
#######################################################
#                                                     #
#                        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   57 (  456),  selected   57 , name one
# Molecule2: number of CA atoms  116 (  942),  selected   57 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:C  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29      58_B - 86_B        4.86    16.48
  LCS_AVERAGE:     19.69

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      60_B - 73_B        1.81    17.06
  LCS_AVERAGE:      8.42

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     8      65_B - 72_B        0.90    17.68
  LCS_AVERAGE:      4.67

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   57
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     R    44_C     R    44_B      4    7   11      3    4    4    5    7    9   10   11   13   14   16   18   21   22   23   24   26   28   29   30 
LCS_GDT     S    45_C     S    45_B      4    7   11      3    4    4    6    8    9   10   11   13   14   16   18   21   22   23   24   26   28   29   30 
LCS_GDT     T    46_C     T    46_B      4    7   11      3    4    4    5    7    9   10   11   13   14   16   18   21   22   23   24   26   28   29   30 
LCS_GDT     T    47_C     T    47_B      4    7   11      0    4    5    6    8    9   10   11   13   14   16   18   21   22   23   24   26   28   29   30 
LCS_GDT     E    48_C     E    48_B      3    7   14      3    4    5    6    8    9   10   11   13   14   16   18   21   22   23   24   26   28   29   30 
LCS_GDT     R    49_C     R    49_B      3    7   14      3    4    6    6    7    8   10   11   13   14   16   17   21   22   23   24   26   28   29   30 
LCS_GDT     S    50_C     S    50_B      4    7   14      3    3    6    6    8    9   10   11   13   14   16   17   21   22   23   24   26   28   29   30 
LCS_GDT     G    51_C     G    51_B      4    6   14      3    3    4    4    6    8   10   11   13   14   16   16   17   21   23   24   26   28   29   30 
LCS_GDT     G    52_C     G    52_B      4    5   14      3    4    4    4    5    6    8   11   11   12   13   13   14   16   17   19   24   25   26   28 
LCS_GDT     I    53_C     I    53_B      4    5   14      3    4    4    4    5    6    8    9   11   12   13   13   14   16   17   19   21   24   26   28 
LCS_GDT     P    54_C     P    54_B      4    5   14      3    4    4    4    5    8    9   11   11   12   13   13   17   20   22   23   25   26   27   28 
LCS_GDT     E    55_C     E    55_B      4    6   16      3    4    4    6    6    8    9   11   11   12   13   14   17   21   22   23   25   26   27   27 
LCS_GDT     G    56_C     G    56_B      5    6   18      3    5    5    6    6    8    9   11   11   12   16   18   20   21   22   23   25   26   27   28 
LCS_GDT     D    57_C     D    57_B      5    6   19      3    5    5    6    6    8    9   11   11   12   13   18   20   21   22   23   25   27   29   31 
LCS_GDT     I    58_C     I    58_B      5    6   29      3    5    5    6    6    8    9   11   15   17   18   19   22   28   29   30   31   33   34   35 
LCS_GDT     Y    59_C     Y    59_B      5    6   29      3    5    5    6    6    8    9   15   15   17   18   19   22   28   29   30   31   33   34   35 
LCS_GDT     L    60_C     L    60_B      5   14   29      4    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     E    61_C     E    61_B      3   14   29      3    3   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     S    62_C     S    62_B      3   14   29      3    5   10   14   14   15   16   17   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     N    63_C     N    63_B      3   14   29      3    3   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     L    64_C     L    64_B      6   14   29      3    3    5    7   10   11   14   16   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     F    65_C     F    65_B      8   14   29      3    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     L    66_C     L    66_B      8   14   29      3    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     D    67_C     D    67_B      8   14   29      3    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     F    68_C     F    68_B      8   14   29      4    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     N    69_C     N    69_B      8   14   29      4    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     P    70_C     P    70_B      8   14   29      4    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     Y    71_C     Y    71_B      8   14   29      3    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     G    72_C     G    72_B      8   14   29      3    6   10   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     L    73_C     L    73_B      6   14   29      3    4    8   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     S    74_C     S    74_B      4   12   29      3    4    6    6    8    9   12   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     G    75_C     G    75_B      5   12   29      4    4    7    8   10   11   12   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     Y    76_C     Y    76_B      5    7   29      4    4    5    7    8   11   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     L    77_C     L    77_B      5    7   29      4    4    5    7    8    9   11   16   20   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     L    78_C     L    78_B      5    7   29      4    4    5    7    8   11   12   13   14   16   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     S    79_C     S    79_B      5    7   29      3    4    5    7    8   11   12   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     E    80_C     E    80_B      3    7   29      2    3    5    7    8   11   12   16   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     P    81_C     P    81_B      3    7   29      2    3    4    5    9   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     N    82_C     N    82_B      3    9   29      2    3    9   14   14   15   16   18   21   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     C    83_C     C    83_B      7    9   29      3    6    8    9   10   12   15   16   20   23   23   24   26   28   29   30   31   33   34   35 
LCS_GDT     V    84_C     V    84_B      7    9   29      3    6    8    9   10   11   13   15   15   18   19   24   26   28   29   30   31   33   34   35 
LCS_GDT     D    85_C     D    85_B      7    9   29      4    6    8    9   10   11   13   15   15   17   18   22   26   28   29   30   31   33   34   35 
LCS_GDT     L    86_C     L    86_B      7    9   29      4    6    8    9   10   10   12   15   15   17   18   19   21   23   27   29   31   33   34   35 
LCS_GDT     L    87_C     L    87_B      7    9   19      3    6    8    9   10   11   12   15   15   15   16   18   20   21   21   23   26   28   33   35 
LCS_GDT     I    88_C     I    88_B      7   11   19      4    6    8    9   10   12   13   15   15   15   16   17   20   21   21   23   26   30   33   35 
LCS_GDT     E    89_C     E    89_B      7   11   19      4    6    8    9   10   12   13   15   15   15   16   17   18   19   21   22   26   28   30   31 
LCS_GDT     P    90_C     P    90_B      6   11   19      4    5    7    9   10   11   13   15   15   15   16   17   18   19   21   23   26   28   30   35 
LCS_GDT     N    91_C     N    91_B      6   11   19      4    5    7    8   10   12   13   15   15   15   16   17   18   19   21   23   26   30   33   35 
LCS_GDT     N    92_C     N    92_B      6   11   19      4    5    7    8   10   12   13   15   15   15   16   19   22   25   27   29   31   32   34   35 
LCS_GDT     Y    93_C     Y    93_B      6   11   19      4    5    7    8   10   12   13   15   15   16   17   19   21   25   27   30   31   33   34   35 
LCS_GDT     V    94_C     V    94_B      6   11   19      4    5    7    8   10   12   13   15   15   17   18   19   22   25   29   30   31   33   34   34 
LCS_GDT     R    95_C     R    95_B      6   11   19      3    5    7    8   10   12   14   15   15   16   18   19   22   24   29   29   31   33   34   34 
LCS_GDT     L    96_C     L    96_B      6   11   19      3    5    7    8   10   12   13   15   15   15   16   18   21   23   25   27   31   33   34   34 
LCS_GDT     R    97_C     R    97_B      6   11   19      3    5    7    8   10   12   13   15   15   15   15   17   18   22   23   24   27   30   30   31 
LCS_GDT     L    98_C     L    98_B      6   11   19      3    5    7    8   10   12   13   15   15   15   15   16   17   19   21   22   26   28   30   31 
LCS_GDT     I    99_C     I    99_B      6   10   19      3    5    7    8   10   12   13   15   15   15   15   16   17   19   21   22   26   28   30   31 
LCS_GDT     E   100_C     E   100_B      6   10   19      3    3    7    8   10   12   13   15   15   15   15   16   17   19   19   21   24   28   30   31 
LCS_AVERAGE  LCS_A:  10.93  (   4.67    8.42   19.69 )

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      4      6     10     14     14     15     16     18     21     23     23     24     26     28     29     30     31     33     34     35 
GDT PERCENT_AT   3.45   5.17   8.62  12.07  12.07  12.93  13.79  15.52  18.10  19.83  19.83  20.69  22.41  24.14  25.00  25.86  26.72  28.45  29.31  30.17
GDT RMS_LOCAL    0.25   0.63   0.99   1.40   1.40   1.63   2.00   2.79   3.08   3.38   3.38   3.56   4.10   4.59   4.86   5.06   5.21   5.62   5.92   6.90
GDT RMS_ALL_AT  23.74  17.29  17.07  17.19  17.19  17.25  17.22  17.01  17.17  17.13  17.13  17.07  16.87  16.58  16.36  16.39  16.23  16.12  16.16  16.46

# Checking swapping
#   possible swapping detected:  E    48_C      E    48_B
#   possible swapping detected:  D    57_C      D    57_B
#   possible swapping detected:  Y    59_C      Y    59_B
#   possible swapping detected:  E    61_C      E    61_B
#   possible swapping detected:  F    65_C      F    65_B
#   possible swapping detected:  F    68_C      F    68_B
#   possible swapping detected:  Y    71_C      Y    71_B
#   possible swapping detected:  E    89_C      E    89_B
#   possible swapping detected:  E   100_C      E   100_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    R    44_C      R    44_B    23.708     0    0.070   0.308    32.818    0.000    0.000
LGA    S    45_C      S    45_B    27.227     0    0.090   0.691    30.319    0.000    0.000
LGA    T    46_C      T    46_B    31.355     0    0.667   0.559    33.044    0.000    0.000
LGA    T    47_C      T    47_B    34.932     0    0.685   1.336    38.213    0.000    0.000
LGA    E    48_C      E    48_B    38.793     0    0.661   0.563    45.345    0.000    0.000
LGA    R    49_C      R    49_B    35.462     0    0.615   1.283    36.643    0.000    0.000
LGA    S    50_C      S    50_B    33.944     0    0.569   0.717    35.404    0.000    0.000
LGA    G    51_C      G    51_B    31.432     0    0.284   0.284    32.526    0.000    0.000
LGA    G    52_C      G    52_B    32.006     0    0.217   0.217    32.006    0.000    0.000
LGA    I    53_C      I    53_B    27.591     0    0.025   0.209    30.273    0.000    0.000
LGA    P    54_C      P    54_B    23.685     0    0.134   0.381    24.543    0.000    0.000
LGA    E    55_C      E    55_B    24.453     0    0.566   0.941    28.254    0.000    0.000
LGA    G    56_C      G    56_B    21.567     0    0.670   0.670    22.741    0.000    0.000
LGA    D    57_C      D    57_B    17.487     0    0.029   0.842    20.296    0.000    0.000
LGA    I    58_C      I    58_B     9.945     0    0.214   1.057    12.696    0.595    5.536
LGA    Y    59_C      Y    59_B     8.945     0    0.640   1.056    14.141    9.048    3.016
LGA    L    60_C      L    60_B     2.474     0    0.675   1.103     5.135   60.476   54.583
LGA    E    61_C      E    61_B     2.532     0    0.597   0.632     6.101   67.024   43.704
LGA    S    62_C      S    62_B     2.777     0    0.080   0.544     3.286   53.571   54.762
LGA    N    63_C      N    63_B     2.429     0    0.614   1.249     4.355   54.167   54.821
LGA    L    64_C      L    64_B     5.525     0    0.660   0.680    11.555   36.310   19.226
LGA    F    65_C      F    65_B     2.442     0    0.483   1.050     3.661   59.405   56.753
LGA    L    66_C      L    66_B     1.968     0    0.137   1.242     2.516   77.143   70.000
LGA    D    67_C      D    67_B     0.928     0    0.041   0.957     3.340   85.952   73.750
LGA    F    68_C      F    68_B     1.549     0    0.114   0.193     2.722   75.000   70.736
LGA    N    69_C      N    69_B     2.510     0    0.229   0.312     3.817   60.952   53.810
LGA    P    70_C      P    70_B     2.762     0    0.013   0.201     2.852   57.143   57.143
LGA    Y    71_C      Y    71_B     2.198     0    0.315   1.349    10.303   64.762   35.714
LGA    G    72_C      G    72_B     2.394     0    0.098   0.098     2.394   66.786   66.786
LGA    L    73_C      L    73_B     1.974     0    0.549   1.136     6.383   58.571   43.452
LGA    S    74_C      S    74_B     4.619     0    0.578   0.814     8.371   42.262   31.825
LGA    G    75_C      G    75_B     4.619     0    0.673   0.673     4.791   40.714   40.714
LGA    Y    76_C      Y    76_B     3.295     0    0.035   1.365     9.958   30.119   20.397
LGA    L    77_C      L    77_B     6.246     0    0.124   0.991     8.704   27.976   17.440
LGA    L    78_C      L    78_B     7.153     0    0.104   1.116    11.926   14.643    7.500
LGA    S    79_C      S    79_B     4.493     0    0.472   0.871     5.489   30.238   33.571
LGA    E    80_C      E    80_B     5.240     0    0.080   0.524    11.811   34.881   16.296
LGA    P    81_C      P    81_B     2.513     0    0.114   0.300     2.848   65.000   61.633
LGA    N    82_C      N    82_B     0.783     0    0.437   0.439     3.174   73.690   72.381
LGA    C    83_C      C    83_B     5.465     0    0.653   0.549     9.128   21.071   16.905
LGA    V    84_C      V    84_B     8.647     0    0.193   1.247    11.857    8.571    5.170
LGA    D    85_C      D    85_B     9.744     0    0.222   0.928    12.485    0.238    0.119
LGA    L    86_C      L    86_B    11.665     0    0.053   0.116    12.662    0.000    0.060
LGA    L    87_C      L    87_B    16.280     0    0.081   0.099    21.936    0.000    0.000
LGA    I    88_C      I    88_B    16.068     0    0.074   0.173    17.870    0.000    0.179
LGA    E    89_C      E    89_B    21.587     0    0.049   0.384    26.520    0.000    0.000
LGA    P    90_C      P    90_B    21.919     0    0.066   0.411    23.797    0.000    0.000
LGA    N    91_C      N    91_B    19.755     0    0.204   0.897    23.707    0.000    0.000
LGA    N    92_C      N    92_B    14.177     0    0.116   1.241    16.332    0.000    0.000
LGA    Y    93_C      Y    93_B    11.776     0    0.115   0.804    13.638    0.119    0.040
LGA    V    94_C      V    94_B     9.623     0    0.157   0.838    10.359    0.238    0.340
LGA    R    95_C      R    95_B    10.083     0    0.004   0.951    14.029    0.357    0.130
LGA    L    96_C      L    96_B    10.385     0    0.230   0.342    12.649    0.000    0.655
LGA    R    97_C      R    97_B    12.621     0    0.156   0.952    15.798    0.000    0.000
LGA    L    98_C      L    98_B    14.110     0    0.135   1.251    16.574    0.000    0.000
LGA    I    99_C      I    99_B    17.643     0    0.040   1.261    19.786    0.000    0.000
LGA    E   100_C      E   100_B    19.782     0    0.666   0.859    27.405    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       57     228    228  100.00     456    456  100.00               116
SUMMARY(RMSD_GDC):    12.796         12.662                 13.841           11.009    9.389

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   57  116    4.0     18    2.79    14.655    13.502     0.622

LGA_LOCAL      RMSD:   2.795  Number of atoms:   18  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  17.013  Number of assigned atoms:   57 
Std_ASGN_ATOMS RMSD:  12.796  Standard rmsd on all 57 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.641032 * X  +  -0.461853 * Y  +  -0.613000 * Z  +  49.200966
  Y_new =   0.597004 * X  +   0.801987 * Y  +   0.020063 * Z  + -100.396706
  Z_new =   0.482352 * X  +  -0.378825 * Y  +   0.789828 * Z  + -93.440575 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.749850 -0.503338 -0.447219   [DEG:   42.9632  -28.8392  -25.6237 ]
ZXZ: -1.603514  0.660268  2.236552   [DEG:  -91.8746   37.8306  128.1450 ]
 
# END of job
