
#######################################################
#                                                     #
#                        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   44 (  354),  selected   44 , name one
# Molecule2: number of CA atoms  132 ( 1073),  selected   44 , 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:    32      37_A - 68_A        4.72    16.16
  LONGEST_CONTINUOUS_SEGMENT:    32      38_A - 69_A        4.87    15.80
  LCS_AVERAGE:     21.97

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      47_A - 64_A        1.97    18.51
  LONGEST_CONTINUOUS_SEGMENT:    18      48_A - 65_A        1.95    18.12
  LONGEST_CONTINUOUS_SEGMENT:    18      49_A - 66_A        1.51    17.55
  LCS_AVERAGE:      8.97

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      49_A - 63_A        0.98    18.47
  LONGEST_CONTINUOUS_SEGMENT:    15      50_A - 64_A        0.89    18.31
  LCS_AVERAGE:      6.40

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   44
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     F    37_A     F    37_A      3    4   32      0    3    3    4    4    4    5    5    7   11   13   13   22   27   29   32   33   34   34   35 
LCS_GDT     H    38_A     H    38_A      3    4   32      0    3    3    4    4    4    7   11   12   12   25   25   25   30   31   32   33   34   34   35 
LCS_GDT     N    39_A     N    39_A      3    5   32      1    3    3    5    7    8   12   22   24   25   26   28   28   30   31   32   33   34   34   35 
LCS_GDT     N    40_A     N    40_A      3    5   32      0    3    3    5    7    8   10   17   18   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     N    41_A     N    41_A      3    7   32      3    3    4    5    7    9   10   17   18   21   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     Q    42_A     Q    42_A      3    7   32      3    3    3    5    7    9   10   14   18   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     L    43_A     L    43_A      6    9   32      3    4    6    6   12   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     A    44_A     A    44_A      6   10   32      3    5    6    7   11   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     E    45_A     E    45_A      6   12   32      3    5    6    9   13   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     S    46_A     S    46_A      6   12   32      3    5    6    8   12   18   21   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     N    47_A     N    47_A      6   18   32      3    5    6    9   16   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     D    48_A     D    48_A      6   18   32      3    5    6    6    8   13   15   17   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     T    49_A     T    49_A     15   18   32      3    4    9   15   16   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     D    50_A     D    50_A     15   18   32      4   13   14   15   17   19   22   23   24   25   27   28   28   29   31   32   33   34   34   35 
LCS_GDT     Y    51_A     Y    51_A     15   18   32      4   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     F    52_A     F    52_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     S    53_A     S    53_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     C    54_A     C    54_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     F    55_A     F    55_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     A    56_A     A    56_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     D    57_A     D    57_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     L    58_A     L    58_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     R    59_A     R    59_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     N    60_A     N    60_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     Q    61_A     Q    61_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     L    62_A     L    62_A     15   18   32     11   13   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     K    63_A     K    63_A     15   18   32      3   12   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     N    64_A     N    64_A     15   18   32      3    6   14   15   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     I    65_A     I    65_A      7   18   32      3    6    8   13   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     I    66_A     I    66_A      7   18   32      3    6    8   13   17   19   22   23   24   25   27   28   28   30   31   32   33   34   34   35 
LCS_GDT     F    67_A     F    67_A      3    4   32      3    3    3    3    5    7   10   12   12   15   19   24   28   30   31   32   33   34   34   35 
LCS_GDT     L    68_A     L    68_A      3    6   32      3    3    3    4    6    8    9   11   13   15   19   24   25   30   31   32   33   34   34   35 
LCS_GDT     C    69_A     C    69_A      6    7   32      5    5    6    6    7    9   10   12   13   15   19   23   25   27   31   32   33   34   34   35 
LCS_GDT     K    70_A     K    70_A      6    7   20      5    5    6    6    7    9   10   12   13   15   19   19   24   26   28   29   33   34   34   35 
LCS_GDT     G    71_A     G    71_A      6    7   20      5    5    6    6    7    9   10   12   13   14   15   16   17   21   23   24   25   27   30   32 
LCS_GDT     A    72_A     A    72_A      6    7   20      5    5    6    6    7    9   10   12   13   14   15   16   20   21   23   24   25   29   30   32 
LCS_GDT     K    73_A     K    73_A      6    7   20      5    5    6    6    7    9   10   12   13   14   17   18   20   21   25   29   29   31   34   35 
LCS_GDT     I    74_A     I    74_A      6    7   20      3    3    6    6    7    9   10   12   13   14   15   16   17   19   23   24   25   27   28   32 
LCS_GDT     N    75_A     N    75_A      3    7   20      3    3    3    5    7    9   10   12   13   14   15   16   17   19   20   24   25   25   27   28 
LCS_GDT     V    76_A     V    76_A      4    6   20      3    4    4    5    7    9   10   12   13   14   15   16   17   18   19   19   21   23   26   26 
LCS_GDT     Y    77_A     Y    77_A      4    6   20      3    4    4    4    6    8   10   12   13   14   15   16   17   18   19   19   20   21   23   23 
LCS_GDT     P    78_A     P    78_A      4    6   20      3    4    4    5    7    9   10   12   13   14   15   16   17   18   19   19   20   21   21   22 
LCS_GDT     S    79_A     S    79_A      4    6   20      3    4    4    5    7    9   10   12   13   14   15   16   17   18   19   19   20   21   21   22 
LCS_GDT     A    80_A     A    80_A      3    3   20      0    3    3    3    3    4    4    4   12   14   15   16   17   18   19   19   20   21   21   22 
LCS_AVERAGE  LCS_A:  12.45  (   6.40    8.97   21.97 )

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     11     13     14     15     17     19     22     23     24     25     27     28     28     30     31     32     33     34     34     35 
GDT PERCENT_AT   8.33   9.85  10.61  11.36  12.88  14.39  16.67  17.42  18.18  18.94  20.45  21.21  21.21  22.73  23.48  24.24  25.00  25.76  25.76  26.52
GDT RMS_LOCAL    0.16   0.39   0.61   0.89   1.40   1.77   2.19   2.32   2.52   2.75   3.29   3.44   3.44   4.51   4.52   4.87   5.04   5.43   5.43   5.90
GDT RMS_ALL_AT  18.85  18.73  18.56  18.31  17.55  17.58  17.56  17.62  17.68  17.74  17.48  17.32  17.32  16.11  16.25  15.80  15.71  15.20  15.20  14.71

# Checking swapping
#   possible swapping detected:  F    37_A      F    37_A
#   possible swapping detected:  E    45_A      E    45_A
#   possible swapping detected:  D    48_A      D    48_A
#   possible swapping detected:  F    52_A      F    52_A
#   possible swapping detected:  F    67_A      F    67_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    F    37_A      F    37_A    13.083     0    0.658   1.410    16.378    0.000    0.000
LGA    H    38_A      H    38_A    11.813     0    0.652   1.250    12.810    1.905    0.762
LGA    N    39_A      N    39_A     8.991     0    0.497   1.107    13.873    1.786    1.071
LGA    N    40_A      N    40_A     9.369     0    0.648   1.131    11.280    2.262    1.131
LGA    N    41_A      N    41_A     8.905     0    0.657   0.951     9.543    4.048    3.631
LGA    Q    42_A      Q    42_A     6.278     0    0.269   0.907    12.952   24.762   11.958
LGA    L    43_A      L    43_A     3.208     0    0.653   1.306     7.575   50.000   33.869
LGA    A    44_A      A    44_A     3.336     0    0.058   0.080     3.810   50.000   48.667
LGA    E    45_A      E    45_A     3.343     0    0.097   0.489     4.013   45.119   46.349
LGA    S    46_A      S    46_A     4.075     0    0.045   0.089     5.794   43.452   36.905
LGA    N    47_A      N    47_A     2.813     0    0.000   1.255     7.463   44.167   36.131
LGA    D    48_A      D    48_A     5.694     0    0.643   0.967    11.182   33.214   17.202
LGA    T    49_A      T    49_A     1.772     0    0.176   0.164     3.418   73.690   68.912
LGA    D    50_A      D    50_A     2.139     0    0.358   0.725     3.791   70.833   64.167
LGA    Y    51_A      Y    51_A     1.777     0    0.082   0.142     2.065   70.833   72.897
LGA    F    52_A      F    52_A     1.496     0    0.000   0.158     1.779   79.286   75.195
LGA    S    53_A      S    53_A     1.437     0    0.073   0.656     4.061   81.429   72.619
LGA    C    54_A      C    54_A     1.457     0    0.000   0.724     3.875   79.286   72.222
LGA    F    55_A      F    55_A     0.403     0    0.028   0.932     5.871   95.238   66.147
LGA    A    56_A      A    56_A     0.236     0    0.051   0.046     0.680   97.619   98.095
LGA    D    57_A      D    57_A     1.073     0    0.000   0.938     2.760   83.690   78.452
LGA    L    58_A      L    58_A     1.270     0    0.036   0.257     2.763   79.286   76.250
LGA    R    59_A      R    59_A     1.285     0    0.039   0.947     2.734   77.143   72.381
LGA    N    60_A      N    60_A     1.582     0    0.061   0.914     3.797   70.952   63.631
LGA    Q    61_A      Q    61_A     2.262     0    0.051   0.639     2.972   64.881   63.122
LGA    L    62_A      L    62_A     2.526     0    0.265   0.246     4.646   60.952   51.488
LGA    K    63_A      K    63_A     1.747     0    0.642   0.973     6.391   68.929   56.402
LGA    N    64_A      N    64_A     2.712     0    0.152   1.174     7.527   57.143   41.071
LGA    I    65_A      I    65_A     3.021     0    0.562   0.955     5.950   42.976   47.619
LGA    I    66_A      I    66_A     3.309     0    0.610   0.649     6.147   36.429   48.155
LGA    F    67_A      F    67_A    10.486     0    0.598   1.417    16.804    1.786    0.649
LGA    L    68_A      L    68_A    13.860     0    0.499   1.340    16.137    0.000    0.000
LGA    C    69_A      C    69_A    15.046     0    0.620   0.622    16.175    0.000    0.000
LGA    K    70_A      K    70_A    17.828     0    0.048   0.807    20.281    0.000    0.000
LGA    G    71_A      G    71_A    22.506     0    0.115   0.115    23.965    0.000    0.000
LGA    A    72_A      A    72_A    20.656     0    0.000   0.000    21.279    0.000    0.000
LGA    K    73_A      K    73_A    20.635     0    0.638   0.619    24.798    0.000    0.000
LGA    I    74_A      I    74_A    24.949     0    0.624   1.198    27.706    0.000    0.000
LGA    N    75_A      N    75_A    30.994     0    0.591   1.157    33.275    0.000    0.000
LGA    V    76_A      V    76_A    32.928     0    0.060   0.165    35.055    0.000    0.000
LGA    Y    77_A      Y    77_A    39.566     0    0.046   1.111    44.362    0.000    0.000
LGA    P    78_A      P    78_A    43.368     0    0.676   0.651    44.673    0.000    0.000
LGA    S    79_A      S    79_A    47.993     0    0.672   0.918    51.982    0.000    0.000
LGA    A    80_A      A    80_A    47.733     0    0.542   0.559    48.641    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       44     176    176  100.00     354    354  100.00               132
SUMMARY(RMSD_GDC):    11.672         11.586                 12.230           12.069   10.812

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   44  132    4.0     23    2.32    15.720    14.324     0.951

LGA_LOCAL      RMSD:   2.317  Number of atoms:   23  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.616  Number of assigned atoms:   44 
Std_ASGN_ATOMS RMSD:  11.672  Standard rmsd on all 44 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.354531 * X  +   0.688894 * Y  +  -0.632245 * Z  +  76.724648
  Y_new =  -0.606793 * X  +  -0.683955 * Y  +  -0.404978 * Z  + 381.234406
  Z_new =  -0.711414 * X  +   0.240064 * Y  +   0.660499 * Z  + -117.978386 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.099569  0.791508  0.348614   [DEG: -120.2965   45.3501   19.9741 ]
ZXZ: -1.001100  0.849313 -1.245348   [DEG:  -57.3588   48.6621  -71.3532 ]
 
# END of job
