
#######################################################
#                                                     #
#                        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   57 (  443),  selected   57 , name one
# Molecule2: number of CA atoms  132 ( 1073),  selected   57 , 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:    26      54_A - 79_A        4.90    21.42
  LCS_AVERAGE:     15.96

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      54_A - 71_A        1.96    22.69
  LCS_AVERAGE:      7.56

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    10      55_A - 64_A        0.88    22.57
  LCS_AVERAGE:      4.05

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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     C    54_A     C    54_A      3   18   26      3    3    8   11   15   17   18   19   20   20   21   21   22   22   23   24   25   25   26   28 
LCS_GDT     F    55_A     F    55_A     10   18   26      3    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     A    56_A     A    56_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     D    57_A     D    57_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     L    58_A     L    58_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     R    59_A     R    59_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     N    60_A     N    60_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     Q    61_A     Q    61_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     L    62_A     L    62_A     10   18   26      8    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   25   28   29 
LCS_GDT     K    63_A     K    63_A     10   18   26      8    9    9   11   14   17   18   19   20   20   21   21   22   22   23   24   25   25   28   29 
LCS_GDT     N    64_A     N    64_A     10   18   26      4    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   25   26   26 
LCS_GDT     I    65_A     I    65_A      5   18   26      4    4    8   14   15   17   18   19   20   20   21   21   22   22   23   24   25   25   26   26 
LCS_GDT     I    66_A     I    66_A      5   18   26      3    4    8   14   15   17   18   19   20   20   21   21   22   22   23   24   25   25   26   26 
LCS_GDT     F    67_A     F    67_A      5   18   26      3    4    8   14   15   17   18   19   20   20   21   21   22   22   23   24   25   25   28   29 
LCS_GDT     L    68_A     L    68_A      5   18   26      3    4    5    5   13   17   18   19   20   20   21   21   22   22   23   24   25   25   28   30 
LCS_GDT     C    69_A     C    69_A      5   18   26      3    4    5   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     K    70_A     K    70_A      4   18   26      4    9   10   14   15   17   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     G    71_A     G    71_A      4   18   26      3    3    4    5    5   14   18   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     A    72_A     A    72_A      3    6   26      3    3    3    4    4    6    7    8    9   10   11   13   15   18   23   24   25   25   29   30 
LCS_GDT     K    73_A     K    73_A      4    6   26      4    4    4    5    5    6    7    9   13   13   17   18   22   22   23   24   25   27   29   30 
LCS_GDT     I    74_A     I    74_A      4    6   26      4    4    4    5    5    6    8    9   10   11   15   15   16   18   22   24   25   27   29   30 
LCS_GDT     N    75_A     N    75_A      5    7   26      4    4    5    6    7    7    8    9   14   18   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     V    76_A     V    76_A      5    7   26      4    9    9   10   12   13   16   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     Y    77_A     Y    77_A      5    7   26      4    4    5   11   12   14   16   19   20   20   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     P    78_A     P    78_A      5    7   26      4    4    5    6    7    7    8    9   10   16   21   21   22   22   23   24   25   27   29   30 
LCS_GDT     S    79_A     S    79_A      5    7   26      4    4    5    6    7    7    8    9   10   10   12   16   19   21   22   23   24   27   29   30 
LCS_GDT     A    80_A     A    80_A      4    7   16      3    4    4    6    7    7    8    9   10   10   12   14   17   18   20   21   23   25   29   30 
LCS_GDT     M    81_A     M    81_A      3    7   16      1    4    5    6    7    7    8    9   10   11   12   14   17   17   20   21   22   25   28   29 
LCS_GDT     S    82_A     S    82_A      3    3   16      0    4    4    4    6    6    9   10   11   12   13   14   17   18   20   21   23   27   29   30 
LCS_GDT     R    83_A     R    83_A      3    3   16      3    4    4    5    6    8   10   11   12   12   13   14   17   18   20   22   23   27   29   30 
LCS_GDT     D    84_A     D    84_A      5    5   16      3    4    5    5    6    7   10   11   12   12   13   14   17   18   20   22   23   27   29   30 
LCS_GDT     M    85_A     M    85_A      5    5   16      3    4    5    5    6    8   10   11   12   12   13   14   17   18   20   22   23   27   29   30 
LCS_GDT     S    86_A     S    86_A      5    5   15      3    4    5    5    6    8   10   11   12   12   13   14   17   17   19   21   23   27   29   30 
LCS_GDT     D    87_A     D    87_A      5    5   15      3    4    5    5    6    8   10   11   12   12   13   14   17   17   19   22   23   27   29   30 
LCS_GDT     G    88_A     G    88_A      5    7   15      3    3    5    6    7    8   10   11   12   12   13   14   17   17   19   22   23   27   29   30 
LCS_GDT     I    89_A     I    89_A      3    7   15      3    4    5    6    7    8   10   11   12   12   13   14   17   17   19   22   23   27   29   30 
LCS_GDT     V    90_A     V    90_A      3    7   15      3    3    4    6    7    8   10   11   12   12   13   14   17   17   19   22   23   27   29   30 
LCS_GDT     A    91_A     A    91_A      4    7   15      4    4    5    5    7    8   10   11   12   12   13   14   17   17   19   22   23   27   29   30 
LCS_GDT     Y    92_A     Y    92_A      4    7   15      4    4    5    6    7    8   10   11   12   12   13   14   17   17   19   22   23   25   28   30 
LCS_GDT     E    93_A     E    93_A      4    7   18      4    4    5    6    7    8    9   11   12   12   13   16   17   17   20   22   23   24   25   26 
LCS_GDT     T    94_A     T    94_A      4    7   18      4    4    5    6    7    8    9   10   12   13   14   16   17   17   20   22   23   24   25   26 
LCS_GDT     T    95_A     T    95_A      4    7   18      4    4    5    6    7    7    9   11   11   13   14   16   16   17   20   22   23   24   25   26 
LCS_GDT     L    96_A     L    96_A      5    7   18      4    4    5    6    7    7    9   11   11   13   13   16   16   17   20   22   23   24   25   26 
LCS_GDT     G    97_A     G    97_A      5    7   18      4    4    5    6    7    7    9   11   11   13   14   16   16   17   20   22   23   24   25   26 
LCS_GDT     Q    98_A     Q    98_A      5    7   18      4    4    5    6    6    7    8   11   11   13   14   16   16   17   20   22   23   24   25   26 
LCS_GDT     P    99_A     P    99_A      5    7   18      4    4    5    5    6    7    8   11   11   13   14   16   16   17   20   22   23   24   25   26 
LCS_GDT     G   100_A     G   100_A      5    7   18      3    4    5    5    6    7    7   11   12   13   14   16   16   17   20   20   22   24   25   26 
LCS_GDT     L   101_A     L   101_A      5    7   18      4    5    5    5    7    8   10   11   12   13   14   16   16   17   20   20   21   22   24   26 
LCS_GDT     P   102_A     P   102_A      5    7   18      4    5    5    5    7    8   10   11   12   13   14   16   17   17   20   20   21   22   23   25 
LCS_GDT     E   103_A     E   103_A      5    7   18      4    5    5    5    7    8   10   10   12   13   14   16   17   17   20   20   21   22   23   25 
LCS_GDT     N   104_A     N   104_A      5    7   18      4    5    5    5    7    8   10   11   12   13   14   16   16   17   20   20   21   22   23   25 
LCS_GDT     Q   105_A     Q   105_A      5    7   18      4    5    5    5    7    8   10   11   12   13   14   16   16   17   20   20   20   22   23   25 
LCS_GDT     V   106_A     V   106_A      3    7   18      3    3    4    5    7    8   10   11   12   13   14   16   16   17   20   20   20   22   23   25 
LCS_GDT     H   107_A     H   107_A      4    7   18      4    4    5    6    7    8    9   11   12   13   14   16   16   17   20   20   20   22   23   25 
LCS_GDT     I   108_A     I   108_A      4    4   18      4    4    5    6    6    8   10   10   12   13   14   16   16   17   20   20   20   22   23   25 
LCS_GDT     F   109_A     F   109_A      4    4   18      4    4    5    6    6    6    6    7   10   10   13   14   16   17   18   21   22   23   23   24 
LCS_GDT     D   110_A     D   110_A      4    4   18      4    4    5    6    6    7   10   10   11   13   13   15   16   17   18   18   20   21   22   22 
LCS_AVERAGE  LCS_A:   9.19  (   4.05    7.56   15.96 )

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      8      9     10     14     15     17     18     19     20     20     21     21     22     22     23     24     25     27     29     30 
GDT PERCENT_AT   6.06   6.82   7.58  10.61  11.36  12.88  13.64  14.39  15.15  15.15  15.91  15.91  16.67  16.67  17.42  18.18  18.94  20.45  21.97  22.73
GDT RMS_LOCAL    0.22   0.36   0.82   1.44   1.52   1.78   1.96   2.24   2.44   2.44   2.79   2.79   3.40   3.40   3.64   4.02   4.40   6.96   9.25   7.33
GDT RMS_ALL_AT  22.51  22.56  22.44  22.40  22.58  22.66  22.69  22.44  22.08  22.08  21.78  21.78  21.91  21.91  21.69  21.87  21.84  16.94  16.94  16.73

# Checking swapping
#   possible swapping detected:  F    67_A      F    67_A
#   possible swapping detected:  Y    77_A      Y    77_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
#   possible swapping detected:  E   103_A      E   103_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    C    54_A      C    54_A     2.751     0    0.054   0.062     4.297   65.000   57.857
LGA    F    55_A      F    55_A     0.634     0    0.449   1.068     5.423   83.810   64.372
LGA    A    56_A      A    56_A     0.519     0    0.172   0.178     1.053   95.238   92.476
LGA    D    57_A      D    57_A     0.955     0    0.004   0.935     3.449   90.476   76.012
LGA    L    58_A      L    58_A     0.437     0    0.044   0.356     1.375   95.238   91.786
LGA    R    59_A      R    59_A     0.776     0    0.041   1.415     5.026   90.595   77.576
LGA    N    60_A      N    60_A     1.183     0    0.017   0.869     3.626   81.548   69.762
LGA    Q    61_A      Q    61_A     1.297     0    0.015   0.860     5.922   79.286   62.381
LGA    L    62_A      L    62_A     1.372     0    0.325   0.280     1.815   77.143   79.286
LGA    K    63_A      K    63_A     2.503     0    0.101   0.985     8.365   64.881   42.434
LGA    N    64_A      N    64_A     0.236     0    0.068   1.127     5.673   86.190   64.643
LGA    I    65_A      I    65_A     2.591     0    0.651   0.929     5.301   51.548   54.464
LGA    I    66_A      I    66_A     2.741     0    0.351   0.752     4.371   67.024   54.405
LGA    F    67_A      F    67_A     2.621     0    0.095   1.272     3.806   53.690   62.511
LGA    L    68_A      L    68_A     3.299     0    0.444   0.429     4.544   47.143   48.571
LGA    C    69_A      C    69_A     2.656     0    0.070   0.792     5.447   69.286   57.778
LGA    K    70_A      K    70_A     0.927     0    0.649   0.987     3.845   73.690   66.455
LGA    G    71_A      G    71_A     3.759     0    0.672   0.672     7.720   31.190   31.190
LGA    A    72_A      A    72_A    10.200     0    0.599   0.547    12.290    1.786    1.429
LGA    K    73_A      K    73_A     9.266     0    0.616   0.626    10.132    1.071   10.423
LGA    I    74_A      I    74_A    13.284     0    0.159   1.325    19.609    0.000    0.000
LGA    N    75_A      N    75_A    10.604     0    0.177   1.385    14.282    2.381    1.190
LGA    V    76_A      V    76_A     4.486     0    0.611   0.536     6.947   31.190   27.279
LGA    Y    77_A      Y    77_A     5.529     0    0.121   1.411    14.502   22.857    8.095
LGA    P    78_A      P    78_A     7.544     0    0.157   0.324    11.202    7.143   12.653
LGA    S    79_A      S    79_A    13.571     0    0.612   0.941    15.234    0.000    0.000
LGA    A    80_A      A    80_A    18.934     0    0.571   0.571    21.553    0.000    0.000
LGA    M    81_A      M    81_A    21.155     0    0.618   0.952    26.570    0.000    0.000
LGA    S    82_A      S    82_A    21.303     0    0.603   0.738    21.584    0.000    0.000
LGA    R    83_A      R    83_A    23.087     0    0.554   1.466    25.239    0.000    0.000
LGA    D    84_A      D    84_A    29.896     0    0.573   0.464    36.750    0.000    0.000
LGA    M    85_A      M    85_A    31.993     0    0.670   1.139    33.400    0.000    0.000
LGA    S    86_A      S    86_A    31.582     0    0.041   0.691    31.748    0.000    0.000
LGA    D    87_A      D    87_A    30.922     0    0.119   0.143    34.904    0.000    0.000
LGA    G    88_A      G    88_A    26.553     0    0.701   0.701    28.124    0.000    0.000
LGA    I    89_A      I    89_A    20.724     0    0.612   1.008    23.202    0.000    0.000
LGA    V    90_A      V    90_A    20.021     0    0.064   1.063    23.732    0.000    0.000
LGA    A    91_A      A    91_A    17.411     0    0.134   0.192    18.703    0.000    0.000
LGA    Y    92_A      Y    92_A    20.480     0    0.019   1.211    27.385    0.000    0.000
LGA    E    93_A      E    93_A    20.824     0    0.640   1.111    24.796    0.000    0.000
LGA    T    94_A      T    94_A    27.519     0    0.086   1.105    29.372    0.000    0.000
LGA    T    95_A      T    95_A    33.479     0    0.121   0.118    36.426    0.000    0.000
LGA    L    96_A      L    96_A    39.778     0    0.051   1.406    42.664    0.000    0.000
LGA    G    97_A      G    97_A    45.363     0    0.029   0.029    47.031    0.000    0.000
LGA    Q    98_A      Q    98_A    42.927     0    0.203   0.841    43.634    0.000    0.000
LGA    P    99_A      P    99_A    43.546     0    0.568   0.792    47.783    0.000    0.000
LGA    G   100_A      G   100_A    39.673     0    0.573   0.573    41.002    0.000    0.000
LGA    L   101_A      L   101_A    37.513     0    0.595   0.582    38.973    0.000    0.000
LGA    P   102_A      P   102_A    36.752     0    0.085   0.079    39.840    0.000    0.000
LGA    E   103_A      E   103_A    39.080     0    0.079   1.039    46.856    0.000    0.000
LGA    N   104_A      N   104_A    33.555     0    0.138   1.130    37.314    0.000    0.000
LGA    Q   105_A      Q   105_A    28.201     0    0.573   0.564    30.644    0.000    0.000
LGA    V   106_A      V   106_A    27.344     0    0.609   1.127    30.518    0.000    0.000
LGA    H   107_A      H   107_A    24.601     0    0.640   0.857    27.383    0.000    0.000
LGA    I   108_A      I   108_A    17.667     0    0.105   1.518    19.986    0.000    0.000
LGA    F   109_A      F   109_A    16.258     0    0.023   1.284    18.791    0.000    0.000
LGA    D   110_A      D   110_A    23.351     0    0.647   1.112    26.303    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     443    443  100.00               132
SUMMARY(RMSD_GDC):    13.293         13.226                 14.066           10.374    9.205

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57  132    4.0     19    2.24    12.500    11.570     0.812

LGA_LOCAL      RMSD:   2.241  Number of atoms:   19  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  22.444  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  13.293  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.141114 * X  +   0.771742 * Y  +   0.620082 * Z  + -123.979454
  Y_new =  -0.967461 * X  +  -0.025371 * Y  +   0.251745 * Z  +  75.481186
  Z_new =   0.210014 * X  +  -0.635430 * Y  +   0.743050 * Z  +  39.908798 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.425957 -0.211589 -0.707485   [DEG:  -81.7013  -12.1232  -40.5359 ]
ZXZ:  1.956453  0.733180  2.822388   [DEG:  112.0965   42.0081  161.7109 ]
 
# END of job
