
#######################################################
#                                                     #
#                        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   53 (  441),  selected   53 , name one
# Molecule2: number of CA atoms  141 ( 1112),  selected   53 , 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:    35      17_A - 51_A        4.77     9.25
  LCS_AVERAGE:     21.41

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    17      29_A - 45_A        1.48    12.95
  LCS_AVERAGE:      8.47

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    15      30_A - 44_A        0.86    14.27
  LCS_AVERAGE:      6.02

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   53
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     L    17_A     L    17_A      8   11   35      7    8    8   10   13   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     A    18_A     A    18_A      8   11   35      7    8    8   10   13   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     E    19_A     E    19_A      8   11   35      7    8    8   10   12   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     I    20_A     I    20_A      8   11   35      7    8    8   10   13   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     F    21_A     F    21_A      8   11   35      7    8    8   10   13   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     K    22_A     K    22_A      8   11   35      7    8    8   10   13   19   23   24   28   29   31   32   34   35   38   43   45   48   50   51 
LCS_GDT     K    23_A     K    23_A      8   11   35      7    8    8   10   13   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     I    24_A     I    24_A      8   11   35      6    8    8   10   13   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     G    25_A     G    25_A      4   11   35      4    4    7   12   15   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     S    26_A     S    26_A      5   11   35      4    4    7    9   11   17   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     K    27_A     K    27_A      5   11   35      4    4    5    6    7    8   11   13   16   25   30   32   34   35   39   43   45   48   50   51 
LCS_GDT     E    28_A     E    28_A      5    6   35      4    4    5    6    6   12   13   19   25   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     N    29_A     N    29_A      5   17   35      4    8   10   14   15   17   22   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     T    30_A     T    30_A     15   17   35      5   12   15   15   16   16   18   19   26   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     K    31_A     K    31_A     15   17   35      7   12   15   15   16   17   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     E    32_A     E    32_A     15   17   35      6   12   15   15   16   17   19   23   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     G    33_A     G    33_A     15   17   35      6   12   15   15   16   17   19   23   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     L    34_A     L    34_A     15   17   35      6   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     A    35_A     A    35_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     E    36_A     E    36_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     L    37_A     L    37_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     Y    38_A     Y    38_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     E    39_A     E    39_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     Y    40_A     Y    40_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     K    41_A     K    41_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     K    42_A     K    42_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   38   41   45   48   50   51 
LCS_GDT     K    43_A     K    43_A     15   17   35      7   12   15   15   16   19   23   24   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     Y    44_A     Y    44_A     15   17   35      7   12   15   15   16   17   23   24   26   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     S    45_A     S    45_A     13   17   35      4    5   12   15   16   19   23   24   28   29   31   32   34   35   37   40   43   47   49   51 
LCS_GDT     D    46_A     D    46_A      4    6   35      3    3    5    6    7   15   18   23   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     A    47_A     A    47_A      4    6   35      3    3    5    8   12   15   18   22   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     D    48_A     D    48_A      4    6   35      3    4    5    6    7   10   16   23   28   29   31   32   34   35   39   43   45   48   50   51 
LCS_GDT     I    49_A     I    49_A      4    6   35      3    4    5    6    6    7    8   11   13   16   17   21   23   27   35   42   45   48   50   51 
LCS_GDT     E    50_A     E    50_A      5    8   35      4    5    5    5    8    9   11   13   15   15   17   20   26   32   38   42   45   48   50   51 
LCS_GDT     P    51_A     P    51_A      5    8   35      4    5    5    5    8    9   11   13   15   17   21   25   29   35   39   43   45   48   50   51 
LCS_GDT     F    52_A     F    52_A      5    8   25      4    5    6    6    8    9   11   13   15   17   20   24   29   33   39   43   45   48   50   51 
LCS_GDT     L    53_A     L    53_A      5    8   25      4    5    6    6    8    9   10   13   15   17   22   26   32   35   39   43   45   48   50   51 
LCS_GDT     K    54_A     K    54_A      5    8   25      4    5    6    6    8    9   10   11   16   18   20   25   29   35   39   43   45   48   50   51 
LCS_GDT     N    55_A     N    55_A      5    8   25      3    4    6    6    8    9   10   11   13   16   20   22   25   30   35   39   43   47   50   51 
LCS_GDT     S    56_A     S    56_A      5    8   25      3    4    6    6    8    9   10   12   14   17   20   22   27   33   35   38   41   46   50   51 
LCS_GDT     S    57_A     S    57_A      5    8   25      3    4    6    6    8    9   12   14   16   19   22   25   29   33   35   39   44   48   50   51 
LCS_GDT     Q    58_A     Q    58_A      4    8   25      3    3    4    5    7   10   13   14   16   19   22   25   29   35   39   43   45   48   50   51 
LCS_GDT     F    59_A     F    59_A      4   11   20      3    3    5    8    8   12   13   16   16   19   22   25   29   35   39   43   45   48   50   51 
LCS_GDT     F    60_A     F    60_A      6   11   20      5    6    6   10   10   12   13   16   16   19   22   24   29   33   38   42   45   48   50   51 
LCS_GDT     Q    61_A     Q    61_A      6   11   20      5    6    6   10   10   12   13   16   16   19   22   25   29   32   38   43   45   48   50   51 
LCS_GDT     S    62_A     S    62_A      6   11   20      5    6    6   10   10   10   12   16   16   18   22   24   29   33   39   43   45   48   50   51 
LCS_GDT     Y    63_A     Y    63_A      6   11   20      5    6    6   10   10   10   13   16   16   19   23   26   31   35   39   43   45   48   50   51 
LCS_GDT     V    64_A     V    64_A      6   11   20      5    6    6   10   10   12   13   16   17   21   25   30   34   35   39   43   45   48   50   51 
LCS_GDT     E    65_A     E    65_A      6   11   16      5    6    6   10   10   12   13   16   16   19   22   26   32   35   39   43   45   48   50   51 
LCS_GDT     R    66_A     R    66_A      6   11   16      4    5    6   10   10   12   13   16   16   19   22   30   34   35   39   43   45   48   50   51 
LCS_GDT     G    67_A     G    67_A      6   11   16      4    5    6   10   10   12   13   16   16   19   28   30   34   35   39   43   45   48   50   51 
LCS_GDT     L    68_A     L    68_A      6   11   16      4    5    6   10   10   12   13   16   16   19   22   24   29   32   33   38   42   44   47   51 
LCS_GDT     R    69_A     R    69_A      6   11   16      4    5    6   10   10   12   13   16   16   19   22   24   28   31   33   35   39   42   44   47 
LCS_AVERAGE  LCS_A:  11.97  (   6.02    8.47   21.41 )

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      7     12     15     15     16     19     23     24     28     29     31     32     34     35     39     43     45     48     50     51 
GDT PERCENT_AT   4.96   8.51  10.64  10.64  11.35  13.48  16.31  17.02  19.86  20.57  21.99  22.70  24.11  24.82  27.66  30.50  31.91  34.04  35.46  36.17
GDT RMS_LOCAL    0.15   0.60   0.86   0.86   1.10   2.22   2.55   2.68   3.28   3.32   3.54   3.67   4.27   4.50   5.64   5.89   6.03   6.30   6.52   6.60
GDT RMS_ALL_AT  14.87  13.43  14.27  14.27  13.61  11.11  11.23  11.29  10.66  10.77  10.64  10.61   9.48   8.99   6.95   6.96   6.98   6.93   6.91   6.92

# Checking swapping
#   possible swapping detected:  E    19_A      E    19_A
#   possible swapping detected:  E    28_A      E    28_A
#   possible swapping detected:  E    32_A      E    32_A
#   possible swapping detected:  E    39_A      E    39_A
#   possible swapping detected:  Y    40_A      Y    40_A
#   possible swapping detected:  D    46_A      D    46_A
#   possible swapping detected:  D    48_A      D    48_A
#   possible swapping detected:  E    50_A      E    50_A
#   possible swapping detected:  F    59_A      F    59_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    L    17_A      L    17_A     3.205     0    0.079   1.417     5.958   51.905   45.714
LGA    A    18_A      A    18_A     2.876     0    0.056   0.055     3.391   57.143   55.714
LGA    E    19_A      E    19_A     3.379     0    0.032   0.428     6.036   53.571   38.624
LGA    I    20_A      I    20_A     2.745     0    0.052   0.170     4.065   60.952   53.036
LGA    F    21_A      F    21_A     2.540     0    0.048   1.399     7.717   59.048   39.957
LGA    K    22_A      K    22_A     2.890     0    0.047   0.065     6.134   57.143   44.074
LGA    K    23_A      K    23_A     2.259     0    0.152   1.082     4.069   64.762   60.899
LGA    I    24_A      I    24_A     2.067     0    0.039   0.152     4.514   70.952   59.107
LGA    G    25_A      G    25_A     1.495     0    0.072   0.072     3.146   71.667   71.667
LGA    S    26_A      S    26_A     3.403     0    0.678   0.835     4.771   48.810   46.111
LGA    K    27_A      K    27_A     6.964     0    0.046   0.678    16.016   19.405    8.783
LGA    E    28_A      E    28_A     6.659     0    0.315   1.038    14.753   20.595    9.312
LGA    N    29_A      N    29_A     4.391     0    0.532   0.939     6.773   29.762   25.298
LGA    T    30_A      T    30_A     5.944     0    0.624   1.080     9.203   31.786   20.816
LGA    K    31_A      K    31_A     3.855     0    0.079   1.101     9.048   40.238   30.053
LGA    E    32_A      E    32_A     5.348     0    0.062   0.863     7.657   30.238   19.101
LGA    G    33_A      G    33_A     5.117     0    0.131   0.131     5.117   31.667   31.667
LGA    L    34_A      L    34_A     2.969     0    0.042   1.428     4.671   59.524   58.155
LGA    A    35_A      A    35_A     1.843     0    0.013   0.030     2.850   72.976   69.810
LGA    E    36_A      E    36_A     2.661     0    0.039   0.524     3.495   60.952   59.788
LGA    L    37_A      L    37_A     2.632     0    0.117   0.978     7.246   60.952   44.524
LGA    Y    38_A      Y    38_A     1.282     0    0.116   1.256     9.950   79.286   46.230
LGA    E    39_A      E    39_A     1.033     0    0.063   0.076     1.909   79.405   85.608
LGA    Y    40_A      Y    40_A     2.385     0    0.050   1.493    10.912   61.190   32.976
LGA    K    41_A      K    41_A     2.301     0    0.051   0.545     2.811   64.762   66.614
LGA    K    42_A      K    42_A     1.851     0    0.026   0.829     5.243   68.810   65.079
LGA    K    43_A      K    43_A     2.430     0    0.077   1.096     6.565   59.167   48.995
LGA    Y    44_A      Y    44_A     3.052     0    0.315   1.413    10.409   59.167   32.857
LGA    S    45_A      S    45_A     1.975     0    0.350   0.553     3.530   59.524   58.810
LGA    D    46_A      D    46_A     6.847     0    0.376   1.227    11.331   18.452    9.405
LGA    A    47_A      A    47_A     7.081     0    0.180   0.196     7.806   11.071   12.286
LGA    D    48_A      D    48_A     5.828     0    0.593   1.515    10.603   13.929   18.274
LGA    I    49_A      I    49_A    12.446     0    0.038   1.063    16.606    0.119    0.060
LGA    E    50_A      E    50_A    12.272     0    0.586   1.682    13.475    0.000    0.000
LGA    P    51_A      P    51_A    15.628     0    0.029   0.244    17.022    0.000    0.000
LGA    F    52_A      F    52_A    15.588     0    0.100   1.166    23.646    0.000    0.000
LGA    L    53_A      L    53_A    12.921     0    0.185   0.380    15.435    0.000    0.000
LGA    K    54_A      K    54_A    17.730     0    0.127   1.008    21.869    0.000    0.000
LGA    N    55_A      N    55_A    23.546     0    0.203   0.284    27.063    0.000    0.000
LGA    S    56_A      S    56_A    24.082     0    0.573   0.733    25.396    0.000    0.000
LGA    S    57_A      S    57_A    23.471     0    0.045   0.107    24.126    0.000    0.000
LGA    Q    58_A      Q    58_A    22.167     0    0.172   0.175    24.367    0.000    0.000
LGA    F    59_A      F    59_A    20.181     0    0.582   1.378    20.929    0.000    0.000
LGA    F    60_A      F    60_A    19.310     0    0.665   1.499    22.377    0.000    0.000
LGA    Q    61_A      Q    61_A    17.357     0    0.050   1.447    21.438    0.000    0.000
LGA    S    62_A      S    62_A    19.665     0    0.041   0.620    22.316    0.000    0.000
LGA    Y    63_A      Y    63_A    16.422     0    0.051   0.186    17.621    0.000    0.000
LGA    V    64_A      V    64_A    12.676     0    0.072   0.928    14.029    0.000    0.000
LGA    E    65_A      E    65_A    15.479     0    0.522   1.203    18.166    0.000    0.000
LGA    R    66_A      R    66_A    13.893     0    0.236   0.869    14.852    0.000    0.000
LGA    G    67_A      G    67_A    10.339     0    0.135   0.135    11.861    0.119    0.119
LGA    L    68_A      L    68_A    13.226     0    0.095   1.040    16.683    0.000    0.000
LGA    R    69_A      R    69_A    14.153     0    0.620   1.217    17.071    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       53     212    212  100.00     441    441  100.00               141
SUMMARY(RMSD_GDC):     6.874          6.716                  8.035           11.554    9.713

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   53  141    4.0     24    2.68    16.667    14.663     0.864

LGA_LOCAL      RMSD:   2.678  Number of atoms:   24  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  11.285  Number of assigned atoms:   53 
Std_ASGN_ATOMS RMSD:   6.874  Standard rmsd on all 53 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.787270 * X  +  -0.558265 * Y  +   0.261815 * Z  +  29.538408
  Y_new =   0.614118 * X  +   0.748025 * Y  +  -0.251631 * Z  + -47.698879
  Z_new =  -0.055368 * X  +   0.358886 * Y  +   0.931738 * Z  + -54.338863 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  0.662464  0.055396  0.367665   [DEG:   37.9564    3.1740   21.0657 ]
ZXZ:  0.805231  0.371627 -0.153069   [DEG:   46.1363   21.2927   -8.7702 ]
 
# END of job
