
#######################################################
#                                                     #
#                        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:    46      32_A - 83_A        4.75     9.73
  LCS_AVERAGE:     72.99

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      53_A - 76_A        1.78     9.37
  LCS_AVERAGE:     35.34

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    20      33_A - 52_A        0.95     9.12
  LONGEST_CONTINUOUS_SEGMENT:    20      57_A - 76_A        0.62     9.59
  LCS_AVERAGE:     28.92

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   23   46      3    3    3    3    4    5   19   22   23   29   32   32   34   40   40   44   44   45   45   45 
LCS_GDT     T    33_A     T    33_A     20   23   46      8   15   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     M    34_A     M    34_A     20   23   46      8   15   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    35_A     A    35_A     20   23   46      8   15   19   22   23   27   31   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     D    36_A     D    36_A     20   23   46      8   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     L    37_A     L    37_A     20   23   46      8   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     K    38_A     K    38_A     20   23   46      8   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     M    39_A     M    39_A     20   23   46      8   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     Q    40_A     Q    40_A     20   23   46      8   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    41_A     A    41_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     V    42_A     V    42_A     20   23   46      5   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     K    43_A     K    43_A     20   23   46      7   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     E    44_A     E    44_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     I    45_A     I    45_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     C    46_A     C    46_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     Y    47_A     Y    47_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     E    48_A     E    48_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     V    49_A     V    49_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    50_A     A    50_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     L    51_A     L    51_A     20   23   46      9   16   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    52_A     A    52_A     20   23   46      4   15   19   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     D    53_A     D    53_A     18   24   46      3   10   15   19   22   25   31   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     F    54_A     F    54_A     18   24   46      3   12   15   19   23   24   29   34   38   40   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     R    55_A     R    55_A      4   24   46      3    3   14   18   22   26   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     H    56_A     H    56_A      4   24   46      0    3    4    4    6    8   25   34   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     G    57_A     G    57_A     20   24   46      8   18   20   20   22   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     R    58_A     R    58_A     20   24   46     15   18   20   20   22   26   30   34   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    59_A     A    59_A     20   24   46     15   18   20   20   22   26   30   34   36   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     E    60_A     E    60_A     20   24   46     15   18   20   20   22   26   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     I    61_A     I    61_A     20   24   46     15   18   20   20   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     E    62_A     E    62_A     20   24   46     15   18   20   20   22   26   30   35   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    63_A     A    63_A     20   24   46     15   18   20   20   22   26   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     L    64_A     L    64_A     20   24   46     15   18   20   20   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    65_A     A    65_A     20   24   46     15   18   20   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     A    66_A     A    66_A     20   24   46     14   18   20   20   22   26   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     L    67_A     L    67_A     20   24   46     15   18   20   20   22   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     K    68_A     K    68_A     20   24   46     15   18   20   20   22   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     M    69_A     M    69_A     20   24   46     15   18   20   22   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     R    70_A     R    70_A     20   24   46     15   18   20   20   24   27   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     E    71_A     E    71_A     20   24   46     15   18   20   20   22   26   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     L    72_A     L    72_A     20   24   46     15   18   20   20   22   26   30   34   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     C    73_A     C    73_A     20   24   46     15   18   20   20   22   26   31   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     R    74_A     R    74_A     20   24   46      4   18   20   20   22   26   33   36   40   41   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     T    75_A     T    75_A     20   24   46      4   17   20   20   22   25   27   32   34   37   40   44   44   44   44   44   44   45   47   49 
LCS_GDT     Y    76_A     Y    76_A     20   24   46      3   14   20   20   22   26   30   32   34   37   43   44   44   44   44   44   44   45   47   49 
LCS_GDT     G    83_A     G    83_A      4   16   46      3    3    4    6   17   18   20   24   29   33   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     D    84_A     D    84_A     15   16   40      3    4    9   15   17   18   20   24   28   33   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     A    85_A     A    85_A     15   16   40      4   11   14   15   17   18   21   25   31   33   36   36   37   38   39   39   41   41   44   49 
LCS_GDT     W    86_A     W    86_A     15   16   40      6   13   14   15   17   18   20   25   31   33   36   36   37   38   39   39   41   41   44   49 
LCS_GDT     R    87_A     R    87_A     15   16   40      5   13   14   15   17   18   20   24   31   33   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     A    88_A     A    88_A     15   16   40      7   13   14   15   17   18   20   24   31   33   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     V    89_A     V    89_A     15   16   40      7   13   14   15   17   18   21   25   31   33   36   36   37   38   39   39   41   44   47   49 
LCS_GDT     A    90_A     A    90_A     15   16   40      7   13   14   15   17   18   21   25   31   33   36   36   37   38   39   39   41   42   47   49 
LCS_GDT     R    91_A     R    91_A     15   16   40      7   13   14   15   17   18   20   24   31   33   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     D    92_A     D    92_A     15   16   40      7   13   14   15   17   18   18   23   31   33   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     V    93_A     V    93_A     15   16   40      7   13   14   15   17   18   20   25   31   33   36   36   37   38   39   39   41   42   47   49 
LCS_GDT     W    94_A     W    94_A     15   16   40      6   13   14   15   17   18   20   25   31   33   36   36   37   38   39   39   41   42   45   46 
LCS_GDT     D    95_A     D    95_A     15   16   40      7   13   14   15   17   18   18   23   30   33   36   36   37   38   39   39   40   41   42   43 
LCS_GDT     T    96_A     T    96_A     15   16   40      3   13   14   15   17   18   18   21   25   31   36   36   37   38   39   39   41   41   42   43 
LCS_GDT     V    97_A     V    97_A     15   16   40      3   13   14   15   17   18   20   25   31   33   36   36   37   38   39   39   41   41   45   46 
LCS_GDT     G    98_A     G    98_A     15   16   40      3   13   14   15   17   18   20   24   31   33   36   36   37   38   39   39   41   41   42   43 
LCS_AVERAGE  LCS_A:  45.75  (  28.92   35.34   72.99 )

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     15     18     20     22     24     27     33     36     40     41     43     44     44     44     44     44     44     45     47     49 
GDT PERCENT_AT  24.59  29.51  32.79  36.07  39.34  44.26  54.10  59.02  65.57  67.21  70.49  72.13  72.13  72.13  72.13  72.13  72.13  73.77  77.05  80.33
GDT RMS_LOCAL    0.29   0.48   0.62   1.19   1.69   1.94   2.51   2.66   2.97   3.05   3.26   3.35   3.35   3.35   3.35   3.35   3.35   3.68   4.60   5.25
GDT RMS_ALL_AT   9.55   9.54   9.59   9.05   9.37   9.47   9.85   9.77   9.82   9.86   9.79   9.80   9.80   9.80   9.80   9.80   9.80   9.87   9.49   9.35

# Checking swapping
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  E    71_A      E    71_A
#   possible swapping detected:  Y    76_A      Y    76_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     9.652     0    0.274   0.275    11.547    6.071    4.857
LGA    T    33_A      T    33_A     2.424     0    0.602   1.243     4.956   60.476   60.272
LGA    M    34_A      M    34_A     1.666     0    0.080   0.690     4.202   70.833   61.548
LGA    A    35_A      A    35_A     3.412     0    0.092   0.091     4.541   53.571   49.143
LGA    D    36_A      D    36_A     2.767     0    0.105   0.249     4.702   59.048   48.988
LGA    L    37_A      L    37_A     1.979     0    0.038   0.105     3.872   72.857   63.333
LGA    K    38_A      K    38_A     1.601     0    0.077   0.989     9.002   79.286   52.910
LGA    M    39_A      M    39_A     2.644     0    0.085   1.263     9.143   62.976   41.429
LGA    Q    40_A      Q    40_A     3.057     0    0.020   0.787     4.914   55.357   43.968
LGA    A    41_A      A    41_A     2.581     0    0.060   0.056     3.270   64.881   61.905
LGA    V    42_A      V    42_A     1.758     0    0.133   0.192     4.179   79.286   64.966
LGA    K    43_A      K    43_A     2.444     0    0.087   0.138     6.536   68.929   46.349
LGA    E    44_A      E    44_A     3.021     0    0.120   0.283     6.295   55.476   39.048
LGA    I    45_A      I    45_A     2.131     0    0.068   0.092     4.554   72.976   58.393
LGA    C    46_A      C    46_A     1.469     0    0.108   0.110     3.318   85.952   76.429
LGA    Y    47_A      Y    47_A     1.742     0    0.058   1.394    12.483   79.286   36.468
LGA    E    48_A      E    48_A     2.154     0    0.020   0.666     6.814   70.833   44.709
LGA    V    49_A      V    49_A     2.325     0    0.035   0.070     4.040   68.810   57.959
LGA    A    50_A      A    50_A     1.785     0    0.071   0.074     2.326   77.143   74.667
LGA    L    51_A      L    51_A     0.852     0    0.102   0.252     3.002   90.595   76.845
LGA    A    52_A      A    52_A     1.118     0    0.544   0.515     3.846   70.000   66.000
LGA    D    53_A      D    53_A     4.109     0    0.378   0.346     6.018   30.952   40.536
LGA    F    54_A      F    54_A     4.803     0    0.306   1.270    12.809   36.071   14.156
LGA    R    55_A      R    55_A     3.718     0    0.681   1.338    11.430   48.452   22.684
LGA    H    56_A      H    56_A     5.486     0    0.539   0.575    13.015   34.524   15.571
LGA    G    57_A      G    57_A     2.910     0    0.568   0.568     4.457   46.905   46.905
LGA    R    58_A      R    58_A     5.509     0    0.070   1.274    12.879   25.119   11.558
LGA    A    59_A      A    59_A     6.364     0    0.038   0.036     7.464   21.667   19.333
LGA    E    60_A      E    60_A     3.558     0    0.029   0.898     7.432   52.500   37.143
LGA    I    61_A      I    61_A     2.006     0    0.042   0.701     5.034   62.857   52.738
LGA    E    62_A      E    62_A     4.706     0    0.039   0.827     9.545   37.262   21.323
LGA    A    63_A      A    63_A     4.029     0    0.037   0.035     4.844   47.143   44.000
LGA    L    64_A      L    64_A     1.227     0    0.232   0.574     4.412   75.119   66.667
LGA    A    65_A      A    65_A     2.833     0    0.051   0.056     4.362   61.071   56.286
LGA    A    66_A      A    66_A     3.611     0    0.081   0.083     4.939   55.714   50.857
LGA    L    67_A      L    67_A     2.179     0    0.064   1.088     6.311   66.786   51.845
LGA    K    68_A      K    68_A     2.649     0    0.042   1.221     6.590   59.762   40.370
LGA    M    69_A      M    69_A     3.018     0    0.059   0.941     5.043   57.381   49.048
LGA    R    70_A      R    70_A     0.816     0    0.086   0.741     7.277   83.690   51.082
LGA    E    71_A      E    71_A     3.285     0    0.086   1.218    10.110   49.405   27.725
LGA    L    72_A      L    72_A     5.141     0    0.068   0.104     7.567   28.214   21.488
LGA    C    73_A      C    73_A     3.909     0    0.076   0.237     5.409   43.452   41.667
LGA    R    74_A      R    74_A     3.561     0    0.280   1.162     9.475   37.024   24.545
LGA    T    75_A      T    75_A     7.783     0    0.138   0.235    10.559    9.048    5.578
LGA    Y    76_A      Y    76_A     8.051     0    0.666   0.820    12.873    9.762    3.810
LGA    G    83_A      G    83_A    20.560     0    0.114   0.114    20.872    0.000    0.000
LGA    D    84_A      D    84_A    21.808     0    0.288   1.158    28.012    0.000    0.000
LGA    A    85_A      A    85_A    15.321     0    0.171   0.180    17.381    0.000    0.000
LGA    W    86_A      W    86_A    14.012     0    0.095   1.259    19.616    0.000    0.000
LGA    R    87_A      R    87_A    20.296     0    0.000   1.303    30.861    0.000    0.000
LGA    A    88_A      A    88_A    20.381     0    0.101   0.107    21.199    0.000    0.000
LGA    V    89_A      V    89_A    13.386     0    0.089   0.163    15.686    0.000    0.680
LGA    A    90_A      A    90_A    13.683     0    0.090   0.095    15.788    0.000    0.000
LGA    R    91_A      R    91_A    20.169     0    0.045   1.172    27.730    0.000    0.000
LGA    D    92_A      D    92_A    19.345     0    0.083   1.183    19.345    0.000    0.000
LGA    V    93_A      V    93_A    13.093     0    0.064   0.080    14.961    0.000    0.884
LGA    W    94_A      W    94_A    15.998     0    0.055   1.624    20.589    0.000    0.000
LGA    D    95_A      D    95_A    22.229     0    0.248   1.083    27.088    0.000    0.000
LGA    T    96_A      T    96_A    20.249     0    0.127   1.135    20.957    0.000    0.000
LGA    V    97_A      V    97_A    14.498     0    0.533   0.463    16.143    0.000    0.000
LGA    G    98_A      G    98_A    18.087     0    0.247   0.247    19.214    0.000    0.000

# 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):     8.789          8.609                 10.078           40.730   31.945

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     36    2.66    49.180    47.956     1.302

LGA_LOCAL      RMSD:   2.664  Number of atoms:   36  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.767  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   8.789  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.598858 * X  +  -0.042866 * Y  +  -0.799707 * Z  +  34.947384
  Y_new =  -0.559143 * X  +  -0.737273 * Y  +  -0.379193 * Z  +  85.975792
  Z_new =  -0.573349 * X  +   0.674233 * Y  +  -0.465490 * Z  + -81.993675 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.751116  0.610587  2.175049   [DEG:  -43.0357   34.9841  124.6211 ]
ZXZ: -1.128030  2.054984 -0.704709   [DEG:  -64.6313  117.7419  -40.3769 ]
 
# END of job
