
#######################################################
#                                                     #
#                        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   58 (  481),  selected   58 , name one
# Molecule2: number of CA atoms   58 (  481),  selected   58 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:A  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      30_A - 58_A        4.52    14.88
  LCS_AVERAGE:     43.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      34_A - 58_A        1.62    15.11
  LCS_AVERAGE:     33.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      35_A - 58_A        0.91    15.12
  LCS_AVERAGE:     28.83

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   58
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     1_A     A     1_A      3   14   17      3    3    3    5   16   21   30   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     E     2_A     E     2_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     Y     3_A     Y     3_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     V     4_A     V     4_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     R     5_A     R     5_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     A     6_A     A     6_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     L     7_A     L     7_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     F     8_A     F     8_A     12   14   17     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     D     9_A     D     9_A     12   14   17     22   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     H    10_A     H    10_A     12   14   17     22   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     T    11_A     T    11_A     12   14   17     16   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     G    12_A     G    12_A     12   14   25      3    6   19   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     H    13_A     H    13_A     12   14   25      3    6   24   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     D    14_A     D    14_A      3   17   25     23   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     E    15_A     E    15_A      3   17   25      3    3    4    5   21   24   27   33   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     Q    16_A     Q    16_A     15   17   25      8   14   14   14   15   15   23   25   35   39   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     E    17_A     E    17_A     15   17   25     10   14   14   14   15   15   17   19   21   22   22   22   24   33   35   40   42   45   46   46 
LCS_GDT     L    18_A     L    18_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   31   37   38 
LCS_GDT     P    19_A     P    19_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     F    20_A     F    20_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     K    21_A     K    21_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   25   28   29   30 
LCS_GDT     K    22_A     K    22_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   25   28   29   30 
LCS_GDT     G    23_A     G    23_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     E    24_A     E    24_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     I    25_A     I    25_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     L    26_A     L    26_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     R    27_A     R    27_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   24   27   28   29   30 
LCS_GDT     I    28_A     I    28_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   24   25   28   31   35   36 
LCS_GDT     R    29_A     R    29_A     15   17   25     12   14   14   14   15   15   17   19   21   22   22   22   23   23   25   28   33   34   37   41 
LCS_GDT     D    30_A     D    30_A     15   17   29      3    4    8   14   15   15   17   19   21   22   23   24   27   30   34   41   44   45   46   46 
LCS_GDT     K    31_A     K    31_A      4   16   29      3    3    4    5    8   12   17   19   21   22   23   24   34   39   44   44   44   45   46   46 
LCS_GDT     P    32_A     P    32_A      4    7   29      3    3    4    5   10   15   17   19   21   22   22   22   36   43   44   44   44   45   46   46 
LCS_GDT     E    33_A     E    33_A      4    7   29      3    3    4    5    7    9   12   25   32   36   40   42   42   43   44   44   44   45   46   46 
LCS_GDT     E    34_A     E    34_A      4   25   29      3    4    5    5    6    8   22   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     Q    35_A     Q    35_A     24   25   29      3   24   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     L    36_A     L    36_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     W    37_A     W    37_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     N    38_A     N    38_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     A    39_A     A    39_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     E    40_A     E    40_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     N    41_A     N    41_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     V    42_A     V    42_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     E    43_A     E    43_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     G    44_A     G    44_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     K    45_A     K    45_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     R    46_A     R    46_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     G    47_A     G    47_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     L    48_A     L    48_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     I    49_A     I    49_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     H    50_A     H    50_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     V    51_A     V    51_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     V    52_A     V    52_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     L    53_A     L    53_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     V    54_A     V    54_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     E    55_A     E    55_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     K    56_A     K    56_A     24   25   29     27   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     Y    57_A     Y    57_A     24   25   29     26   33   34   35   36   36   36   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_GDT     G    58_A     G    58_A     24   25   29      3    3    6    8   21   24   35   37   38   40   41   42   42   43   44   44   44   45   46   46 
LCS_AVERAGE  LCS_A:  35.41  (  28.83   33.47   43.94 )

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     27     33     34     35     36     36     36     37     38     40     41     42     42     43     44     44     44     45     46     46 
GDT PERCENT_AT  46.55  56.90  58.62  60.34  62.07  62.07  62.07  63.79  65.52  68.97  70.69  72.41  72.41  74.14  75.86  75.86  75.86  77.59  79.31  79.31
GDT RMS_LOCAL    0.27   0.40   0.47   0.66   0.85   0.85   0.85   1.09   1.52   2.09   2.37   2.76   2.76   3.22   3.64   3.64   3.64   3.99   4.39   4.39
GDT RMS_ALL_AT  15.12  15.15  15.14  15.16  15.19  15.19  15.19  15.18  15.10  14.99  14.89  14.86  14.86  14.81  14.72  14.72  14.72  14.60  14.49  14.49

# Checking swapping
#   possible swapping detected:  E     2_A      E     2_A
#   possible swapping detected:  D    14_A      D    14_A
#   possible swapping detected:  E    15_A      E    15_A
#   possible swapping detected:  E    17_A      E    17_A
#   possible swapping detected:  F    20_A      F    20_A
#   possible swapping detected:  E    24_A      E    24_A
#   possible swapping detected:  D    30_A      D    30_A
#   possible swapping detected:  E    34_A      E    34_A
#   possible swapping detected:  E    40_A      E    40_A
#   possible swapping detected:  E    43_A      E    43_A
#   possible swapping detected:  Y    57_A      Y    57_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A     1_A      A     1_A     6.794     0    0.026   0.028     8.620   21.190   19.619
LGA    E     2_A      E     2_A     0.133     0    0.636   0.991     7.291   89.286   55.926
LGA    Y     3_A      Y     3_A     0.235     0    0.039   0.071     0.474  100.000  100.000
LGA    V     4_A      V     4_A     0.242     0    0.038   0.081     0.355  100.000  100.000
LGA    R     5_A      R     5_A     0.350     0    0.053   0.813     1.867   97.619   89.913
LGA    A     6_A      A     6_A     0.529     0    0.036   0.041     0.537   92.857   92.381
LGA    L     7_A      L     7_A     0.548     0    0.098   0.229     1.098   90.476   91.726
LGA    F     8_A      F     8_A     0.544     0    0.040   0.139     1.210   90.476   88.831
LGA    D     9_A      D     9_A     0.562     0    0.047   0.357     1.761   90.476   86.012
LGA    H    10_A      H    10_A     0.632     0    0.030   0.109     0.960   90.476   90.476
LGA    T    11_A      T    11_A     0.829     0    0.545   1.074     2.627   86.071   79.524
LGA    G    12_A      G    12_A     3.155     0    0.081   0.081     3.155   63.333   63.333
LGA    H    13_A      H    13_A     2.634     0    0.534   1.484     6.106   53.810   42.857
LGA    D    14_A      D    14_A     0.873     0    0.036   1.016     5.755   65.595   52.857
LGA    E    15_A      E    15_A     7.002     0    0.644   0.695    13.885   16.071    7.513
LGA    Q    16_A      Q    16_A     8.221     0    0.632   1.163    10.615    3.810    3.069
LGA    E    17_A      E    17_A    12.185     0    0.081   0.704    15.739    0.000    0.000
LGA    L    18_A      L    18_A    19.323     0    0.083   1.406    23.700    0.000    0.000
LGA    P    19_A      P    19_A    24.701     0    0.048   0.271    27.429    0.000    0.000
LGA    F    20_A      F    20_A    30.619     0    0.055   1.433    32.676    0.000    0.000
LGA    K    21_A      K    21_A    37.283     0    0.049   1.095    40.434    0.000    0.000
LGA    K    22_A      K    22_A    40.228     0    0.050   1.037    47.671    0.000    0.000
LGA    G    23_A      G    23_A    42.401     0    0.072   0.072    42.401    0.000    0.000
LGA    E    24_A      E    24_A    38.660     0    0.010   0.872    39.449    0.000    0.000
LGA    I    25_A      I    25_A    36.334     0    0.054   0.138    42.500    0.000    0.000
LGA    L    26_A      L    26_A    30.155     0    0.038   0.133    32.072    0.000    0.000
LGA    R    27_A      R    27_A    28.307     0    0.038   0.214    32.248    0.000    0.000
LGA    I    28_A      I    28_A    21.212     0    0.065   0.172    23.961    0.000    0.000
LGA    R    29_A      R    29_A    20.923     0    0.620   0.931    28.319    0.000    0.000
LGA    D    30_A      D    30_A    16.941     0    0.674   1.097    19.672    0.000    0.000
LGA    K    31_A      K    31_A    14.875     0    0.256   0.644    22.757    0.000    0.000
LGA    P    32_A      P    32_A    13.791     0    0.103   0.111    17.533    0.000    0.000
LGA    E    33_A      E    33_A    10.885     0    0.718   1.038    14.166    0.476    0.212
LGA    E    34_A      E    34_A     7.049     0    0.234   1.037    10.572   17.500    9.048
LGA    Q    35_A      Q    35_A     1.277     0    0.585   1.321     3.010   79.881   70.794
LGA    L    36_A      L    36_A     0.657     0    0.119   1.305     2.818   90.595   82.202
LGA    W    37_A      W    37_A     0.799     0    0.010   0.226     1.744   90.476   84.082
LGA    N    38_A      N    38_A     0.596     0    0.000   0.657     2.479   90.476   81.845
LGA    A    39_A      A    39_A     0.323     0    0.028   0.038     0.395  100.000  100.000
LGA    E    40_A      E    40_A     0.372     0    0.028   0.548     1.387  100.000   92.698
LGA    N    41_A      N    41_A     0.349     0    0.047   0.110     0.457  100.000  100.000
LGA    V    42_A      V    42_A     0.248     0    0.714   0.999     3.545   81.190   77.007
LGA    E    43_A      E    43_A     0.357     0    0.083   0.964     4.080   97.619   76.878
LGA    G    44_A      G    44_A     0.599     0    0.032   0.032     0.709   92.857   92.857
LGA    K    45_A      K    45_A     0.535     0    0.077   0.991     5.652   90.476   70.582
LGA    R    46_A      R    46_A     0.223     0    0.035   0.833     2.832  100.000   93.506
LGA    G    47_A      G    47_A     0.315     0    0.024   0.024     0.349  100.000  100.000
LGA    L    48_A      L    48_A     0.417     0    0.021   0.085     0.602   95.238   96.429
LGA    I    49_A      I    49_A     0.603     0    0.000   0.103     1.170   95.238   90.595
LGA    H    50_A      H    50_A     0.640     0    0.023   0.931     2.997   90.476   81.095
LGA    V    51_A      V    51_A     0.605     0    0.036   0.103     0.708   95.238   93.197
LGA    V    52_A      V    52_A     0.540     0    0.110   1.059     3.004   92.857   83.469
LGA    L    53_A      L    53_A     0.537     0    0.112   1.051     3.240   95.238   84.464
LGA    V    54_A      V    54_A     0.323     0    0.034   0.107     0.578  100.000   98.639
LGA    E    55_A      E    55_A     0.158     0    0.038   0.177     1.065  100.000   94.762
LGA    K    56_A      K    56_A     0.169     0    0.105   0.524     2.236  100.000   88.889
LGA    Y    57_A      Y    57_A     0.723     0    0.617   0.870     2.535   81.786   73.929
LGA    G    58_A      G    58_A     4.056     0    0.085   0.085     6.459   31.429   31.429

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       58     232    232  100.00     481    481  100.00                58
SUMMARY(RMSD_GDC):    12.984         12.895                 13.363           57.941   53.666

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58   58    4.0     37    1.09    64.224    56.969     3.121

LGA_LOCAL      RMSD:   1.086  Number of atoms:   37  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  15.178  Number of assigned atoms:   58 
Std_ASGN_ATOMS RMSD:  12.984  Standard rmsd on all 58 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.424787 * X  +   0.450043 * Y  +  -0.785504 * Z  + -117.677063
  Y_new =   0.211110 * X  +  -0.893002 * Y  +  -0.397468 * Z  + 120.550346
  Z_new =  -0.880334 * X  +   0.003011 * Y  +  -0.474344 * Z  +  90.863602 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.461228  1.076566  3.135245   [DEG:   26.4264   61.6827  179.6363 ]
ZXZ: -1.102358  2.065016 -1.567376   [DEG:  -63.1604  118.3167  -89.8040 ]
 
# END of job
