
#######################################################
#                                                     #
#                        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   70 (  573),  selected   61 , name one
# Molecule2: number of CA atoms   61 (  491),  selected   61 , name two
# PARAMETERS: input.pdb  -ie  -3  -d:4  -sda  -swap  -ch1:B  -ch2:B  
# FIXED Atom-Atom correspondence
# GDT and LCS analysis 

LCS - RMSD CUTOFF   5.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    45       1_B - 45_B        4.95     8.95
  LCS_AVERAGE:     60.95

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    24      19_B - 42_B        1.98    10.13
  LCS_AVERAGE:     26.31

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    22      20_B - 41_B        0.47    10.73
  LCS_AVERAGE:     21.93

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     D     1_B     D     1_B     16   18   45     12   15   15   16   17   25   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     Y     2_B     Y     2_B     16   18   45     12   15   15   16   17   25   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     I     3_B     I     3_B     16   18   45     12   15   15   16   17   20   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     R     4_B     R     4_B     16   18   45     12   15   15   17   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     E     5_B     E     5_B     16   18   45     12   15   15   19   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L     6_B     L     6_B     16   18   45     12   15   15   16   22   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     R     7_B     R     7_B     16   18   45     12   15   15   16   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A     8_B     A     8_B     16   18   45     12   15   15   18   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A     9_B     A     9_B     16   18   45     12   15   15   16   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L    10_B     L    10_B     16   18   45     12   15   15   16   18   27   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     I    11_B     I    11_B     16   18   45     12   15   15   16   22   27   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L    12_B     L    12_B     16   18   45     12   15   15   16   19   27   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L    13_B     L    13_B     16   18   45     11   15   15   16   17   23   30   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A    14_B     A    14_B     16   18   45     10   15   15   16   17   18   24   30   35   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L    15_B     L    15_B     16   18   45      3   15   15   16   17   18   24   28   35   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     K    16_B     K    16_B     16   18   45      3    3   11   16   17   18   18   18   29   37   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     K    17_B     K    17_B      4   18   45      3    3    4    7   17   18   18   18   20   20   33   39   42   43   45   47   47   49   50   50 
LCS_GDT     Q    18_B     Q    18_B      3   18   45      3    3    4    5    5   10   13   18   20   35   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     H    19_B     H    19_B      3   24   45      3    3    4    5    9   17   24   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A    20_B     A    20_B     22   24   45      3    5   22   22   24   28   30   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     E    21_B     E    21_B     22   24   45     13   21   22   22   24   28   30   34   36   37   39   41   42   42   45   47   47   49   50   50 
LCS_GDT     D    22_B     D    22_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     P    23_B     P    23_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     D    24_B     D    24_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A    25_B     A    25_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     Q    26_B     Q    26_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     R    27_B     R    27_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     V    28_B     V    28_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A    29_B     A    29_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     D    30_B     D    30_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     E    31_B     E    31_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L    32_B     L    32_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     M    33_B     M    33_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     K    34_B     K    34_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     K    35_B     K    35_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     L    36_B     L    36_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     F    37_B     F    37_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     D    38_B     D    38_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A    39_B     A    39_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     A    40_B     A    40_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     H    41_B     H    41_B     22   24   45     20   21   22   22   24   28   31   34   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     R    42_B     R    42_B      4   24   45      3    4    5    9   15   20   31   32   36   38   39   41   42   43   45   47   47   49   50   50 
LCS_GDT     N    43_B     N    43_B      4    6   45      3    4    5    6    6    7   10   13   17   21   26   36   38   42   43   45   47   49   50   50 
LCS_GDT     D    44_B     D    44_B      4    6   45      3    4    4    5    6    7   11   16   17   18   20   25   29   38   41   44   47   49   50   50 
LCS_GDT     K    45_B     K    45_B      4    6   45      3    3    5    6    6    7    9   10   12   15   18   19   21   24   25   27   29   30   37   40 
LCS_GDT     D    46_B     D    46_B      4    6   23      3    3    5    6    6    7    9   11   12   15   18   19   21   24   26   27   29   30   37   45 
LCS_GDT     K    47_B     K    47_B      4    6   21      3    3    5    5    6    7    9   11   12   14   18   20   21   24   26   27   29   37   41   45 
LCS_GDT     V    48_B     V    48_B      3    4   21      3    3    5    5    6    7    9   11   12   14   15   20   21   24   26   27   29   30   41   45 
LCS_GDT     K    49_B     K    49_B      3    4   20      3    3    5    5    5    5    6    8   12   13   15   19   20   22   24   26   29   30   31   33 
LCS_GDT     K    50_B     K    50_B      3    4   20      3    3    4    4    4    5    6    8   12   13   15   19   20   22   24   26   29   30   31   33 
LCS_GDT     V    51_B     V    51_B      3    4   20      3    3    4    4    4    5    6    9   11   13   15   17   19   24   26   27   29   30   31   33 
LCS_GDT     V    52_B     V    52_B      3    4   15      3    3    3    4    4    4    5    7    9   10   12   15   16   20   22   24   27   29   31   33 
LCS_GDT     E    53_B     E    53_B      3    4   15      3    3    3    4    4    4    5    7    8    9   13   17   19   21   23   25   27   29   31   33 
LCS_GDT     E    54_B     E    54_B      3    4   15      0    3    3    4    4    4    6    9   11   13   15   17   19   22   26   27   29   30   33   35 
LCS_GDT     A    55_B     A    55_B      3    3   15      0    3    3    3    3    3    5    9   11   13   18   20   21   28   42   45   47   49   50   50 
LCS_GDT     K    56_B     K    56_B      3    3   11      3    3    3    3    3    6    6    7   11   14   26   34   40   42   45   47   47   49   50   50 
LCS_GDT     K    57_B     K    57_B      3    3   11      3    3    3    5    9   10   19   25   33   36   39   41   42   42   45   47   47   49   50   50 
LCS_GDT     V    58_B     V    58_B      3    3    9      3    3    3    5   17   18   18   18   20   20   28   36   42   43   45   47   47   49   50   50 
LCS_GDT     V    59_B     V    59_B      3    3    9      3    3    3    3    4    6    6    7    9    9   21   35   42   43   45   47   47   49   50   50 
LCS_GDT     S    60_B     S    60_B      3    3    9      1    3    3    3    3    3    5    7    8    9   23   25   41   43   45   47   47   49   50   50 
LCS_GDT     T    61_B     T    61_B      3    3    9      0    3    3    3    3    3    5    5    6    7    9   22   23   27   33   35   38   41   45   49 
LCS_AVERAGE  LCS_A:  36.40  (  21.93   26.31   60.95 )

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     20     21     22     22     24     28     31     34     36     38     39     41     42     43     45     47     47     49     50     50 
GDT PERCENT_AT  32.79  34.43  36.07  36.07  39.34  45.90  50.82  55.74  59.02  62.30  63.93  67.21  68.85  70.49  73.77  77.05  77.05  80.33  81.97  81.97
GDT RMS_LOCAL    0.27   0.30   0.47   0.47   1.57   1.96   2.32   2.45   2.62   3.00   3.05   3.34   3.51   3.82   4.05   4.27   4.27   4.84   5.01   5.01
GDT RMS_ALL_AT  10.83  10.86  10.73  10.73   9.99   9.84   9.64   9.67   9.62   9.41   9.44   9.38   9.37   9.34   9.37   9.38   9.38   9.07   9.04   9.04

# Checking swapping
#   possible swapping detected:  Y     2_B      Y     2_B
#   possible swapping detected:  E     5_B      E     5_B
#   possible swapping detected:  E    21_B      E    21_B
#   possible swapping detected:  E    31_B      E    31_B
#   possible swapping detected:  D    46_B      D    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    D     1_B      D     1_B     3.769     0    0.563   1.407     6.003   41.905   45.119
LGA    Y     2_B      Y     2_B     3.456     0    0.049   0.173     6.460   48.333   35.198
LGA    I     3_B      I     3_B     3.936     0    0.068   0.181     6.972   48.452   36.429
LGA    R     4_B      R     4_B     2.139     0    0.054   0.523     4.903   69.048   55.022
LGA    E     5_B      E     5_B     1.153     0    0.018   0.811     3.476   75.000   69.894
LGA    L     6_B      L     6_B     2.806     0    0.045   1.050     6.220   59.048   49.702
LGA    R     7_B      R     7_B     2.504     0    0.021   0.239     5.349   59.048   47.922
LGA    A     8_B      A     8_B     1.624     0    0.034   0.038     2.471   68.810   71.333
LGA    A     9_B      A     9_B     2.599     0    0.022   0.024     3.599   53.810   54.476
LGA    L    10_B      L    10_B     3.844     0    0.016   0.115     4.809   43.452   40.357
LGA    I    11_B      I    11_B     3.691     0    0.057   0.078     4.804   38.810   47.143
LGA    L    12_B      L    12_B     4.110     0    0.092   0.176     5.415   34.524   39.762
LGA    L    13_B      L    13_B     4.895     0    0.211   0.352     5.346   28.810   32.262
LGA    A    14_B      A    14_B     6.726     0    0.017   0.045     7.467   12.619   12.762
LGA    L    15_B      L    15_B     7.291     0    0.347   0.468     8.803    8.333   10.000
LGA    K    16_B      K    16_B     7.665     0    0.433   0.907     8.383    7.262    8.254
LGA    K    17_B      K    17_B    10.162     0    0.476   0.809    19.958    0.476    0.212
LGA    Q    18_B      Q    18_B     8.912     0    0.636   1.468    15.233   12.262    5.450
LGA    H    19_B      H    19_B     4.632     0    0.637   0.788    11.600   38.929   17.333
LGA    A    20_B      A    20_B     2.899     0    0.657   0.594     5.217   62.857   55.524
LGA    E    21_B      E    21_B     3.020     0    0.221   0.426     6.588   63.214   40.000
LGA    D    22_B      D    22_B     1.591     0    0.017   0.344     3.800   77.143   63.631
LGA    P    23_B      P    23_B     1.750     0    0.084   0.317     2.888   75.000   71.837
LGA    D    24_B      D    24_B     2.750     0    0.056   0.358     5.599   62.857   48.810
LGA    A    25_B      A    25_B     2.276     0    0.043   0.046     2.690   68.810   66.476
LGA    Q    26_B      Q    26_B     1.190     0    0.049   1.342     6.610   81.429   57.513
LGA    R    27_B      R    27_B     1.796     0    0.017   0.414     4.130   75.000   57.489
LGA    V    28_B      V    28_B     2.282     0    0.022   0.035     3.444   68.810   61.769
LGA    A    29_B      A    29_B     1.804     0    0.018   0.019     2.100   75.000   72.952
LGA    D    30_B      D    30_B     1.457     0    0.038   0.663     2.267   81.429   76.131
LGA    E    31_B      E    31_B     1.835     0    0.017   0.180     4.191   75.000   58.995
LGA    L    32_B      L    32_B     2.022     0    0.031   0.039     4.021   70.833   58.869
LGA    M    33_B      M    33_B     1.666     0    0.025   0.755     4.880   79.286   61.845
LGA    K    34_B      K    34_B     1.424     0    0.064   0.880     8.185   81.429   53.545
LGA    K    35_B      K    35_B     1.710     0    0.023   0.287     3.952   77.143   63.016
LGA    L    36_B      L    36_B     1.869     0    0.037   1.261     6.580   75.000   55.833
LGA    F    37_B      F    37_B     1.831     0    0.028   0.067     3.636   75.000   60.519
LGA    D    38_B      D    38_B     1.577     0    0.054   0.258     3.402   79.286   67.381
LGA    A    39_B      A    39_B     1.727     0    0.068   0.068     2.417   75.000   72.952
LGA    A    40_B      A    40_B     2.341     0    0.157   0.156     2.891   64.881   63.333
LGA    H    41_B      H    41_B     2.113     0    0.302   1.239     8.414   61.190   37.667
LGA    R    42_B      R    42_B     6.907     0    0.630   1.090    14.684   13.452    5.758
LGA    N    43_B      N    43_B    12.690     0    0.428   0.686    17.870    0.000    0.000
LGA    D    44_B      D    44_B    14.683     0    0.303   1.216    16.844    0.000    0.000
LGA    K    45_B      K    45_B    20.602     0    0.088   0.237    26.442    0.000    0.000
LGA    D    46_B      D    46_B    21.749     0    0.588   1.211    25.545    0.000    0.000
LGA    K    47_B      K    47_B    19.448     0    0.615   0.915    20.498    0.000    0.000
LGA    V    48_B      V    48_B    17.928     0    0.590   0.627    20.032    0.000    0.000
LGA    K    49_B      K    49_B    24.188     0    0.040   0.527    31.023    0.000    0.000
LGA    K    50_B      K    50_B    23.879     0    0.615   0.785    34.576    0.000    0.000
LGA    V    51_B      V    51_B    18.072     0    0.631   0.608    20.101    0.000    0.000
LGA    V    52_B      V    52_B    18.909     0    0.096   0.341    20.538    0.000    0.000
LGA    E    53_B      E    53_B    18.965     0    0.633   0.780    23.687    0.000    0.000
LGA    E    54_B      E    54_B    15.049     0    0.614   1.171    16.916    0.000    0.000
LGA    A    55_B      A    55_B    10.656     0    0.572   0.554    11.906    5.000    4.000
LGA    K    56_B      K    56_B     8.608     0    0.592   0.573    18.459    5.119    2.275
LGA    K    57_B      K    57_B     6.941     0    0.604   0.707    13.340   19.405    9.312
LGA    V    58_B      V    58_B     8.862     0    0.630   0.526    12.757    2.619    1.497
LGA    V    59_B      V    59_B     9.283     0    0.630   1.447     9.976    2.024    2.109
LGA    S    60_B      S    60_B     9.614     0    0.600   0.793    10.918    0.476    0.556
LGA    T    61_B      T    61_B    13.277     0    0.599   1.234    16.413    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     491    491  100.00                61
SUMMARY(RMSD_GDC):     8.452          8.398                  9.571           39.387   33.282

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   70   61    4.0     34    2.45    50.820    45.232     1.331

LGA_LOCAL      RMSD:   2.455  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   9.672  Number of assigned atoms:   61 
Std_ASGN_ATOMS RMSD:   8.452  Standard rmsd on all 61 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.269643 * X  +   0.644622 * Y  +  -0.715370 * Z  +  -5.717501
  Y_new =  -0.723469 * X  +   0.625891 * Y  +   0.291297 * Z  +  -7.554174
  Z_new =   0.635520 * X  +   0.439002 * Y  +   0.635131 * Z  +   3.719607 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -1.214036 -0.688682  0.604794   [DEG:  -69.5591  -39.4586   34.6522 ]
ZXZ: -1.957492  0.882618  0.966288   [DEG: -112.1560   50.5703   55.3642 ]
 
# END of job
