
#######################################################
#                                                     #
#                        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        4.49     9.78
  LCS_AVERAGE:     72.18

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    25      52_A - 76_A        1.96    10.67
  LCS_AVERAGE:     36.55

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    21      34_A - 54_A        0.98     8.76
  LCS_AVERAGE:     30.31

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    3    6    9   14   20   28   39   39   43   43   44   44   45   46   48   49 
LCS_GDT     T    33_A     T    33_A     20   24   46      8   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     M    34_A     M    34_A     21   24   46      8   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     A    35_A     A    35_A     21   24   46      8   17   21   23   27   33   37   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     D    36_A     D    36_A     21   24   46      8   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     L    37_A     L    37_A     21   24   46      8   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     K    38_A     K    38_A     21   24   46      8   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     M    39_A     M    39_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     Q    40_A     Q    40_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     A    41_A     A    41_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     V    42_A     V    42_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     K    43_A     K    43_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     E    44_A     E    44_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     I    45_A     I    45_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     C    46_A     C    46_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     Y    47_A     Y    47_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     E    48_A     E    48_A     21   24   46     10   17   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     V    49_A     V    49_A     21   24   46     10   16   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     A    50_A     A    50_A     21   24   46     10   16   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     L    51_A     L    51_A     21   24   46     10   16   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   45   48   49 
LCS_GDT     A    52_A     A    52_A     21   25   46     10   16   21   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     D    53_A     D    53_A     21   25   46     10   16   20   23   26   32   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     F    54_A     F    54_A     21   25   46      6   16   20   23   25   27   30   35   40   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     R    55_A     R    55_A      4   25   46      3    4   14   21   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     H    56_A     H    56_A      4   25   46      3    4    4    5   13   17   29   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     G    57_A     G    57_A     20   25   46      7   17   18   21   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     R    58_A     R    58_A     20   25   46      6   17   18   21   26   32   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     A    59_A     A    59_A     20   25   46      6   16   18   21   26   32   38   41   41   42   44   44   44   44   44   44   45   45   47   47 
LCS_GDT     E    60_A     E    60_A     20   25   46      7   17   18   21   27   33   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     I    61_A     I    61_A     20   25   46      7   17   18   21   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     E    62_A     E    62_A     20   25   46     10   17   18   21   25   31   35   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     A    63_A     A    63_A     20   25   46     10   17   18   21   26   32   38   41   41   42   44   44   44   44   44   44   45   45   47   47 
LCS_GDT     L    64_A     L    64_A     20   25   46      8   17   18   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     A    65_A     A    65_A     20   25   46     10   17   18   21   26   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     A    66_A     A    66_A     20   25   46     10   17   18   21   26   32   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     L    67_A     L    67_A     20   25   46     10   17   18   23   27   33   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     K    68_A     K    68_A     20   25   46     10   17   19   23   27   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     M    69_A     M    69_A     20   25   46     10   17   21   23   26   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     R    70_A     R    70_A     20   25   46     10   17   18   23   27   33   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     E    71_A     E    71_A     20   25   46     10   17   18   23   27   33   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     L    72_A     L    72_A     20   25   46     10   17   18   21   26   32   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     C    73_A     C    73_A     20   25   46     10   17   18   21   26   33   38   41   41   42   44   44   44   44   44   44   45   46   48   49 
LCS_GDT     R    74_A     R    74_A     20   25   46     10   17   18   23   27   33   38   41   41   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     T    75_A     T    75_A     20   25   46      4   15   18   19   23   26   29   35   39   42   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     Y    76_A     Y    76_A     20   25   46      4    5   12   17   20   23   28   33   35   38   44   44   44   44   44   44   45   45   47   48 
LCS_GDT     G    83_A     G    83_A     16   16   46      3    3    7   16   20   20   21   25   27   31   34   35   36   36   36   37   37   37   46   49 
LCS_GDT     D    84_A     D    84_A     16   16   38      4   10   15   17   20   20   21   25   26   30   34   35   36   36   36   37   42   46   48   49 
LCS_GDT     A    85_A     A    85_A     16   16   38      4   11   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     W    86_A     W    86_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     R    87_A     R    87_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     A    88_A     A    88_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   36   37   42   43   48   49 
LCS_GDT     V    89_A     V    89_A     16   16   38      5   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     A    90_A     A    90_A     16   16   38      6   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   43   46   48   49 
LCS_GDT     R    91_A     R    91_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     D    92_A     D    92_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     V    93_A     V    93_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     W    94_A     W    94_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     D    95_A     D    95_A     16   16   38      7   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     T    96_A     T    96_A     16   16   38      4   12   15   17   20   20   21   25   26   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     V    97_A     V    97_A     16   16   38      4   12   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_GDT     G    98_A     G    98_A     16   16   38      3    3   15   17   20   20   21   25   27   31   34   35   36   36   39   40   42   46   48   49 
LCS_AVERAGE  LCS_A:  46.35  (  30.31   36.55   72.18 )

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     10     17     21     23     27     33     38     41     41     42     44     44     44     44     44     44     45     46     48     49 
GDT PERCENT_AT  16.39  27.87  34.43  37.70  44.26  54.10  62.30  67.21  67.21  68.85  72.13  72.13  72.13  72.13  72.13  72.13  73.77  75.41  78.69  80.33
GDT RMS_LOCAL    0.24   0.60   0.98   1.10   1.57   1.99   2.33   2.47   2.47   2.58   2.90   2.90   2.90   2.90   2.90   2.90   3.21   6.09   6.18   6.26
GDT RMS_ALL_AT   8.84  10.82   8.70   8.69   9.72   9.75  10.06  10.09  10.09  10.04  10.03  10.03  10.03  10.03  10.03  10.03  10.02   8.46   8.51   8.58

# Checking swapping
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  Y    47_A      Y    47_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  D    92_A      D    92_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A     9.249     0    0.372   0.368    10.341    7.024    5.619
LGA    T    33_A      T    33_A     2.675     0    0.606   1.252     4.903   54.524   48.095
LGA    M    34_A      M    34_A     2.401     0    0.057   0.796     2.630   60.952   66.964
LGA    A    35_A      A    35_A     3.277     0    0.096   0.102     3.852   53.571   51.524
LGA    D    36_A      D    36_A     2.384     0    0.109   0.218     3.348   62.857   57.321
LGA    L    37_A      L    37_A     1.178     0    0.070   0.105     1.708   79.286   80.357
LGA    K    38_A      K    38_A     1.399     0    0.481   0.890     6.093   69.405   49.206
LGA    M    39_A      M    39_A     2.521     0    0.075   1.161     6.068   62.857   48.393
LGA    Q    40_A      Q    40_A     2.038     0    0.047   0.782     2.933   70.952   64.974
LGA    A    41_A      A    41_A     0.656     0    0.055   0.052     1.012   90.595   90.571
LGA    V    42_A      V    42_A     1.478     0    0.110   0.183     3.346   83.690   73.469
LGA    K    43_A      K    43_A     1.941     0    0.051   0.881     4.267   72.857   60.423
LGA    E    44_A      E    44_A     1.447     0    0.175   0.296     2.708   79.286   68.730
LGA    I    45_A      I    45_A     0.984     0    0.071   0.672     4.845   90.476   73.512
LGA    C    46_A      C    46_A     1.632     0    0.076   0.814     3.277   81.548   73.492
LGA    Y    47_A      Y    47_A     1.399     0    0.046   0.191     4.287   85.952   62.222
LGA    E    48_A      E    48_A     1.268     0    0.026   0.748     7.005   81.548   55.079
LGA    V    49_A      V    49_A     2.749     0    0.072   0.122     4.604   61.071   52.721
LGA    A    50_A      A    50_A     2.608     0    0.118   0.115     3.046   64.881   61.905
LGA    L    51_A      L    51_A     0.981     0    0.206   0.296     1.683   88.214   84.881
LGA    A    52_A      A    52_A     2.340     0    0.291   0.294     3.269   61.190   61.905
LGA    D    53_A      D    53_A     3.772     0    0.048   0.935     5.561   35.238   38.810
LGA    F    54_A      F    54_A     5.706     0    0.403   0.914    14.015   29.405   11.212
LGA    R    55_A      R    55_A     2.311     0    0.629   1.637    11.027   73.214   33.593
LGA    H    56_A      H    56_A     4.045     0    0.541   0.462    11.412   48.810   23.143
LGA    G    57_A      G    57_A     2.093     0    0.731   0.731     2.303   66.786   66.786
LGA    R    58_A      R    58_A     3.214     0    0.083   1.133    10.477   51.786   28.788
LGA    A    59_A      A    59_A     3.338     0    0.032   0.032     3.467   50.000   50.000
LGA    E    60_A      E    60_A     2.227     0    0.059   1.366     6.840   66.905   50.529
LGA    I    61_A      I    61_A     2.511     0    0.068   1.659     4.651   59.048   52.262
LGA    E    62_A      E    62_A     3.880     0    0.064   0.116     7.400   46.667   30.688
LGA    A    63_A      A    63_A     3.308     0    0.059   0.066     3.647   55.476   53.048
LGA    L    64_A      L    64_A     1.023     0    0.192   0.785     1.811   77.143   79.345
LGA    A    65_A      A    65_A     2.784     0    0.079   0.071     3.704   59.048   55.905
LGA    A    66_A      A    66_A     3.081     0    0.061   0.074     3.935   61.190   57.619
LGA    L    67_A      L    67_A     1.500     0    0.038   0.355     2.879   79.405   71.190
LGA    K    68_A      K    68_A     1.727     0    0.079   1.255     3.303   71.310   68.942
LGA    M    69_A      M    69_A     3.122     0    0.074   0.789     5.612   55.476   42.262
LGA    R    70_A      R    70_A     1.753     0    0.059   1.030     9.096   81.667   42.165
LGA    E    71_A      E    71_A     1.920     0    0.088   1.338     8.353   67.619   43.069
LGA    L    72_A      L    72_A     3.861     0    0.038   1.365     6.861   43.810   40.000
LGA    C    73_A      C    73_A     3.596     0    0.071   0.253     4.928   46.667   43.571
LGA    R    74_A      R    74_A     1.750     0    0.299   1.232     7.324   63.214   46.840
LGA    T    75_A      T    75_A     6.104     0    0.094   0.201     8.638   18.810   14.014
LGA    Y    76_A      Y    76_A     7.964     0    0.591   1.512     8.627    8.690   18.810
LGA    G    83_A      G    83_A    21.937     0    0.179   0.179    21.937    0.000    0.000
LGA    D    84_A      D    84_A    23.516     0    0.295   1.170    29.506    0.000    0.000
LGA    A    85_A      A    85_A    17.911     0    0.032   0.030    19.724    0.000    0.000
LGA    W    86_A      W    86_A    14.772     0    0.149   1.190    19.564    0.000    0.000
LGA    R    87_A      R    87_A    20.454     0    0.063   1.025    28.746    0.000    0.000
LGA    A    88_A      A    88_A    21.755     0    0.142   0.139    22.785    0.000    0.000
LGA    V    89_A      V    89_A    15.118     0    0.147   0.207    17.201    0.000    0.000
LGA    A    90_A      A    90_A    13.427     0    0.097   0.095    15.611    0.000    0.000
LGA    R    91_A      R    91_A    20.014     0    0.061   1.220    28.101    0.000    0.000
LGA    D    92_A      D    92_A    20.522     0    0.101   0.233    24.947    0.000    0.000
LGA    V    93_A      V    93_A    14.515     0    0.061   0.084    16.191    0.000    0.000
LGA    W    94_A      W    94_A    15.634     0    0.060   1.546    18.259    0.000    0.000
LGA    D    95_A      D    95_A    22.520     0    0.240   0.963    25.970    0.000    0.000
LGA    T    96_A      T    96_A    21.743     0    0.140   1.148    22.964    0.000    0.000
LGA    V    97_A      V    97_A    16.485     0    0.533   1.314    17.768    0.000    0.000
LGA    G    98_A      G    98_A    18.583     0    0.267   0.267    18.732    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):     7.966          7.758                  8.897           45.576   38.589

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     41    2.47    51.230    50.452     1.597

LGA_LOCAL      RMSD:   2.468  Number of atoms:   41  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.095  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   7.966  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.599213 * X  +   0.605890 * Y  +   0.523299 * Z  +  49.383686
  Y_new =   0.173264 * X  +  -0.540007 * Y  +   0.823634 * Z  +  38.621422
  Z_new =   0.781616 * X  +   0.584201 * Y  +   0.218600 * Z  +  -7.366034 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.860117 -0.897252  1.212739   [DEG:  163.8727  -51.4088   69.4848 ]
ZXZ:  2.575583  1.350416  0.928944   [DEG:  147.5700   77.3732   53.2246 ]
 
# END of job
