
#######################################################
#                                                     #
#                        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:    42      35_A - 76_A        4.90    11.45
  LCS_AVERAGE:     65.25

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      57_A - 74_A        1.63    11.30
  LCS_AVERAGE:     22.71

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    16      58_A - 73_A        0.75    11.98
  LCS_AVERAGE:     19.78

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     10   10   17      7    9   10   10   10   10   11   14   16   18   19   23   26   31   35   37   41   44   45   45 
LCS_GDT     T    33_A     T    33_A     10   10   17      7    9   10   10   10   10   11   19   20   23   24   27   28   32   37   38   40   42   45   45 
LCS_GDT     M    34_A     M    34_A     10   10   22      7    9   10   10   10   10   11   14   20   23   24   27   34   35   37   38   41   44   45   45 
LCS_GDT     A    35_A     A    35_A     10   10   42      7    9   10   10   10   14   16   19   22   25   28   31   32   34   36   38   42   44   45   45 
LCS_GDT     D    36_A     D    36_A     10   10   42      7    9   10   10   10   14   18   21   25   28   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     L    37_A     L    37_A     10   10   42      7    9   10   10   10   14   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     K    38_A     K    38_A     10   10   42      7    9   10   10   10   13   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     M    39_A     M    39_A     10   10   42      4    9   10   10   10   10   14   15   17   27   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     Q    40_A     Q    40_A     10   10   42      4    9   10   10   10   12   14   20   25   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    41_A     A    41_A     10   13   42      3    5   10   10   10   10   14   16   22   25   32   35   38   40   41   41   42   44   45   45 
LCS_GDT     V    42_A     V    42_A     12   13   42      4   10   12   12   12   12   17   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     K    43_A     K    43_A     12   13   42      5   11   12   12   12   12   14   17   22   26   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     E    44_A     E    44_A     12   13   42      5   11   12   12   12   12   15   17   22   25   28   31   35   40   41   41   42   44   45   45 
LCS_GDT     I    45_A     I    45_A     12   13   42      5   11   12   12   12   12   14   17   25   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     C    46_A     C    46_A     12   13   42      5   11   12   12   12   12   17   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     Y    47_A     Y    47_A     12   13   42      5   11   12   12   12   12   15   19   22   25   30   37   38   40   41   41   42   44   45   45 
LCS_GDT     E    48_A     E    48_A     12   13   42      6   11   12   12   12   12   15   19   23   26   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     V    49_A     V    49_A     12   13   42      6   11   12   12   12   12   14   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    50_A     A    50_A     12   13   42      6   11   12   12   12   12   14   18   23   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     L    51_A     L    51_A     12   13   42      6   11   12   12   12   12   14   15   16   23   27   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    52_A     A    52_A     12   13   42      6   11   12   12   12   12   15   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     D    53_A     D    53_A     12   13   42      6   11   12   12   12   12   17   20   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     F    54_A     F    54_A      5   13   42      3    4    5    5   10   14   17   20   22   26   30   33   35   40   41   41   42   44   45   45 
LCS_GDT     R    55_A     R    55_A      5    6   42      4    4    5    8   10   14   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     H    56_A     H    56_A      5    6   42      4    4    5   10   10   16   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     G    57_A     G    57_A      5   18   42      4    4    5   12   16   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     R    58_A     R    58_A     16   18   42      4   14   16   16   17   17   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    59_A     A    59_A     16   18   42      4   14   16   16   17   17   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     E    60_A     E    60_A     16   18   42      4   14   16   16   17   17   18   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     I    61_A     I    61_A     16   18   42      4   14   16   16   17   17   18   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     E    62_A     E    62_A     16   18   42      7   14   16   16   17   17   18   22   26   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    63_A     A    63_A     16   18   42      7   14   16   16   17   17   18   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     L    64_A     L    64_A     16   18   42      7   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    65_A     A    65_A     16   18   42      7   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     A    66_A     A    66_A     16   18   42      7   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     L    67_A     L    67_A     16   18   42      7   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     K    68_A     K    68_A     16   18   42      4   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     M    69_A     M    69_A     16   18   42      4   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     R    70_A     R    70_A     16   18   42      4   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     E    71_A     E    71_A     16   18   42      7   14   16   16   17   17   18   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     L    72_A     L    72_A     16   18   42      6   14   16   16   17   17   18   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     C    73_A     C    73_A     16   18   42      6   14   16   16   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     R    74_A     R    74_A      8   18   42      3    8   11   14   17   17   19   24   28   30   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     T    75_A     T    75_A      3    3   42      3    4    5    7   10   12   17   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     Y    76_A     Y    76_A      3    4   42      3    5   12   15   15   15   18   22   26   29   32   37   38   40   41   41   42   44   45   45 
LCS_GDT     G    83_A     G    83_A      3    5   38      0    3    3    5    6    9   12   14   20   23   25   27   32   34   36   36   38   38   39   40 
LCS_GDT     D    84_A     D    84_A      3   15   38      2    3    3    4    6    9   11   14   20   23   28   30   33   34   36   37   38   38   39   42 
LCS_GDT     A    85_A     A    85_A     14   15   38      4   12   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     W    86_A     W    86_A     14   15   38      7   13   14   15   15   15   18   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     R    87_A     R    87_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     A    88_A     A    88_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     V    89_A     V    89_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     A    90_A     A    90_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     R    91_A     R    91_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     D    92_A     D    92_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     V    93_A     V    93_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     W    94_A     W    94_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     D    95_A     D    95_A     14   15   38      3   13   14   15   15   15   18   23   28   30   32   34   34   35   37   37   40   42   43   43 
LCS_GDT     T    96_A     T    96_A     14   15   38      6   13   14   15   15   15   18   22   27   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     V    97_A     V    97_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_GDT     G    98_A     G    98_A     14   15   38      8   13   14   15   15   15   19   24   28   30   32   34   34   35   37   38   40   42   43   43 
LCS_AVERAGE  LCS_A:  35.91  (  19.78   22.71   65.25 )

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      8     14     16     16     17     17     19     24     28     30     32     37     38     40     41     41     42     44     45     45 
GDT PERCENT_AT  13.11  22.95  26.23  26.23  27.87  27.87  31.15  39.34  45.90  49.18  52.46  60.66  62.30  65.57  67.21  67.21  68.85  72.13  73.77  73.77
GDT RMS_LOCAL    0.30   0.66   0.75   0.75   1.07   1.07   2.62   3.09   3.35   3.50   3.82   4.29   4.35   4.53   4.65   4.65   4.90   5.30   5.50   5.50
GDT RMS_ALL_AT   9.71  11.85  11.98  11.98  12.04  12.04  11.19  11.31  11.39  11.38  11.06  11.56  11.49  11.66  11.57  11.57  11.45  11.26  11.17  11.17

# Checking swapping
#   possible swapping detected:  D    36_A      D    36_A
#   possible swapping detected:  Y    47_A      Y    47_A
#   possible swapping detected:  E    48_A      E    48_A
#   possible swapping detected:  D    53_A      D    53_A
#   possible swapping detected:  F    54_A      F    54_A
#   possible swapping detected:  E    60_A      E    60_A
#   possible swapping detected:  E    62_A      E    62_A
#   possible swapping detected:  Y    76_A      Y    76_A
#   possible swapping detected:  D    84_A      D    84_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    A    32_A      A    32_A    17.819     0    0.570   0.575    20.043    0.000    0.000
LGA    T    33_A      T    33_A    12.519     0    0.103   1.292    14.576    0.000    0.000
LGA    M    34_A      M    34_A    10.074     0    0.054   0.606    11.306    0.000    0.595
LGA    A    35_A      A    35_A    12.563     0    0.112   0.116    15.599    0.000    0.000
LGA    D    36_A      D    36_A    16.128     0    0.111   1.115    18.321    0.000    0.000
LGA    L    37_A      L    37_A    14.512     0    0.095   0.121    16.563    0.000    0.000
LGA    K    38_A      K    38_A    13.789     0    0.098   1.326    20.332    0.000    0.000
LGA    M    39_A      M    39_A    20.477     0    0.073   0.641    28.013    0.000    0.000
LGA    Q    40_A      Q    40_A    21.267     0    0.580   1.383    26.687    0.000    0.000
LGA    A    41_A      A    41_A    18.881     0    0.022   0.032    19.810    0.000    0.000
LGA    V    42_A      V    42_A    19.280     0    0.535   0.946    19.712    0.000    0.000
LGA    K    43_A      K    43_A    20.462     0    0.057   0.783    29.667    0.000    0.000
LGA    E    44_A      E    44_A    20.608     0    0.152   0.903    26.698    0.000    0.000
LGA    I    45_A      I    45_A    17.338     0    0.044   1.091    18.276    0.000    0.000
LGA    C    46_A      C    46_A    15.940     0    0.089   0.839    16.510    0.000    0.000
LGA    Y    47_A      Y    47_A    18.583     0    0.041   0.127    23.426    0.000    0.000
LGA    E    48_A      E    48_A    19.558     0    0.069   0.830    21.786    0.000    0.000
LGA    V    49_A      V    49_A    17.390     0    0.050   0.104    17.857    0.000    0.000
LGA    A    50_A      A    50_A    16.743     0    0.038   0.057    17.256    0.000    0.000
LGA    L    51_A      L    51_A    18.773     0    0.233   1.388    22.943    0.000    0.000
LGA    A    52_A      A    52_A    19.468     0    0.302   0.297    19.956    0.000    0.000
LGA    D    53_A      D    53_A    18.028     0    0.437   1.474    22.642    0.000    0.000
LGA    F    54_A      F    54_A    10.483     0    0.468   1.352    13.288    0.833    0.346
LGA    R    55_A      R    55_A     9.955     0    0.563   1.642    14.178    2.500    0.952
LGA    H    56_A      H    56_A     6.868     0    0.088   0.921    14.204   23.810   10.000
LGA    G    57_A      G    57_A     3.472     0    0.080   0.080     6.503   32.976   32.976
LGA    R    58_A      R    58_A     8.075     0    0.562   1.225    19.057   10.833    3.983
LGA    A    59_A      A    59_A     7.945     0    0.062   0.070     8.684    9.643    8.286
LGA    E    60_A      E    60_A     5.290     0    0.050   1.016     6.194   27.976   35.926
LGA    I    61_A      I    61_A     4.796     0    0.036   0.562     6.734   30.119   26.607
LGA    E    62_A      E    62_A     6.043     0    0.056   1.278    11.129   24.048   12.381
LGA    A    63_A      A    63_A     4.880     0    0.040   0.060     5.365   36.071   34.095
LGA    L    64_A      L    64_A     2.921     0    0.191   0.547     3.639   55.595   56.429
LGA    A    65_A      A    65_A     3.545     0    0.048   0.062     4.329   50.119   47.524
LGA    A    66_A      A    66_A     3.096     0    0.089   0.113     3.456   55.476   54.381
LGA    L    67_A      L    67_A     2.483     0    0.074   0.839     3.005   64.881   63.036
LGA    K    68_A      K    68_A     2.235     0    0.019   1.329     7.298   64.762   49.048
LGA    M    69_A      M    69_A     3.205     0    0.062   1.313     7.935   51.786   40.893
LGA    R    70_A      R    70_A     2.772     0    0.076   1.358     8.947   51.905   35.671
LGA    E    71_A      E    71_A     3.614     0    0.080   0.955     4.165   43.452   46.455
LGA    L    72_A      L    72_A     4.101     0    0.041   1.069     5.071   37.262   37.440
LGA    C    73_A      C    73_A     4.027     0    0.627   0.691     6.180   32.262   31.984
LGA    R    74_A      R    74_A     4.252     0    0.569   1.383    11.607   30.000   20.952
LGA    T    75_A      T    75_A     8.448     0    0.093   0.158    12.857    8.095    4.626
LGA    Y    76_A      Y    76_A     7.357     0    0.187   0.368    18.898   14.643    4.921
LGA    G    83_A      G    83_A     9.074     0    0.240   0.240     9.074    3.214    3.214
LGA    D    84_A      D    84_A     7.254     0    0.505   1.214    12.791   20.000   10.357
LGA    A    85_A      A    85_A     2.528     0    0.630   0.610     4.763   57.619   52.381
LGA    W    86_A      W    86_A     3.608     0    0.135   1.200     4.861   51.905   51.054
LGA    R    87_A      R    87_A     2.506     0    0.070   1.186    11.616   65.000   34.459
LGA    A    88_A      A    88_A     1.693     0    0.117   0.119     1.906   72.857   72.857
LGA    V    89_A      V    89_A     2.407     0    0.083   0.180     2.976   64.881   61.565
LGA    A    90_A      A    90_A     2.156     0    0.034   0.039     2.409   66.786   66.381
LGA    R    91_A      R    91_A     2.345     0    0.018   1.091     3.496   62.976   62.468
LGA    D    92_A      D    92_A     3.350     0    0.076   0.161     4.777   51.786   45.298
LGA    V    93_A      V    93_A     2.963     0    0.083   0.155     3.208   55.357   55.102
LGA    W    94_A      W    94_A     2.526     0    0.048   1.526    10.525   55.476   27.959
LGA    D    95_A      D    95_A     4.938     0    0.196   0.613     6.845   30.595   25.000
LGA    T    96_A      T    96_A     5.991     0    0.159   0.963     7.305   26.310   21.429
LGA    V    97_A      V    97_A     3.200     0    0.458   1.335     4.437   45.119   51.633
LGA    G    98_A      G    98_A     3.509     0    0.093   0.093     6.727   33.214   33.214

# 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):     9.440          9.318                 10.335           24.953   21.867

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   99   61    4.0     24    3.09    38.934    35.401     0.752

LGA_LOCAL      RMSD:   3.092  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.312  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   9.440  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.361113 * X  +   0.926444 * Y  +   0.106297 * Z  +  13.674300
  Y_new =  -0.826572 * X  +   0.370769 * Y  +  -0.423449 * Z  +  24.371412
  Z_new =  -0.431713 * X  +   0.065051 * Y  +   0.899662 * Z  + -13.394044 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.158906  0.446392  0.072181   [DEG:  -66.4004   25.5764    4.1356 ]
ZXZ:  0.245944  0.451801 -1.421240   [DEG:   14.0915   25.8863  -81.4311 ]
 
# END of job
