881   61.111
LGA    L     6_B      L     6_B     2.677     0    0.035   0.872     3.237   60.952   60.060
LGA    E     7_B      E     7_B     2.316     0    0.033   1.105     7.051   68.810   52.011
LGA    T     8_B      T     8_B     0.859     0    0.059   1.231     2.791   88.214   81.020
LGA    K     9_B      K     9_B     1.038     0    0.009   0.129     2.306   83.690   76.825
LGA    K    10_B      K    10_B     1.461     0    0.013   0.943     5.521   81.429   65.767
LGA    A    11_B      A    11_B     1.466     0    0.016   0.017     1.671   81.429   79.714
LGA    Y    12_B      Y    12_B     0.752     0    0.038   0.094     2.752   90.476   78.968
LGA    A    13_B      A    13_B     0.451     0    0.004   0.012     0.816   95.238   94.286
LGA    A    14_B      A    14_B     1.396     0    0.037   0.041     1.970   79.405   78.095
LGA    R    15_B      R    15_B     1.927     0    0.019   1.206     5.083   70.833   64.935
LGA    T    16_B      T    16_B     1.808     0    0.066   0.080     2.085   72.857   72.925
LGA    R    17_B      R    17_B     0.950     0    0.035   1.054     5.995   83.690   60.779
LGA    R    18_B      R    18_B     1.543     0    0.021   1.259     6.767   75.000   55.238
LGA    S    19_B      S    19_B     2.281     0    0.038   0.699     2.814   66.786   66.190
LGA    N    20_B      N    20_B     1.832     0    0.041   0.358     2.136   77.143   73.988
LGA    Y    21_B      Y    21_B     0.528     0    0.080   0.197     4.673   90.476   69.127
LGA    A    22_B      A    22_B     1.125     0    0.003   0.013     1.640   85.952   83.333
LGA    A    23_B      A    23_B     1.481     0    0.022   0.022     1.900   81.429   79.714
LGA    S    24_B      S    24_B     1.305     0    0.066   0.728     1.407   81.429   82.937
LGA    L    25_B      L    25_B     0.779     0    0.035   0.057     1.084   90.476   89.345
LGA    R    26_B      R    26_B     0.727     0    0.051   1.046     4.688   90.476   70.087
LGA    L    27_B      L    27_B     1.098     0    0.026   0.209     1.999   83.690   81.488
LGA    E    28_B      E    28_B     1.039     0    0.030   1.104     5.073   83.690   73.757
LGA    G    29_B      G    29_B     0.843     0    0.091   0.091     0.858   90.476   90.476
LGA    F    30_B      F    30_B     0.836     0    0.021   0.044     1.335   90.476   85.541
LGA    K    31_B      K    31_B     0.807     0    0.213   0.864     6.701   90.476   60.476
LGA    V    32_B      V    32_B     0.771     0    0.022   0.231     2.368   81.786   78.027
LGA    T    33_B      T    33_B     2.273     0    0.058   1.103     5.350   75.119   61.973
LGA    F    34_B      F    34_B     1.977     0    0.018   1.108     8.396   77.381   42.121
LGA    A    35_B      A    35_B     2.159     0    0.040   0.044     3.046   68.810   65.048
LGA    D    36_B      D    36_B     2.092     0    0.119   0.130     3.179   64.881   65.000
LGA    G    37_B      G    37_B     1.870     0    0.082   0.082     2.337   70.833   70.833
LGA    E    38_B      E    38_B     1.537     0    0.051   0.854     4.340   69.048   64.074
LGA    R    39_B      R    39_B     3.234     0    0.132   1.349     5.890   50.119   40.563
LGA    K    40_B      K    40_B     4.535     0    0.059   0.856    12.335   33.095   18.942
LGA    M    41_B      M    41_B     5.351     0    0.031   1.274     6.138   22.976   35.357
LGA    P    42_B      P    42_B     7.286     0    0.033   0.050     7.735    9.405    9.320
LGA    T    43_B      T    43_B     8.866     0    0.079   1.110    11.172    2.381    1.633
LGA    R    44_B      R    44_B     9.754     0    0.601   1.432    10.366    1.190   12.035
LGA    E    45_B      E    45_B    13.427     0    0.426   1.364    20.019    0.000    0.000
LGA    E    46_B      E    46_B    14.416     0    0.594   1.432    16.409    0.000    0.000
LGA    V    47_B      V    47_B    14.521     0    0.428   1.368    16.132    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):     3.815          3.736                  4.506           65.742   59.375

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   56   43    4.0     36    1.76    73.837    78.884     1.931

LGA_LOCAL      RMSD:   1.764  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.741  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.815  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.135861 * X  +  -0.895564 * Y  +  -0.423682 * Z  +  19.761869
  Y_new =  -0.805095 * X  +   0.349024 * Y  +  -0.479587 * Z  + -56.839386
  Z_new =   0.577376 * X  +   0.275947 * Y  +  -0.768433 * Z  +  10.160863 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.737973 -0.615512  2.796831   [DEG:  -99.5785  -35.2662  160.2466 ]
ZXZ: -0.723585  2.447186  1.124958   [DEG:  -41.4584  140.2134   64.4554 ]
 
# END of job
