
#######################################################
#                                                     #
#                        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   61 (  460),  selected   60 , name one
# Molecule2: number of CA atoms   60 (  451),  selected   60 , 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:    60       1_A - 60_A        3.68     3.68
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22       1_A - 22_A        1.87     4.27
  LONGEST_CONTINUOUS_SEGMENT:    22       2_A - 23_A        1.90     4.01
  LONGEST_CONTINUOUS_SEGMENT:    22      12_A - 33_A        1.99     6.40
  LCS_AVERAGE:     33.44

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18       5_A - 22_A        1.00     4.27
  LCS_AVERAGE:     24.39

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     1_A     D     1_A      7   22   60      3    4    7    8   24   29   30   38   40   40   52   53   55   59   59   60   60   60   60   60 
LCS_GDT     D     2_A     D     2_A     12   22   60      6   14   24   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K     3_A     K     3_A     13   22   60      6   15   24   32   34   35   38   45   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A     4_A     A     4_A     17   22   60      6   16   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A     5_A     A     5_A     18   22   60      6    9   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     C     6_A     C     6_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A     7_A     A     7_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     D     8_A     D     8_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     G     9_A     G     9_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     I    10_A     I    10_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    11_A     A    11_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    12_A     A    12_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     V    13_A     V    13_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K    14_A     K    14_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    15_A     A    15_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     R    16_A     R    16_A     18   22   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     V    17_A     V    17_A     18   22   60      9   17   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     E    18_A     E    18_A     18   22   60      9   17   25   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K    19_A     K    19_A     18   22   60      9   17   25   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     L    20_A     L    20_A     18   22   60      8   17   24   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    21_A     A    21_A     18   22   60      3   14   20   26   31   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     P    22_A     P    22_A     18   22   60      3    8   17   22   31   34   38   43   48   53   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     E    23_A     E    23_A      4   22   60      3    4    4    5   20   30   35   43   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    24_A     A    24_A      4   22   60      3    4    4    5    5   12   25   37   41   49   54   57   59   59   59   60   60   60   60   60 
LCS_GDT     V    25_A     V    25_A      4   22   60      3    4    4   11   21   29   36   43   48   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     P    26_A     P    26_A     14   22   60      3   10   14   15   15   24   31   45   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     Q    27_A     Q    27_A     14   22   60     11   13   14   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K    28_A     K    28_A     14   22   60      9   13   14   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     L    29_A     L    29_A     14   22   60     11   13   15   22   29   33   41   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K    30_A     K    30_A     14   22   60     11   13   17   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     R    31_A     R    31_A     14   22   60     11   13   17   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    32_A     A    32_A     14   22   60     11   13   17   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     L    33_A     L    33_A     14   22   60     11   13   16   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K    34_A     K    34_A     14   17   60     11   13   17   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     I    35_A     I    35_A     14   17   60     11   13   17   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    36_A     A    36_A     14   17   60     11   13   17   23   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     E    37_A     E    37_A     14   17   60     11   13   14   18   29   33   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     R    38_A     R    38_A     14   17   60     11   13   14   21   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     E    39_A     E    39_A     14   17   60     10   13   15   22   29   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     Q    40_A     Q    40_A      4   17   60      3    3    4    5   11   16   26   30   44   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     G    41_A     G    41_A      4   17   60      3    3    4    7   10   16   25   28   34   44   53   56   59   59   59   60   60   60   60   60 
LCS_GDT     E    42_A     E    42_A      4   18   60      3    3    4    5   11   24   30   44   49   53   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     G    43_A     G    43_A     13   18   60      3    9   12   17   21   25   34   38   40   40   51   56   59   59   59   60   60   60   60   60 
LCS_GDT     E    44_A     E    44_A     16   18   60      3    9   13   18   25   35   38   44   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     F    45_A     F    45_A     16   18   60      4   14   17   22   34   35   39   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     D    46_A     D    46_A     16   18   60      3   14   17   21   34   35   39   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     E    47_A     E    47_A     16   18   60      7   14   24   32   34   35   40   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     C    48_A     C    48_A     16   18   60      7   16   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     L    49_A     L    49_A     16   18   60      7   16   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     E    50_A     E    50_A     16   18   60      7   16   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    51_A     A    51_A     16   18   60      7   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     L    52_A     L    52_A     16   18   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     D    53_A     D    53_A     16   18   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     D    54_A     D    54_A     16   18   60      7   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    55_A     A    55_A     16   18   60      5   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     K    56_A     K    56_A     16   18   60      9   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     R    57_A     R    57_A     16   18   60     11   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     A    58_A     A    58_A     16   18   60     11   19   26   32   34   35   39   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     L    59_A     L    59_A     16   18   60      3   19   26   32   34   35   42   47   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_GDT     P    60_A     P    60_A     16   18   60      0    3    3    3   30   35   38   38   49   54   56   57   59   59   59   60   60   60   60   60 
LCS_AVERAGE  LCS_A:  52.61  (  24.39   33.44  100.00 )

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     19     26     32     34     35     42     47     49     54     56     57     59     59     59     60     60     60     60     60 
GDT PERCENT_AT  18.33  31.67  43.33  53.33  56.67  58.33  70.00  78.33  81.67  90.00  93.33  95.00  98.33  98.33  98.33 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.29   0.64   0.95   1.22   1.39   1.47   2.38   2.66   2.78   3.12   3.25   3.35   3.57   3.57   3.57   3.68   3.68   3.68   3.68   3.68
GDT RMS_ALL_AT   4.17   4.47   4.66   4.59   4.65   4.69   3.95   3.84   3.82   3.74   3.71   3.71   3.69   3.69   3.69   3.68   3.68   3.68   3.68   3.68

# Checking swapping
#   possible swapping detected:  D     1_A      D     1_A
#   possible swapping detected:  E    18_A      E    18_A
#   possible swapping detected:  E    23_A      E    23_A
#   possible swapping detected:  E    42_A      E    42_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_A      D     1_A     8.357     0    0.512   1.262     8.542    7.024    6.488
LGA    D     2_A      D     2_A     3.434     0    0.130   0.262     4.950   49.048   52.202
LGA    K     3_A      K     3_A     4.537     0    0.057   0.714     8.059   40.476   24.974
LGA    A     4_A      A     4_A     3.984     0    0.044   0.045     4.773   48.810   45.333
LGA    A     5_A      A     5_A     2.224     0    0.063   0.061     2.809   71.190   69.905
LGA    C     6_A      C     6_A     1.203     0    0.059   0.126     3.247   79.286   71.984
LGA    A     7_A      A     7_A     1.736     0    0.044   0.054     2.096   77.143   74.667
LGA    D     8_A      D     8_A     1.099     0    0.050   1.011     4.058   85.952   72.083
LGA    G     9_A      G     9_A     0.927     0    0.049   0.049     1.238   85.952   85.952
LGA    I    10_A      I    10_A     1.361     0    0.031   0.629     3.800   81.429   73.512
LGA    A    11_A      A    11_A     1.146     0    0.044   0.049     1.208   81.429   81.429
LGA    A    12_A      A    12_A     0.942     0    0.042   0.047     0.994   90.476   90.476
LGA    V    13_A      V    13_A     0.659     0    0.080   0.136     0.810   90.476   93.197
LGA    K    14_A      K    14_A     1.057     0    0.060   0.972     4.400   81.429   71.958
LGA    A    15_A      A    15_A     1.436     0    0.072   0.071     1.688   81.429   79.714
LGA    R    16_A      R    16_A     1.207     0    0.046   0.559     5.099   81.429   61.732
LGA    V    17_A      V    17_A     1.680     0    0.043   0.072     2.338   72.976   71.769
LGA    E    18_A      E    18_A     2.097     0    0.089   0.665     2.741   64.881   64.021
LGA    K    19_A      K    19_A     1.400     0    0.163   0.834     3.025   79.286   74.286
LGA    L    20_A      L    20_A     1.902     0    0.039   0.779     2.910   66.905   63.929
LGA    A    21_A      A    21_A     2.303     0    0.629   0.609     2.689   64.881   66.476
LGA    P    22_A      P    22_A     5.411     0    0.589   0.533     9.262   32.976   21.156
LGA    E    23_A      E    23_A     5.329     0    0.078   1.287     8.246   23.095   16.085
LGA    A    24_A      A    24_A     7.129     0    0.276   0.276     8.537   12.619   10.667
LGA    V    25_A      V    25_A     5.356     0    0.597   0.586     7.684   24.048   20.272
LGA    P    26_A      P    26_A     4.813     0    0.663   0.706     5.909   38.929   38.299
LGA    Q    27_A      Q    27_A     3.065     0    0.077   0.970     3.609   48.333   59.524
LGA    K    28_A      K    28_A     3.499     0    0.065   1.065     4.428   46.667   46.349
LGA    L    29_A      L    29_A     3.634     0    0.061   0.981     3.685   43.333   54.405
LGA    K    30_A      K    30_A     3.269     0    0.043   1.002     7.993   50.000   34.127
LGA    R    31_A      R    31_A     3.122     0    0.034   1.408     8.040   50.000   33.896
LGA    A    32_A      A    32_A     3.183     0    0.049   0.048     3.394   50.000   50.000
LGA    L    33_A      L    33_A     3.407     0    0.040   1.167     5.484   50.000   42.381
LGA    K    34_A      K    34_A     3.141     0    0.038   0.837     3.225   53.571   67.619
LGA    I    35_A      I    35_A     2.789     0    0.033   1.369     7.133   57.143   48.036
LGA    A    36_A      A    36_A     3.172     0    0.046   0.064     3.507   50.000   48.667
LGA    E    37_A      E    37_A     3.457     0    0.055   1.344     9.660   50.000   30.529
LGA    R    38_A      R    38_A     2.868     0    0.089   1.191     6.631   55.357   46.580
LGA    E    39_A      E    39_A     2.310     0    0.595   1.293     8.359   60.952   40.053
LGA    Q    40_A      Q    40_A     6.195     0    0.641   1.331    10.023   17.500    8.571
LGA    G    41_A      G    41_A     8.869     0    0.528   0.528     8.869    5.476    5.476
LGA    E    42_A      E    42_A     7.000     0    0.574   1.271    11.089   17.976    8.836
LGA    G    43_A      G    43_A     8.273     0    0.708   0.708     8.273    8.810    8.810
LGA    E    44_A      E    44_A     5.980     0    0.202   0.961     8.754   23.095   15.185
LGA    F    45_A      F    45_A     4.579     0    0.069   1.395     8.710   32.976   22.424
LGA    D    46_A      D    46_A     4.337     0    0.055   0.882     5.171   37.262   35.119
LGA    E    47_A      E    47_A     3.959     0    0.086   0.749     7.004   45.119   34.180
LGA    C    48_A      C    48_A     2.909     0    0.065   0.129     3.339   59.167   58.492
LGA    L    49_A      L    49_A     1.890     0    0.085   1.426     4.778   70.833   58.274
LGA    E    50_A      E    50_A     2.373     0    0.054   0.323     5.146   64.762   51.058
LGA    A    51_A      A    51_A     2.235     0    0.038   0.040     2.317   68.810   68.000
LGA    L    52_A      L    52_A     1.171     0    0.048   0.884     3.967   79.286   73.571
LGA    D    53_A      D    53_A     1.331     0    0.023   0.850     2.877   77.143   72.143
LGA    D    54_A      D    54_A     2.576     0    0.045   0.174     3.066   57.262   57.202
LGA    A    55_A      A    55_A     2.969     0    0.031   0.048     3.332   55.357   55.714
LGA    K    56_A      K    56_A     2.429     0    0.052   1.085     4.663   59.167   52.963
LGA    R    57_A      R    57_A     3.346     0    0.119   1.045     4.507   46.905   46.623
LGA    A    58_A      A    58_A     3.839     0    0.159   0.157     4.645   40.357   40.952
LGA    L    59_A      L    59_A     2.772     0    0.574   1.159     4.337   51.905   51.190
LGA    P    60_A      P    60_A     5.527     0    0.657   0.662     9.325   32.024   20.612

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     451    451  100.00                60
SUMMARY(RMSD_GDC):     3.681          3.567                  4.245           53.835   49.169

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   61   60    4.0     47    2.66    65.833    60.313     1.702

LGA_LOCAL      RMSD:   2.661  Number of atoms:   47  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   3.839  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:   3.681  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.230948 * X  +  -0.820851 * Y  +  -0.522366 * Z  +  34.098026
  Y_new =   0.876927 * X  +  -0.408192 * Y  +   0.253730 * Z  +   4.887744
  Z_new =  -0.421500 * X  +  -0.399478 * Y  +   0.814097 * Z  +  13.594100 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  1.828310  0.435099 -0.456181   [DEG:  104.7544   24.9293  -26.1372 ]
ZXZ: -2.022965  0.619623 -2.329377   [DEG: -115.9073   35.5018 -133.4635 ]
 
# END of job
