
#######################################################
#                                                     #
#                        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   60 (  510),  selected   60 , name one
# Molecule2: number of CA atoms  106 (  891),  selected   60 , 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:    26      53_A - 78_A        4.78    16.52
  LONGEST_CONTINUOUS_SEGMENT:    26      54_A - 79_A        4.55    16.46
  LCS_AVERAGE:     20.16

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    14      63_A - 76_A        1.90    15.86
  LONGEST_CONTINUOUS_SEGMENT:    14      64_A - 77_A        1.97    15.57
  LCS_AVERAGE:      9.81

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    12      66_A - 77_A        0.97    16.54
  LCS_AVERAGE:      7.03

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   60
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     K    45_A     K    45_A     11   13   19      7   10   11   11   12   13   14   14   16   17   19   20   23   24   24   25   28   29   31   32 
LCS_GDT     K    46_A     K    46_A     11   13   19      7   10   11   11   12   13   14   14   16   17   18   19   20   21   24   25   28   29   31   32 
LCS_GDT     F    47_A     F    47_A     11   13   19      7   10   11   11   12   13   14   14   16   17   18   19   20   21   23   23   24   25   29   31 
LCS_GDT     M    48_A     M    48_A     11   13   19      7   10   11   11   12   13   14   14   16   17   18   19   20   21   23   23   26   29   31   32 
LCS_GDT     L    49_A     L    49_A     11   13   19      7   10   11   11   12   13   14   14   16   17   18   19   20   21   23   26   28   29   31   32 
LCS_GDT     E    50_A     E    50_A     11   13   19      7   10   11   11   12   13   14   14   16   17   18   19   20   21   23   23   24   25   27   29 
LCS_GDT     N    51_A     N    51_A     11   13   19      7   10   11   11   12   13   14   14   16   17   18   19   20   21   23   23   24   25   26   29 
LCS_GDT     G    52_A     G    52_A     11   13   19      6   10   11   11   12   13   14   14   16   17   18   19   20   21   23   23   24   25   26   29 
LCS_GDT     F    53_A     F    53_A     11   13   26      7   10   11   11   12   13   14   14   16   17   18   19   20   21   23   23   24   28   30   32 
LCS_GDT     E    54_A     E    54_A     11   13   26      3   10   11   11   12   13   14   14   16   17   19   21   23   26   26   28   29   30   31   32 
LCS_GDT     H    55_A     H    55_A     11   13   26      2    4   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     R    56_A     R    56_A      3   13   26      1    3    4    4    5   12   12   14   22   23   25   25   25   26   26   28   29   30   30   32 
LCS_GDT     Q    57_A     Q    57_A      3   13   26      3    3    5    6    9   15   16   19   21   23   25   25   25   26   26   28   29   30   30   32 
LCS_GDT     Y    58_A     Y    58_A      4    9   26      3    3    5    6   10   15   16   20   22   23   25   25   25   26   26   28   29   30   30   32 
LCS_GDT     S    59_A     S    59_A      4    9   26      3    4    8   11   12   15   17   20   22   23   25   25   25   26   26   28   29   30   30   32 
LCS_GDT     G    60_A     G    60_A      5    9   26      4    5    6   12   13   15   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     Y    61_A     Y    61_A      5    9   26      4    5    7   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     T    62_A     T    62_A      5    9   26      4    5    6    9   13   15   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     S    63_A     S    63_A      5   14   26      4    5   10   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     K    64_A     K    64_A      5   14   26      3    5    6    8    9   14   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     E    65_A     E    65_A      3   14   26      3    5   10   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     P    66_A     P    66_A     12   14   26      7   11   11   11   13   16   17   19   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     I    67_A     I    67_A     12   14   26      8   11   11   11   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     N    68_A     N    68_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     E    69_A     E    69_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     R    70_A     R    70_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     R    71_A     R    71_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     V    72_A     V    72_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     I    73_A     I    73_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     R    74_A     R    74_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     I    75_A     I    75_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     I    76_A     I    76_A     12   14   26      9   11   11   12   13   16   17   20   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     N    77_A     N    77_A     12   14   26      3    4    7   10   13   16   17   19   22   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     K    78_A     K    78_A      3    4   26      3    3    3    3    4    5    9   11   13   15   18   21   24   25   26   28   29   30   31   32 
LCS_GDT     L    79_A     L    79_A      3    4   26      1    3    3    4    4    5    6    9   10   13   15   17   21   24   26   27   29   30   30   32 
LCS_GDT     T    80_A     T    80_A      3    3   22      1    3    3    4    4    5    6    9   10   13   15   17   18   19   20   22   23   25   27   31 
LCS_GDT     K    81_A     K    81_A      3    4   18      0    3    4    5    5    6    9   10   11   13   15   17   18   19   20   22   23   23   26   31 
LCS_GDT     K    82_A     K    82_A      3    9   18      1    3    4    5    5    9    9   10   11   13   15   17   18   19   20   22   23   23   26   28 
LCS_GDT     F    83_A     F    83_A      4    9   18      3    4    4    8    8    9    9   11   11   15   17   19   20   21   23   23   24   24   25   27 
LCS_GDT     T    84_A     T    84_A      7    9   18      3    4    7    8    8    9    9   10   11   17   18   19   20   21   23   23   24   24   26   30 
LCS_GDT     W    85_A     W    85_A      7    9   18      5    6    7    8    8    9    9    9   11   13   15   17   18   19   22   22   23   23   26   31 
LCS_GDT     L    86_A     L    86_A      7    9   18      5    6    7    8    8    9    9   10   11   13   15   17   19   21   23   23   24   25   26   31 
LCS_GDT     G    87_A     G    87_A      7    9   18      5    6    7    8    8    9    9   10   11   13   15   17   18   19   23   23   24   25   26   31 
LCS_GDT     E    88_A     E    88_A      7    9   18      5    6    7    8    8    9    9    9   11   13   15   17   18   18   20   22   24   25   26   31 
LCS_GDT     C    89_A     C    89_A      7    9   18      5    6    7    8    8    9    9    9   11   13   15   17   18   18   20   22   23   23   26   31 
LCS_GDT     V    90_A     V    90_A      7    9   18      3    6    7    8    8    9    9   10   11   13   15   17   18   18   20   22   24   25   26   31 
LCS_GDT     K    91_A     K    91_A      3    9   18      3    3    4    4    7    7    9   10   11   13   15   17   18   18   21   22   23   25   26   31 
LCS_GDT     E    92_A     E    92_A      3    5   18      3    3    4    5    5    6    9   10   11   12   15   17   18   18   21   22   23   25   26   31 
LCS_GDT     F    93_A     F    93_A      3    9   18      3    3    5   10   10   12   12   12   13   13   15   17   18   18   21   22   24   25   26   31 
LCS_GDT     D    94_A     D    94_A      7    9   18      3    4    8   10   10   12   12   12   13   13   15   17   19   21   23   23   24   25   27   29 
LCS_GDT     I    95_A     I    95_A      7    9   18      3    6    8   10   11   13   14   14   16   17   18   19   20   21   23   23   24   25   30   31 
LCS_GDT     T    96_A     T    96_A      7    9   16      3    6    8   10   10   12   12   13   14   15   17   21   24   25   26   28   29   30   31   32 
LCS_GDT     E    97_A     E    97_A      7    9   15      4    6    8   10   12   12   12   13   14   15   17   18   20   26   26   28   29   30   31   32 
LCS_GDT     I    98_A     I    98_A      7    9   15      4    6    8   10   10   12   17   19   21   23   25   25   25   26   26   28   29   30   31   32 
LCS_GDT     G    99_A     G    99_A      7    9   15      4    6    8   10   13   14   17   20   21   23   25   25   25   26   26   27   28   30   31   32 
LCS_GDT     E   100_A     E   100_A      7    9   15      4    6    8   10   10   12   12   15   20   21   23   24   25   26   26   27   28   29   31   32 
LCS_GDT     Q   101_A     Q   101_A      5    9   15      0    4    8   10   10   12   12   12   15   18   20   21   23   24   25   27   28   29   31   31 
LCS_GDT     Y   102_A     Y   102_A      3    3   15      3    4    4    4    4    4    4    6   10   12   16   19   22   23   24   26   28   28   29   29 
LCS_GDT     S   103_A     S   103_A      3    3   15      3    4    4    4    4    4    4    6   10   12   13   13   14   16   21   22   23   25   26   29 
LCS_GDT     L   104_A     L   104_A      3    3   15      3    4    4    4    4    4    4    6   10   12   13   13   16   17   21   22   23   25   26   29 
LCS_AVERAGE  LCS_A:  12.33  (   7.03    9.81   20.16 )

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      9     11     11     12     13     16     17     20     22     23     25     25     25     26     26     28     29     30     31     32 
GDT PERCENT_AT   8.49  10.38  10.38  11.32  12.26  15.09  16.04  18.87  20.75  21.70  23.58  23.58  23.58  24.53  24.53  26.42  27.36  28.30  29.25  30.19
GDT RMS_LOCAL    0.33   0.45   0.45   1.19   1.35   1.92   2.10   2.61   2.98   3.03   3.30   3.30   3.30   3.61   3.61   4.66   5.00   5.10   6.06   6.06
GDT RMS_ALL_AT  16.70  16.81  16.81  16.00  15.92  15.57  16.17  16.82  16.78  17.03  17.01  17.01  17.01  17.01  17.01  16.49  16.37  16.40  14.82  15.93

# Checking swapping
#   possible swapping detected:  F    53_A      F    53_A
#   possible swapping detected:  Y    58_A      Y    58_A
#   possible swapping detected:  Y    61_A      Y    61_A
#   possible swapping detected:  E    69_A      E    69_A
#   possible swapping detected:  F    83_A      F    83_A
#   possible swapping detected:  F    93_A      F    93_A
#   possible swapping detected:  D    94_A      D    94_A
#   possible swapping detected:  E    97_A      E    97_A
#   possible swapping detected:  Y   102_A      Y   102_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    K    45_A      K    45_A    12.437     0    0.108   0.893    14.880    0.000    1.323
LGA    K    46_A      K    46_A    14.992     0    0.041   1.140    16.940    0.000    0.000
LGA    F    47_A      F    47_A    20.013     0    0.016   1.346    25.101    0.000    0.000
LGA    M    48_A      M    48_A    15.655     0    0.025   1.161    16.799    0.000    0.000
LGA    L    49_A      L    49_A    14.084     0    0.063   1.313    17.432    0.000    0.000
LGA    E    50_A      E    50_A    20.693     0    0.082   0.196    24.015    0.000    0.000
LGA    N    51_A      N    51_A    22.650     0    0.243   0.479    25.775    0.000    0.000
LGA    G    52_A      G    52_A    20.101     0    0.072   0.072    20.245    0.000    0.000
LGA    F    53_A      F    53_A    13.755     0    0.105   0.356    16.403    0.000    0.000
LGA    E    54_A      E    54_A     8.949     0    0.408   1.103    14.051   10.357    4.656
LGA    H    55_A      H    55_A     3.323     0    0.674   1.182     9.541   48.929   26.810
LGA    R    56_A      R    56_A     6.337     0    0.699   1.600    14.314   22.857    8.615
LGA    Q    57_A      Q    57_A     6.057     0    0.161   0.770     9.867   17.500   10.899
LGA    Y    58_A      Y    58_A     4.417     0    0.514   1.283     5.707   31.786   43.095
LGA    S    59_A      S    59_A     3.411     0    0.098   0.682     4.695   57.738   49.921
LGA    G    60_A      G    60_A     2.689     0    0.648   0.648     5.918   44.762   44.762
LGA    Y    61_A      Y    61_A     3.572     0    0.031   1.123    14.396   61.667   22.976
LGA    T    62_A      T    62_A     2.258     0    0.027   0.090     6.622   61.429   43.197
LGA    S    63_A      S    63_A     1.084     0    0.027   0.592     3.894   75.833   65.000
LGA    K    64_A      K    64_A     3.761     0    0.582   1.212     7.099   48.810   30.053
LGA    E    65_A      E    65_A     2.051     0    0.225   0.902     3.373   59.405   66.032
LGA    P    66_A      P    66_A     5.238     0    0.697   0.645     8.030   34.524   24.762
LGA    I    67_A      I    67_A     3.209     0    0.035   1.285     4.527   47.143   43.929
LGA    N    68_A      N    68_A     1.371     0    0.047   1.245     4.383   79.286   73.869
LGA    E    69_A      E    69_A     2.384     0    0.091   0.956     3.054   62.857   65.132
LGA    R    70_A      R    70_A     2.019     0    0.052   1.545    10.183   73.095   42.078
LGA    R    71_A      R    71_A     0.310     0    0.067   1.037     4.952   95.238   81.082
LGA    V    72_A      V    72_A     1.596     0    0.020   0.277     3.540   77.143   68.776
LGA    I    73_A      I    73_A     2.015     0    0.131   1.510     6.106   68.810   58.750
LGA    R    74_A      R    74_A     1.503     0    0.025   1.277     6.476   79.286   56.580
LGA    I    75_A      I    75_A     0.381     0    0.042   0.178     1.585   92.857   87.202
LGA    I    76_A      I    76_A     2.416     0    0.182   1.551     6.116   54.524   46.548
LGA    N    77_A      N    77_A     5.798     0    0.456   1.388     9.517   15.952   18.214
LGA    K    78_A      K    78_A    11.577     0    0.591   0.481    17.705    0.357    0.159
LGA    L    79_A      L    79_A    13.599     0    0.566   1.498    16.752    0.000    0.000
LGA    T    80_A      T    80_A    16.568     0    0.630   0.538    21.012    0.000    0.000
LGA    K    81_A      K    81_A    22.724     0    0.628   1.117    25.608    0.000    0.000
LGA    K    82_A      K    82_A    24.135     0    0.594   0.828    27.807    0.000    0.000
LGA    F    83_A      F    83_A    25.928     0    0.518   1.339    28.016    0.000    0.000
LGA    T    84_A      T    84_A    31.672     0    0.193   0.957    34.368    0.000    0.000
LGA    W    85_A      W    85_A    30.708     0    0.226   1.047    30.819    0.000    0.000
LGA    L    86_A      L    86_A    26.506     0    0.035   1.253    28.779    0.000    0.000
LGA    G    87_A      G    87_A    32.366     0    0.024   0.024    35.140    0.000    0.000
LGA    E    88_A      E    88_A    35.864     0    0.100   1.222    42.963    0.000    0.000
LGA    C    89_A      C    89_A    30.785     0    0.144   0.167    32.082    0.000    0.000
LGA    V    90_A      V    90_A    30.051     0    0.591   0.933    33.420    0.000    0.000
LGA    K    91_A      K    91_A    33.154     0    0.041   0.643    38.569    0.000    0.000
LGA    E    92_A      E    92_A    28.737     0    0.668   1.153    30.264    0.000    0.000
LGA    F    93_A      F    93_A    25.821     0    0.506   1.510    29.292    0.000    0.000
LGA    D    94_A      D    94_A    20.716     0    0.157   1.212    22.390    0.000    0.000
LGA    I    95_A      I    95_A    15.990     0    0.206   0.602    18.002    0.000    0.000
LGA    T    96_A      T    96_A    13.338     0    0.008   1.149    14.551    0.119    0.068
LGA    E    97_A      E    97_A    10.377     0    0.072   1.295    15.686    5.119    2.275
LGA    I    98_A      I    98_A     4.115     0    0.208   0.788     6.451   28.214   36.905
LGA    G    99_A      G    99_A     3.596     0    0.159   0.159     5.786   36.548   36.548
LGA    E   100_A      E   100_A     7.242     0    0.585   1.005    12.885   12.738    5.979
LGA    Q   101_A      Q   101_A    10.121     0    0.634   0.981    15.330    0.714    0.317
LGA    Y   102_A      Y   102_A    10.890     0    0.621   0.485    13.296    0.000   11.508
LGA    S   103_A      S   103_A    16.831     0    0.120   0.340    19.948    0.000    0.000
LGA    L   104_A      L   104_A    23.061     0    0.707   0.709    26.671    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       60     240    240  100.00     510    510  100.00               106
SUMMARY(RMSD_GDC):    13.557         13.641                 14.037           13.260   11.113

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   60  106    4.0     20    2.61    16.745    15.300     0.737

LGA_LOCAL      RMSD:   2.614  Number of atoms:   20  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  16.822  Number of assigned atoms:   60 
Std_ASGN_ATOMS RMSD:  13.557  Standard rmsd on all 60 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.646132 * X  +   0.090392 * Y  +  -0.757854 * Z  + -16.000761
  Y_new =  -0.762623 * X  +  -0.115922 * Y  +   0.636371 * Z  + -38.310371
  Z_new =  -0.030329 * X  +   0.989137 * Y  +   0.143836 * Z  +   0.771448 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.273691  0.030334  1.426393   [DEG: -130.2729    1.7380   81.7263 ]
ZXZ: -2.269281  1.426460 -0.030653   [DEG: -130.0202   81.7301   -1.7563 ]
 
# END of job
