
#######################################################
#                                                     #
#                        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 (  433),  selected   57 , name one
# Molecule2: number of CA atoms  175 ( 1323),  selected   57 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:D  -ch2:A  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      30_A - 49_A        4.71    19.53
  LONGEST_CONTINUOUS_SEGMENT:    20      31_A - 50_A        4.84    19.05
  LCS_AVERAGE:      9.94

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    13      67_A - 79_A        1.81    21.15
  LCS_AVERAGE:      4.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    11      69_A - 79_A        0.79    22.54
  LCS_AVERAGE:      3.24

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     D    23_D     D    23_A      6    8   15      2    4    6    7    7    8    8    8    9   11   13   13   14   14   14   15   15   15   15   15 
LCS_GDT     T    24_D     T    24_A      6    8   15      3    5    6    7    7    8    9   10   12   13   13   13   14   14   14   15   15   15   15   16 
LCS_GDT     R    25_D     R    25_A      6    8   15      3    5    6    7    7    8    9   10   12   13   13   13   14   14   14   15   15   15   15   15 
LCS_GDT     I    26_D     I    26_A      6    8   15      3    5    6    7    7    8    9   10   12   13   13   13   14   14   14   16   16   18   22   23 
LCS_GDT     P    27_D     P    27_A      6    8   15      3    5    6    7    7    8    9    9   11   13   13   13   14   14   16   20   22   22   24   24 
LCS_GDT     A    28_D     A    28_A      6    8   15      4    5    6    7    7    8    9   10   12   13   13   13   14   18   20   21   22   23   24   24 
LCS_GDT     G    29_D     G    29_A      5    8   17      4    4    5    7    7    8    9   10   12   13   13   13   14   19   20   21   22   23   24   24 
LCS_GDT     E    30_D     E    30_A      5    8   20      4    4    5    6    7    8    9   10   12   14   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     A    31_D     A    31_A      6    7   20      4    5    6    6    7    8    9   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     T    32_D     T    32_A      6    7   20      4    5    6    6    7    7    8   10   12   14   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     A    33_D     A    33_A      6    7   20      4    5    6    6    7    7    8    9   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     A    34_D     A    34_A      6    7   20      4    5    6    6    7    8    9   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     W    35_D     W    35_A      6    7   20      3    5    6    6    7    8    9   10   12   13   16   17   18   19   20   20   21   23   24   24 
LCS_GDT     Q    36_D     Q    36_A      6    7   20      3    5    6    6    7    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     W    37_D     W    37_A      5    7   20      3    5    5    6    7    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     E    38_D     E    38_A      5    7   20      3    5    5    6    7    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     V    39_D     V    39_A      5    7   20      3    5    5    6    7    7   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     S    40_D     S    40_A      5    7   20      1    4    5    6    7    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     R    41_D     R    41_A      4    7   20      3    4    5    6    7    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     D    42_D     D    42_A      4    5   20      3    4    4    4    4    8   10   10   12   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     T    43_D     T    43_A      4    5   20      3    4    5    5    6    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     G    44_D     G    44_A      4    5   20      2    4    5    5    6    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     E    45_D     E    45_A      4    5   20      3    4    4    5    5    6    7    9   10   13   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     V    46_D     V    46_A      4    5   20      3    4    4    5    5    6    6    7   10   12   13   17   18   19   20   21   22   23   24   24 
LCS_GDT     H    47_D     H    47_A      4    5   20      3    4    4    5    5    6    6    8   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     A    48_D     A    48_A      4    5   20      3    4    4    5    6    8   10   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     M    49_D     M    49_A      3    5   20      0    3    4    5    6    7    8   10   14   15   16   17   18   19   20   21   22   23   24   24 
LCS_GDT     L    50_D     L    50_A      3    3   20      2    3    4    4    6    7   10   12   12   13   16   18   18   19   20   20   21   23   24   24 
LCS_GDT     C    51_D     C    51_A      3    3   15      0    3    4    5    6    6    7    9   10   12   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     A    52_D     A    52_A      3    4   15      0    3    4    5    5    6    7    9   10   12   14   17   18   19   20   20   21   21   22   23 
LCS_GDT     C    53_D     C    53_A      3    5   15      3    3    4    5    5    6    7    9    9   11   14   15   17   17   19   20   21   21   22   23 
LCS_GDT     D    54_D     D    54_A      4    5   15      3    3    4    4    5    5    6    7    9   10   10   12   12   17   18   19   19   21   21   23 
LCS_GDT     A    55_D     A    55_A      4    5   15      3    3    4    4    5    5    5    7    9   11   11   14   15   17   18   19   19   21   22   23 
LCS_GDT     H    56_D     H    56_A      4    5   15      3    3    4    5    5    6    7    9   10   12   14   15   17   17   18   19   19   21   22   23 
LCS_GDT     Q    57_D     Q    57_A      4    5   15      3    3    4    4    5    5    6    7   10   12   14   15   17   17   18   19   19   21   22   23 
LCS_GDT     A    58_D     A    58_A      3    4   15      3    3    3    4    4    5    7    9   10   12   14   15   17   17   18   19   19   21   21   22 
LCS_GDT     A    59_D     A    59_A      3    4   14      3    3    3    3    4    5    7    8    9   12   14   15   17   17   18   18   19   21   21   22 
LCS_GDT     A    60_D     A    60_A      3    6   14      3    3    3    5    5    6    7    8    9   10   11   13   14   14   18   18   19   19   20   21 
LCS_GDT     S    61_D     S    61_A      3    6   14      3    3    3    5    5    6    7    8    9   10   11   13   14   14   14   15   16   19   19   23 
LCS_GDT     G    62_D     G    62_A      3    6   14      3    3    3    4    4    6    7    8    9   10   11   13   14   14   14   15   16   19   20   23 
LCS_GDT     T    63_D     T    63_A      4    6   17      4    4    4    5    5    6    7    8   10   11   16   18   18   19   20   20   21   21   21   23 
LCS_GDT     S    64_D     S    64_A      4    6   17      4    4    4    5    5    6    7    8   14   15   16   18   18   19   20   20   21   21   21   24 
LCS_GDT     A    65_D     A    65_A      4    6   17      4    4    4    5    6    6   10   12   14   15   16   18   18   19   20   20   21   21   21   24 
LCS_GDT     P    66_D     P    66_A      4    4   17      4    4    4    4    6    6   10   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     A    67_D     A    67_A      3   13   17      3    3    3    6   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     R    68_D     R    68_A      3   13   17      3    3    4   10   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     R    69_D     R    69_A     11   13   17      4    6   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     M    70_D     M    70_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     E    71_D     E    71_A     11   13   17      4   10   11   11   11   12   13   14   14   15   16   16   18   19   20   20   21   21   22   24 
LCS_GDT     T    72_D     T    72_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     T    73_D     T    73_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     E    74_D     E    74_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     H    75_D     H    75_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     R    76_D     R    76_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     V    77_D     V    77_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     R    78_D     R    78_A     11   13   17      5   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_GDT     S    79_D     S    79_A     11   13   17      6   10   11   11   11   12   13   14   14   15   16   18   18   19   20   20   21   21   22   24 
LCS_AVERAGE  LCS_A:   5.84  (   3.24    4.34    9.94 )

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      6     10     11     11     11     12     13     14     14     15     16     18     18     19     20     21     22     23     24     24 
GDT PERCENT_AT   3.43   5.71   6.29   6.29   6.29   6.86   7.43   8.00   8.00   8.57   9.14  10.29  10.29  10.86  11.43  12.00  12.57  13.14  13.71  13.71
GDT RMS_LOCAL    0.27   0.57   0.79   0.79   0.79   1.36   1.81   2.19   2.19   2.57   3.04   4.26   4.24   4.43   4.71   5.26   5.66   5.76   6.10   6.10
GDT RMS_ALL_AT  21.91  21.94  22.54  22.54  22.54  21.46  21.15  21.50  21.50  21.10  20.75  22.73  19.28  19.41  19.53  19.77  19.83  19.26  19.31  19.31

# Checking swapping
#   possible swapping detected:  D    23_D      D    23_A
#   possible swapping detected:  E    38_D      E    38_A
#   possible swapping detected:  D    42_D      D    42_A
#   possible swapping detected:  E    45_D      E    45_A
#   possible swapping detected:  D    54_D      D    54_A
#   possible swapping detected:  E    71_D      E    71_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D    23_D      D    23_A    46.690     0    0.545   1.049    48.886    0.000    0.000
LGA    T    24_D      T    24_A    41.336     0    0.203   1.088    43.249    0.000    0.000
LGA    R    25_D      R    25_A    37.662     0    0.270   1.638    43.334    0.000    0.000
LGA    I    26_D      I    26_A    34.999     0    0.032   0.585    38.820    0.000    0.000
LGA    P    27_D      P    27_A    31.061     0    0.662   0.828    32.484    0.000    0.000
LGA    A    28_D      A    28_A    31.020     0    0.093   0.141    31.933    0.000    0.000
LGA    G    29_D      G    29_A    32.076     0    0.129   0.129    32.076    0.000    0.000
LGA    E    30_D      E    30_A    29.006     0    0.628   1.119    32.579    0.000    0.000
LGA    A    31_D      A    31_A    28.985     0    0.595   0.590    30.228    0.000    0.000
LGA    T    32_D      T    32_A    28.307     0    0.087   1.199    31.861    0.000    0.000
LGA    A    33_D      A    33_A    25.184     0    0.109   0.108    26.893    0.000    0.000
LGA    A    34_D      A    34_A    19.902     0    0.596   0.539    22.364    0.000    0.000
LGA    W    35_D      W    35_A    15.533     0    0.415   1.129    19.104    0.000    0.000
LGA    Q    36_D      Q    36_A    14.583     0    0.121   1.474    20.856    0.000    0.000
LGA    W    37_D      W    37_A    15.049     0    0.247   1.197    17.426    0.000    0.034
LGA    E    38_D      E    38_A    15.316     0    0.077   0.661    15.404    0.000    0.000
LGA    V    39_D      V    39_A    17.062     0    0.131   1.064    19.430    0.000    0.000
LGA    S    40_D      S    40_A    14.862     0    0.569   0.768    16.965    0.000    0.000
LGA    R    41_D      R    41_A    20.339     0    0.607   1.389    26.997    0.000    0.000
LGA    D    42_D      D    42_A    22.632     0    0.100   1.004    26.385    0.000    0.000
LGA    T    43_D      T    43_A    22.230     0    0.623   1.454    22.688    0.000    0.000
LGA    G    44_D      G    44_A    25.705     0    0.630   0.630    26.279    0.000    0.000
LGA    E    45_D      E    45_A    28.679     0    0.532   1.059    36.344    0.000    0.000
LGA    V    46_D      V    46_A    26.706     0    0.559   0.980    29.114    0.000    0.000
LGA    H    47_D      H    47_A    24.270     0    0.385   1.342    24.994    0.000    0.000
LGA    A    48_D      A    48_A    23.514     0    0.625   0.604    25.087    0.000    0.000
LGA    M    49_D      M    49_A    21.088     0    0.597   1.559    22.511    0.000    0.000
LGA    L    50_D      L    50_A    15.637     0    0.527   1.524    17.452    0.000    0.000
LGA    C    51_D      C    51_A    14.938     0    0.605   0.581    18.217    0.000    0.000
LGA    A    52_D      A    52_A    20.099     0    0.621   0.610    22.184    0.000    0.000
LGA    C    53_D      C    53_A    17.457     0    0.577   1.112    19.714    0.000    0.000
LGA    D    54_D      D    54_A    19.687     0    0.569   1.431    23.589    0.000    0.000
LGA    A    55_D      A    55_A    26.229     0    0.228   0.248    28.655    0.000    0.000
LGA    H    56_D      H    56_A    26.470     0    0.608   1.217    31.067    0.000    0.000
LGA    Q    57_D      Q    57_A    23.522     0    0.620   1.141    25.840    0.000    0.000
LGA    A    58_D      A    58_A    23.212     0    0.656   0.629    23.874    0.000    0.000
LGA    A    59_D      A    59_A    25.709     0    0.601   0.577    27.942    0.000    0.000
LGA    A    60_D      A    60_A    25.341     0    0.734   0.677    25.341    0.000    0.000
LGA    S    61_D      S    61_A    23.628     0    0.593   0.822    24.225    0.000    0.000
LGA    G    62_D      G    62_A    20.253     0    0.628   0.628    21.358    0.000    0.000
LGA    T    63_D      T    63_A    14.593     0    0.594   0.529    16.685    0.000    0.000
LGA    S    64_D      S    64_A     8.941     0    0.072   0.740    10.914    2.619    6.270
LGA    A    65_D      A    65_A     6.294     0    0.604   0.608     7.146   16.667   17.619
LGA    P    66_D      P    66_A     4.252     0    0.561   0.568     5.374   40.238   35.782
LGA    A    67_D      A    67_A     3.093     0    0.583   0.561     3.820   50.119   51.524
LGA    R    68_D      R    68_A     3.295     0    0.614   1.302     6.559   50.357   31.299
LGA    R    69_D      R    69_A     3.736     0    0.576   1.075    14.790   61.548   24.978
LGA    M    70_D      M    70_A     2.242     0    0.153   0.984     4.912   64.881   59.762
LGA    E    71_D      E    71_A     2.219     0    0.060   1.466     3.091   68.810   66.772
LGA    T    72_D      T    72_A     0.908     0    0.032   0.160     1.500   88.214   85.374
LGA    T    73_D      T    73_A     0.991     0    0.075   1.112     3.315   92.857   83.537
LGA    E    74_D      E    74_A     1.129     0    0.044   0.778     1.788   85.952   84.497
LGA    H    75_D      H    75_A     0.687     0    0.023   1.129     3.766   88.214   79.286
LGA    R    76_D      R    76_A     0.589     0    0.029   1.076     8.071   92.857   61.169
LGA    V    77_D      V    77_A     0.502     0    0.057   0.125     1.098   95.238   93.265
LGA    R    78_D      R    78_A     0.400     0    0.079   1.391     6.841   97.619   69.048
LGA    S    79_D      S    79_A     0.545     0    0.338   0.323     1.380   88.214   90.556

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     428    428  100.00               175
SUMMARY(RMSD_GDC):    15.323         15.118                 15.792            6.197    5.376

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   58  175    4.0     14    2.19     8.000     7.013     0.612

LGA_LOCAL      RMSD:   2.188  Number of atoms:   14  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  21.499  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  15.323  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.162886 * X  +  -0.850509 * Y  +   0.500103 * Z  +   0.183836
  Y_new =   0.566887 * X  +   0.495530 * Y  +   0.658095 * Z  + -18.594727
  Z_new =  -0.807531 * X  +   0.176308 * Y  +   0.562858 * Z  +  49.602112 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.291000  0.939955  0.303556   [DEG:   73.9688   53.8554   17.3925 ]
ZXZ:  2.491770  0.972957 -1.355840   [DEG:  142.7679   55.7463  -77.6839 ]
 
# END of job
