
#######################################################
#                                                     #
#                        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   53 (  413),  selected   53 , name one
# Molecule2: number of CA atoms  132 ( 1073),  selected   53 , 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:    21      46_A - 66_A        4.65    18.24
  LONGEST_CONTINUOUS_SEGMENT:    21      47_A - 67_A        4.87    18.46
  LCS_AVERAGE:     13.61

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      49_A - 63_A        1.98    15.17
  LONGEST_CONTINUOUS_SEGMENT:    15      50_A - 64_A        1.48    16.32
  LCS_AVERAGE:      7.26

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      50_A - 63_A        0.74    16.02
  LCS_AVERAGE:      5.40

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   53
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    46_A     S    46_A      3    3   21      3    3    3    4    5    5    5    7   10   12   12   17   17   23   24   28   32   35   36   37 
LCS_GDT     N    47_A     N    47_A      3    4   21      3    3    3    4    5    5    7   10   11   14   19   20   21   23   26   30   32   35   36   39 
LCS_GDT     D    48_A     D    48_A      3    4   21      3    3    3    4    5    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     T    49_A     T    49_A      3   15   21      3    3    4    5    7    9   13   15   18   20   20   21   24   26   28   30   32   35   37   39 
LCS_GDT     D    50_A     D    50_A     14   15   21      3   12   14   14   14   14   14   16   18   20   20   21   22   24   28   30   32   35   37   39 
LCS_GDT     Y    51_A     Y    51_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   23   25   28   30   32   35   37   39 
LCS_GDT     F    52_A     F    52_A     14   15   21      9   12   14   14   14   14   14   15   16   20   20   21   23   24   28   30   32   35   37   39 
LCS_GDT     S    53_A     S    53_A     14   15   21      9   12   14   14   14   14   14   15   18   20   20   21   24   26   28   30   32   35   37   39 
LCS_GDT     C    54_A     C    54_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   32   35   37   39 
LCS_GDT     F    55_A     F    55_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   32   35   37   39 
LCS_GDT     A    56_A     A    56_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   32   35   37   39 
LCS_GDT     D    57_A     D    57_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   32   35   37   39 
LCS_GDT     L    58_A     L    58_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   31   35   37   39 
LCS_GDT     R    59_A     R    59_A     14   15   21      9   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   31   35   37   39 
LCS_GDT     N    60_A     N    60_A     14   15   21      5   12   14   14   14   14   14   16   18   20   20   21   24   26   28   30   31   35   37   39 
LCS_GDT     Q    61_A     Q    61_A     14   15   21      4   12   14   14   14   14   14   16   18   20   20   21   23   26   28   30   31   33   37   39 
LCS_GDT     L    62_A     L    62_A     14   15   21      4   12   14   14   14   14   14   16   18   20   20   21   21   24   26   28   31   33   37   39 
LCS_GDT     K    63_A     K    63_A     14   15   21      4   12   14   14   14   14   14   16   18   20   20   21   21   24   26   27   30   33   37   39 
LCS_GDT     N    64_A     N    64_A      5   15   21      3    5    5    5    6   14   14   15   16   20   20   21   21   24   26   27   30   33   35   39 
LCS_GDT     I    65_A     I    65_A      5    9   21      3    5    5    7    8   10   11   13   15   17   19   21   24   26   28   30   31   33   37   39 
LCS_GDT     I    66_A     I    66_A      5    9   21      3    5    6    8    8   10   11   13   15   17   19   21   24   26   28   30   31   33   37   39 
LCS_GDT     F    67_A     F    67_A      4    9   21      3    4    6    8    8   10   11   11   12   12   13   16   21   26   27   28   31   32   34   34 
LCS_GDT     L    68_A     L    68_A      6    9   17      3    5    6    8    8   10   11   11   12   12   13   14   17   20   25   27   29   30   32   34 
LCS_GDT     C    69_A     C    69_A      6    9   17      3    5    6    8    8   10   11   11   12   12   13   14   14   15   17   19   23   25   26   29 
LCS_GDT     K    70_A     K    70_A      6    9   17      3    5    6    8    8   10   11   11   12   12   13   14   14   15   17   18   21   24   26   29 
LCS_GDT     G    71_A     G    71_A      6    9   17      3    5    6    8    8   10   11   11   12   12   13   14   14   15   17   18   20   21   24   27 
LCS_GDT     A    72_A     A    72_A      6    9   17      3    5    6    8    8   10   11   11   12   12   13   14   14   15   19   24   27   29   30   34 
LCS_GDT     K    73_A     K    73_A      6    9   17      3    5    6    8    8    9   11   11   12   12   16   19   24   26   28   30   31   32   34   38 
LCS_GDT     I    74_A     I    74_A      5    9   17      3    4    5    7    8    8    9   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     N    75_A     N    75_A      5    8   17      3    4    5    6    7    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     V    76_A     V    76_A      4    7   14      3    4    5    5    7    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     Y    77_A     Y    77_A      4    7   14      3    4    4    5    7    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     P    78_A     P    78_A      4    7   14      3    4    5    5    6    7    8    9   14   16   17   20   23   26   28   30   31   34   37   39 
LCS_GDT     S    79_A     S    79_A      3    7   14      3    4    5    5    6    7    8   12   14   16   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     A    80_A     A    80_A      3    7   14      3    3    3    4    6    7    8   12   14   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     M    81_A     M    81_A      3    4   14      3    3    3    4    4    6    8    9   14   16   19   20   24   26   28   30   32   35   37   39 
LCS_GDT     S    82_A     S    82_A      3    4   14      3    3    3    5    7    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     R    83_A     R    83_A      3    3   16      0    3    4    4    6    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     D    84_A     D    84_A      3    3   16      0    3    3    4    6    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     M    85_A     M    85_A      3    6   16      1    3    4    4    6    8   10   13   15   17   19   21   24   26   28   30   32   35   37   39 
LCS_GDT     S    86_A     S    86_A      4    6   16      3    4    4    5    6    7    8    9   11   12   16   18   23   24   27   30   32   35   37   39 
LCS_GDT     D    87_A     D    87_A      4    6   16      3    4    4    5    7    9    9   10   11   11   12   13   16   16   17   20   22   33   35   37 
LCS_GDT     G    88_A     G    88_A      4    8   16      3    4    5    6    7    7    9   10   11   11   12   13   16   16   17   18   21   24   26   31 
LCS_GDT     I    89_A     I    89_A      5    9   16      3    4    7    8    8    9    9   10   11   11   12   14   16   24   24   28   32   34   36   37 
LCS_GDT     V    90_A     V    90_A      7    9   16      3    6    7    8    9   11   13   16   18   20   20   21   21   24   26   28   32   35   37   39 
LCS_GDT     A    91_A     A    91_A      7    9   16      3    4    7    8    8    9   13   16   18   20   20   21   21   24   26   28   32   35   37   39 
LCS_GDT     Y    92_A     Y    92_A      7    9   16      5    6    7    8    8    9    9   16   18   20   20   21   21   24   25   28   32   35   37   39 
LCS_GDT     E    93_A     E    93_A      7    9   16      5    6    7    8    8    9   12   16   18   20   20   21   21   24   26   28   32   35   37   39 
LCS_GDT     T    94_A     T    94_A      7    9   16      5    6    7    8    8    9    9   10   11   11   12   14   16   20   24   28   32   35   37   39 
LCS_GDT     T    95_A     T    95_A      7    9   16      5    6    7    8    8    9    9   10   11   11   12   13   16   19   21   28   32   35   37   39 
LCS_GDT     L    96_A     L    96_A      7    9   16      5    6    7    8    8    9    9   10   11   11   12   14   16   20   24   28   32   35   36   37 
LCS_GDT     G    97_A     G    97_A      3    9   16      3    3    3    6    7    9    9   10   11   11   12   14   17   21   24   28   32   35   36   37 
LCS_GDT     Q    98_A     Q    98_A      3    3   16      0    3    3    3    3    4    4    6    9   10   11   14   16   20   24   28   32   33   35   37 
LCS_AVERAGE  LCS_A:   8.76  (   5.40    7.26   13.61 )

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     12     14     14     14     14     14     16     18     20     20     21     24     26     28     30     32     35     37     39 
GDT PERCENT_AT   6.82   9.09  10.61  10.61  10.61  10.61  10.61  12.12  13.64  15.15  15.15  15.91  18.18  19.70  21.21  22.73  24.24  26.52  28.03  29.55
GDT RMS_LOCAL    0.23   0.51   0.74   0.74   0.74   0.74   0.74   2.69   2.92   3.29   3.29   3.50   4.70   5.10   5.10   5.40   6.49   6.68   6.67   6.91
GDT RMS_ALL_AT  16.51  16.26  16.02  16.02  16.02  16.02  16.02  13.37  13.25  13.28  13.28  13.05  10.13  10.38  10.10  10.06  11.44  10.94  10.12  10.07

# Checking swapping
#   possible swapping detected:  D    48_A      D    48_A
#   possible swapping detected:  D    50_A      D    50_A
#   possible swapping detected:  F    52_A      F    52_A
#   possible swapping detected:  Y    77_A      Y    77_A
#   possible swapping detected:  D    84_A      D    84_A
#   possible swapping detected:  D    87_A      D    87_A
#   possible swapping detected:  Y    92_A      Y    92_A
#   possible swapping detected:  E    93_A      E    93_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S    46_A      S    46_A    14.903     0    0.668   0.846    16.888    0.000    0.000
LGA    N    47_A      N    47_A    13.502     0    0.567   0.673    20.272    0.000    0.000
LGA    D    48_A      D    48_A     9.196     0    0.648   1.149    10.773    4.643    2.560
LGA    T    49_A      T    49_A     4.404     0    0.280   1.016     6.066   44.048   39.524
LGA    D    50_A      D    50_A     1.627     0    0.643   1.381     7.290   72.857   47.917
LGA    Y    51_A      Y    51_A     2.426     0    0.044   1.038    10.513   59.405   31.667
LGA    F    52_A      F    52_A     5.359     0    0.071   0.199    11.139   31.548   13.420
LGA    S    53_A      S    53_A     4.405     0    0.025   0.052     6.253   45.357   37.460
LGA    C    54_A      C    54_A     0.724     0    0.047   0.077     1.930   88.452   89.206
LGA    F    55_A      F    55_A     2.790     0    0.041   1.281     9.396   61.071   31.948
LGA    A    56_A      A    56_A     3.555     0    0.085   0.087     4.898   53.810   49.333
LGA    D    57_A      D    57_A     2.395     0    0.000   0.942     3.254   68.810   63.036
LGA    L    58_A      L    58_A     2.049     0    0.000   1.223     5.950   69.048   56.905
LGA    R    59_A      R    59_A     2.432     0    0.054   1.798     4.348   68.810   66.147
LGA    N    60_A      N    60_A     1.027     0    0.075   0.918     2.558   83.690   73.274
LGA    Q    61_A      Q    61_A     2.438     0    0.129   0.703     4.442   61.190   52.857
LGA    L    62_A      L    62_A     3.273     0    0.407   1.031     7.622   57.262   43.512
LGA    K    63_A      K    63_A     2.619     0    0.728   0.835    11.103   47.143   27.196
LGA    N    64_A      N    64_A     6.682     0    0.136   1.188    12.552   14.048    7.381
LGA    I    65_A      I    65_A     8.015     0    0.129   0.605    10.050    9.167    6.131
LGA    I    66_A      I    66_A    11.600     0    0.232   1.096    15.162    0.000    0.000
LGA    F    67_A      F    67_A    17.631     0    0.397   1.149    19.918    0.000    0.000
LGA    L    68_A      L    68_A    22.979     0    0.391   1.151    25.886    0.000    0.000
LGA    C    69_A      C    69_A    27.313     0    0.080   0.282    29.168    0.000    0.000
LGA    K    70_A      K    70_A    29.112     0    0.600   1.006    34.831    0.000    0.000
LGA    G    71_A      G    71_A    25.778     0    0.110   0.110    26.816    0.000    0.000
LGA    A    72_A      A    72_A    19.461     0    0.276   0.259    21.856    0.000    0.000
LGA    K    73_A      K    73_A    18.879     0    0.644   0.635    25.488    0.000    0.000
LGA    I    74_A      I    74_A    14.877     0    0.515   1.293    16.129    0.000    0.000
LGA    N    75_A      N    75_A    16.268     0    0.611   1.161    19.080    0.000    0.000
LGA    V    76_A      V    76_A    15.336     0    0.072   0.852    17.484    0.000    0.000
LGA    Y    77_A      Y    77_A    13.003     0    0.117   0.739    14.361    0.000    0.000
LGA    P    78_A      P    78_A    14.715     0    0.630   0.588    15.508    0.000    0.000
LGA    S    79_A      S    79_A    14.833     0    0.051   0.105    18.919    0.000    0.000
LGA    A    80_A      A    80_A    15.425     0    0.386   0.371    17.719    0.000    0.000
LGA    M    81_A      M    81_A    16.935     0    0.540   1.079    22.584    0.000    0.000
LGA    S    82_A      S    82_A    13.038     0    0.603   0.545    14.109    0.000    0.000
LGA    R    83_A      R    83_A    10.318     0    0.609   1.435    11.349    0.000   11.905
LGA    D    84_A      D    84_A    13.445     0    0.572   1.480    18.667    0.000    0.000
LGA    M    85_A      M    85_A    11.802     0    0.651   0.798    14.183    0.000    1.607
LGA    S    86_A      S    86_A    12.614     0    0.713   0.682    12.992    0.000    0.000
LGA    D    87_A      D    87_A    16.098     0    0.242   0.229    20.589    0.000    0.000
LGA    G    88_A      G    88_A    13.317     0    0.000   0.000    13.525    0.000    0.000
LGA    I    89_A      I    89_A     8.417     0    0.187   0.760    11.583    9.762    7.917
LGA    V    90_A      V    90_A     2.452     0    0.018   1.175     5.590   41.905   50.884
LGA    A    91_A      A    91_A     3.114     0    0.127   0.191     5.010   67.262   59.048
LGA    Y    92_A      Y    92_A     4.036     0    0.257   0.452     8.813   40.714   18.135
LGA    E    93_A      E    93_A     3.785     0    0.218   1.024     6.983   30.357   44.180
LGA    T    94_A      T    94_A     8.943     0    0.090   0.112    10.171    5.119    2.993
LGA    T    95_A      T    95_A    11.394     0    0.155   0.200    14.095    0.000    0.068
LGA    L    96_A      L    96_A    16.091     0    0.197   0.926    20.704    0.000    0.000
LGA    G    97_A      G    97_A    21.499     0    0.704   0.704    25.236    0.000    0.000
LGA    Q    98_A      Q    98_A    26.033     0    0.179   0.978    28.482    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       53     212    212  100.00     413    413  100.00               132
SUMMARY(RMSD_GDC):     9.729          9.607                 10.161            8.602    7.092

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53  132    4.0     16    2.69    13.636    11.754     0.572

LGA_LOCAL      RMSD:   2.695  Number of atoms:   16  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  13.368  Number of assigned atoms:   53 
Std_ASGN_ATOMS RMSD:   9.729  Standard rmsd on all 53 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.128568 * X  +  -0.564919 * Y  +   0.815069 * Z  + -150.953186
  Y_new =   0.899183 * X  +  -0.280234 * Y  +  -0.336064 * Z  + -10.119250
  Z_new =   0.418259 * X  +   0.776103 * Y  +   0.471936 * Z  + -421.669250 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.428776 -0.431528  1.024453   [DEG:   81.8629  -24.7247   58.6968 ]
ZXZ:  1.179720  1.079310  0.494298   [DEG:   67.5930   61.8399   28.3212 ]
 
# END of job
