
#######################################################
#                                                     #
#                        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   99 (  793),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  480),  selected   61 , 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:    45      32_A - 76_A        4.66     9.47
  LONGEST_CONTINUOUS_SEGMENT:    45      33_A - 83_A        4.76     9.23
  LCS_AVERAGE:     72.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      56_A - 76_A        1.27     8.91
  LONGEST_CONTINUOUS_SEGMENT:    21      57_A - 83_A        1.86     9.78
  LCS_AVERAGE:     28.86

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        0.63     8.98
  LCS_AVERAGE:     24.67

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   61
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     A    32_A     A    32_A      3    3   45      0    3    3    3    3    4    6    8   11   14   16   20   24   27   29   31   39   40   42   45 
LCS_GDT     T    33_A     T    33_A     12   18   45      5    8   13   17   18   20   25   26   29   34   37   40   42   44   44   44   44   45   45   48 
LCS_GDT     M    34_A     M    34_A     12   18   45      5    8   13   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    35_A     A    35_A     14   18   45      4    9   15   17   18   20   25   26   29   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     D    36_A     D    36_A     14   18   45      5    8   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     L    37_A     L    37_A     14   18   45      5    9   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     K    38_A     K    38_A     14   18   45      5    9   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     M    39_A     M    39_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     Q    40_A     Q    40_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    41_A     A    41_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     V    42_A     V    42_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     K    43_A     K    43_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     E    44_A     E    44_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     I    45_A     I    45_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     C    46_A     C    46_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     Y    47_A     Y    47_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     E    48_A     E    48_A     14   18   45      7   11   15   17   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     V    49_A     V    49_A     14   18   45      4   11   15   17   18   21   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    50_A     A    50_A     13   18   45      3    3   12   16   18   20   25   26   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     L    51_A     L    51_A      5   17   45      3    3    3    8   16   18   21   25   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    52_A     A    52_A      5    7   45      3    5    5    8   16   18   21   25   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     D    53_A     D    53_A      5    7   45      3    5    5    8   16   18   21   25   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     F    54_A     F    54_A      5    7   45      3    5    5    8   16   18   21   25   30   34   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     R    55_A     R    55_A      5    7   45      3    5    5   16   17   17   20   24   28   31   36   39   42   44   44   44   44   45   45   48 
LCS_GDT     H    56_A     H    56_A      3   21   45      3    4    6   11   17   21   23   27   32   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     G    57_A     G    57_A     20   21   45      8   19   20   20   20   21   25   30   33   35   37   40   42   44   44   44   44   45   45   48 
LCS_GDT     R    58_A     R    58_A     20   21   45     13   19   20   20   20   21   25   30   33   35   36   39   42   44   44   44   44   45   45   48 
LCS_GDT     A    59_A     A    59_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     E    60_A     E    60_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     I    61_A     I    61_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     E    62_A     E    62_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    63_A     A    63_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     L    64_A     L    64_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    65_A     A    65_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     A    66_A     A    66_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     L    67_A     L    67_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     K    68_A     K    68_A     20   21   45     11   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     M    69_A     M    69_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     R    70_A     R    70_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     E    71_A     E    71_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     L    72_A     L    72_A     20   21   45     13   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     C    73_A     C    73_A     20   21   45     12   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     R    74_A     R    74_A     20   21   45     12   19   20   20   20   21   25   30   33   35   38   40   42   44   44   44   44   45   45   48 
LCS_GDT     T    75_A     T    75_A     20   21   45     10   19   20   20   20   21   24   28   32   35   36   39   41   44   44   44   44   45   45   48 
LCS_GDT     Y    76_A     Y    76_A     20   21   45      3    7   20   20   20   21   22   25   28   34   37   40   42   44   44   44   44   45   45   48 
LCS_GDT     G    83_A     G    83_A     15   21   45      3    3    4    9   17   18   25   30   33   35   36   37   37   38   39   41   42   43   45   46 
LCS_GDT     D    84_A     D    84_A     15   16   41      3    4   14   16   17   18   23   29   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     A    85_A     A    85_A     15   16   41      3    8   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   43   45   48 
LCS_GDT     W    86_A     W    86_A     15   16   41      5   11   14   16   17   18   25   30   33   35   36   37   37   38   40   41   44   45   45   48 
LCS_GDT     R    87_A     R    87_A     15   16   41      4   10   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     A    88_A     A    88_A     15   16   41      4   11   14   16   17   18   24   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     V    89_A     V    89_A     15   16   41      5   11   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   43   45   48 
LCS_GDT     A    90_A     A    90_A     15   16   41      5   11   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   44   45   48 
LCS_GDT     R    91_A     R    91_A     15   16   41      5   11   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     D    92_A     D    92_A     15   16   41      5   11   14   16   17   18   22   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     V    93_A     V    93_A     15   16   41      5   11   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     W    94_A     W    94_A     15   16   41      5   11   14   16   17   18   25   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     D    95_A     D    95_A     15   16   41      5   11   14   16   17   18   20   25   33   35   36   37   37   38   38   39   42   43   44   45 
LCS_GDT     T    96_A     T    96_A     15   16   41      5   11   14   16   17   18   20   24   29   35   36   37   37   38   38   39   42   43   44   45 
LCS_GDT     V    97_A     V    97_A     15   16   41      5   11   14   16   17   18   23   30   33   35   36   37   37   38   39   41   42   43   44   45 
LCS_GDT     G    98_A     G    98_A     15   16   41      3    3   14   16   17   18   23   30   33   35   36   37   37   38   38   40   42   43   44   45 
LCS_AVERAGE  LCS_A:  41.90  (  24.67   28.86   72.16 )

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     13     19     20     20     20     21     25     30     33     35     38     40     42     44     44     44     44     45     45     48 
GDT PERCENT_AT  21.31  31.15  32.79  32.79  32.79  34.43  40.98  49.18  54.10  57.38  62.30  65.57  68.85  72.13  72.13  72.13  72.13  73.77  73.77  78.69
GDT RMS_LOCAL    0.33   0.48   0.63   0.63   0.63   1.27   2.49   2.98   3.16   3.30   3.83   3.95   4.13   4.31   4.31   4.31   4.31   4.57   4.57   5.36
GDT RMS_ALL_AT   9.00   9.01   8.98   8.98   8.98   8.91   9.43  11.27  11.59  11.46   9.35   9.38   9.31   9.33   9.33   9.33   9.33   9.24   9.24   8.99

# Checking swapping
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  E    44_A      E    44_A
#   possible swapping detected:  E    71_A      E    71_A
#   possible swapping detected:  D    84_A      D    84_A
#   possible swapping detected:  D    92_A      D    92_A
#   possible swapping detected:  D    95_A      D    95_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A    26.949     0    0.359   0.366    27.817    0.000    0.000
LGA    T    33_A      T    33_A    22.045     0    0.606   1.184    24.164    0.000    0.000
LGA    M    34_A      M    34_A    17.329     0    0.066   0.315    19.109    0.000    0.000
LGA    A    35_A      A    35_A    21.169     0    0.105   0.118    23.726    0.000    0.000
LGA    D    36_A      D    36_A    22.743     0    0.107   0.231    27.559    0.000    0.000
LGA    L    37_A      L    37_A    17.223     0    0.155   0.167    19.086    0.000    0.000
LGA    K    38_A      K    38_A    14.823     0    0.238   0.706    17.595    0.000    0.000
LGA    M    39_A      M    39_A    19.361     0    0.600   0.977    25.787    0.000    0.000
LGA    Q    40_A      Q    40_A    20.681     0    0.102   1.129    26.155    0.000    0.000
LGA    A    41_A      A    41_A    14.217     0    0.074   0.075    16.268    0.000    0.000
LGA    V    42_A      V    42_A    13.781     0    0.183   0.192    15.573    0.000    0.000
LGA    K    43_A      K    43_A    19.682     0    0.070   0.149    29.510    0.000    0.000
LGA    E    44_A      E    44_A    18.739     0    0.161   1.046    22.639    0.000    0.000
LGA    I    45_A      I    45_A    12.423     0    0.063   0.142    14.395    0.000    2.262
LGA    C    46_A      C    46_A    14.248     0    0.113   0.138    15.939    0.000    0.000
LGA    Y    47_A      Y    47_A    19.426     0    0.078   1.392    29.325    0.000    0.000
LGA    E    48_A      E    48_A    16.584     0    0.420   0.769    21.019    0.000    0.000
LGA    V    49_A      V    49_A    11.503     0    0.601   0.596    13.719    0.000    0.816
LGA    A    50_A      A    50_A    13.711     0    0.179   0.184    16.691    0.000    0.000
LGA    L    51_A      L    51_A    18.227     0    0.453   0.387    25.577    0.000    0.000
LGA    A    52_A      A    52_A    13.832     0    0.433   0.409    14.619    0.000    0.000
LGA    D    53_A      D    53_A    15.197     0    0.366   0.461    19.856    0.000    0.000
LGA    F    54_A      F    54_A    12.891     0    0.406   1.304    20.296    0.000    0.000
LGA    R    55_A      R    55_A    10.213     0    0.150   0.998    11.797    6.071    2.468
LGA    H    56_A      H    56_A     5.201     0    0.605   1.042    11.309   29.167   14.381
LGA    G    57_A      G    57_A     1.429     0    0.538   0.538     3.027   69.286   69.286
LGA    R    58_A      R    58_A     2.906     0    0.082   1.095    12.416   59.048   28.528
LGA    A    59_A      A    59_A     3.406     0    0.033   0.037     4.332   55.357   51.714
LGA    E    60_A      E    60_A     2.117     0    0.050   0.441     5.870   68.810   51.852
LGA    I    61_A      I    61_A     2.017     0    0.060   0.153     4.984   72.976   56.726
LGA    E    62_A      E    62_A     3.115     0    0.055   0.157     6.755   57.262   38.360
LGA    A    63_A      A    63_A     3.168     0    0.037   0.047     3.909   57.262   54.476
LGA    L    64_A      L    64_A     2.114     0    0.201   0.411     5.407   72.976   55.476
LGA    A    65_A      A    65_A     1.991     0    0.045   0.043     2.695   72.857   69.714
LGA    A    66_A      A    66_A     2.753     0    0.072   0.075     3.658   62.857   58.952
LGA    L    67_A      L    67_A     2.936     0    0.062   1.038     5.702   60.952   45.774
LGA    K    68_A      K    68_A     2.275     0    0.057   0.971     5.916   62.857   51.270
LGA    M    69_A      M    69_A     2.303     0    0.082   1.117     9.190   68.810   47.619
LGA    R    70_A      R    70_A     1.825     0    0.049   1.546     3.329   68.810   61.472
LGA    E    71_A      E    71_A     3.555     0    0.070   1.077     5.208   45.238   40.317
LGA    L    72_A      L    72_A     3.973     0    0.067   0.246     6.471   43.452   34.464
LGA    C    73_A      C    73_A     2.842     0    0.104   0.289     3.854   57.143   56.111
LGA    R    74_A      R    74_A     2.947     0    0.285   1.289     9.745   47.262   31.212
LGA    T    75_A      T    75_A     4.709     0    0.103   0.134     5.982   30.595   30.340
LGA    Y    76_A      Y    76_A     6.043     0    0.564   1.547    13.013   22.738   10.119
LGA    G    83_A      G    83_A     3.818     0    0.243   0.243     4.941   40.476   40.476
LGA    D    84_A      D    84_A     5.196     0    0.300   0.414     9.355   35.952   21.012
LGA    A    85_A      A    85_A     2.683     0    0.057   0.055     3.362   59.167   60.286
LGA    W    86_A      W    86_A     2.632     0    0.120   1.314     8.467   62.857   36.735
LGA    R    87_A      R    87_A     3.091     0    0.054   0.980     6.869   53.571   37.316
LGA    A    88_A      A    88_A     3.645     0    0.120   0.146     4.419   48.333   46.095
LGA    V    89_A      V    89_A     2.599     0    0.113   1.162     3.818   59.048   54.286
LGA    A    90_A      A    90_A     2.356     0    0.104   0.106     3.427   64.762   61.810
LGA    R    91_A      R    91_A     3.500     0    0.053   1.727     6.780   46.786   39.957
LGA    D    92_A      D    92_A     4.600     0    0.092   0.232     6.203   37.262   29.405
LGA    V    93_A      V    93_A     3.441     0    0.066   0.156     3.756   46.667   46.190
LGA    W    94_A      W    94_A     3.027     0    0.073   1.266    10.313   50.119   29.116
LGA    D    95_A      D    95_A     5.294     0    0.280   1.305     9.582   27.738   16.131
LGA    T    96_A      T    96_A     6.178     0    0.068   1.052     7.976   19.524   17.143
LGA    V    97_A      V    97_A     4.465     0    0.542   1.213     5.867   43.929   38.776
LGA    G    98_A      G    98_A     3.966     0    0.205   0.205     4.413   40.238   40.238

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       61     244    244  100.00     480    480  100.00                61
SUMMARY(RMSD_GDC):     8.495          8.383                  9.327           31.610   25.880

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     30    2.98    46.311    42.282     0.973

LGA_LOCAL      RMSD:   2.982  Number of atoms:   30  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.271  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   8.495  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.384204 * X  +   0.922646 * Y  +  -0.033333 * Z  + -56.121700
  Y_new =   0.226933 * X  +   0.059379 * Y  +  -0.972099 * Z  +  28.415512
  Z_new =  -0.894924 * X  +  -0.381048 * Y  +  -0.232192 * Z  +  97.660210 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.608071  1.108261 -2.118063   [DEG:  149.4315   63.4987 -121.3561 ]
ZXZ: -0.034276  1.805127 -1.973335   [DEG:   -1.9639  103.4262 -113.0637 ]
 
# END of job
