
#######################################################
#                                                     #
#                        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   62 (  507),  selected   43 , name one
# Molecule2: number of CA atoms   43 (  346),  selected   43 , 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:    43       5_B - 47_B        4.07     4.07
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    26      10_B - 35_B        1.98     5.43
  LCS_AVERAGE:     50.62

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    18      15_B - 32_B        0.99     6.48
  LCS_AVERAGE:     30.72

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   43
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     S     5_B     S     5_B     14   21   43     12   13   15   17   18   20   24   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     14   21   43     12   13   15   17   18   22   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     14   21   43     12   13   15   17   18   25   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     14   23   43     12   13   15   17   23   25   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     14   24   43     12   13   15   19   23   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     14   26   43     12   13   15   19   23   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     14   26   43     12   13   15   19   23   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     14   26   43     12   13   15   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     14   26   43     12   13   15   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     16   26   43     12   13   16   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     18   26   43     12   13   15   18   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     18   26   43     12   16   17   19   24   26   29   32   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     18   26   43      7   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     18   26   43     10   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     18   26   43      9   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     18   26   43      5   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     18   26   43      8   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     18   26   43      5   16   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     18   26   43      5   15   17   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     T    33_B     T    33_B      6   26   43      4    5    7   11   22   25   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     F    34_B     F    34_B      6   26   43      4    5   12   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     A    35_B     A    35_B      5   26   43      4    5    7   10   19   26   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     D    36_B     D    36_B      7   25   43      4    5    7    8   13   17   19   30   34   35   36   37   40   42   42   42   43   43   43   43 
LCS_GDT     G    37_B     G    37_B      8   14   43      4    8    9   12   18   25   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     E    38_B     E    38_B      8   14   43      4    8   12   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     R    39_B     R    39_B      8   12   43      4    8   11   19   24   27   30   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     K    40_B     K    40_B      8   12   43      4    8    9   14   19   27   29   33   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     M    41_B     M    41_B      8   12   43      5   11   15   17   18   20   24   29   36   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     P    42_B     P    42_B      8   12   43      5    8   15   17   18   19   22   26   32   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     T    43_B     T    43_B      8   12   43      5    8    9   13   17   19   22   25   29   35   36   38   40   42   42   42   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      8   12   43      5    8    9   12   15   19   22   24   28   32   36   37   40   42   42   42   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      8   12   43      5    6    7   11   17   19   22   25   29   35   36   38   40   42   42   42   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3   10   43      3    3    3    4    6    6   14   22   31   36   38   38   40   42   42   42   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3    3    3    4    5    5   22   24   28   33   38   40   41   43   43   43   43 
LCS_AVERAGE  LCS_A:  60.45  (  30.72   50.62  100.00 )

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     12     16     17     19     24     27     30     33     36     36     38     38     40     42     42     42     43     43     43     43 
GDT PERCENT_AT  27.91  37.21  39.53  44.19  55.81  62.79  69.77  76.74  83.72  83.72  88.37  88.37  93.02  97.67  97.67  97.67 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.24   0.58   0.65   1.08   1.62   2.01   2.20   2.47   2.75   2.75   3.12   3.12   3.46   3.83   3.83   3.83   4.07   4.07   4.07   4.07
GDT RMS_ALL_AT   8.67   6.84   6.80   6.36   5.39   4.88   5.06   4.86   4.69   4.69   4.36   4.36   4.24   4.09   4.09   4.09   4.07   4.07   4.07   4.07

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  E    28_B      E    28_B
#   possible swapping detected:  F    30_B      F    30_B
#   possible swapping detected:  F    34_B      F    34_B
#   possible swapping detected:  D    36_B      D    36_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     4.788     0    0.641   0.946     8.744   38.810   27.540
LGA    L     6_B      L     6_B     4.008     0    0.064   1.224     6.847   45.357   40.298
LGA    E     7_B      E     7_B     3.425     0    0.045   0.822     6.831   53.810   37.937
LGA    T     8_B      T     8_B     2.401     0    0.050   1.208     5.149   69.048   58.503
LGA    K     9_B      K     9_B     1.854     0    0.009   0.151     4.093   75.119   60.635
LGA    K    10_B      K    10_B     0.907     0    0.013   0.963     5.295   88.214   72.011
LGA    A    11_B      A    11_B     1.524     0    0.013   0.014     2.113   77.143   74.667
LGA    Y    12_B      Y    12_B     0.945     0    0.016   1.217     8.537   81.786   52.659
LGA    A    13_B      A    13_B     1.745     0    0.011   0.012     2.644   71.071   71.429
LGA    A    14_B      A    14_B     2.213     0    0.064   0.070     3.798   57.738   59.143
LGA    R    15_B      R    15_B     3.498     0    0.049   1.197     4.707   45.476   54.719
LGA    T    16_B      T    16_B     4.290     0    0.205   1.065     6.642   41.786   37.415
LGA    R    17_B      R    17_B     3.072     0    0.044   0.790     7.184   51.905   32.944
LGA    R    18_B      R    18_B     2.783     0    0.020   1.298     4.607   57.143   48.485
LGA    S    19_B      S    19_B     3.638     0    0.044   0.718     4.429   50.119   46.825
LGA    N    20_B      N    20_B     3.149     0    0.021   0.325     4.342   57.381   51.250
LGA    Y    21_B      Y    21_B     1.222     0    0.075   0.085     2.506   81.548   81.111
LGA    A    22_B      A    22_B     1.611     0    0.015   0.019     2.303   75.000   72.952
LGA    A    23_B      A    23_B     2.201     0    0.010   0.016     2.986   68.810   66.476
LGA    S    24_B      S    24_B     1.945     0    0.131   0.529     2.335   72.976   70.238
LGA    L    25_B      L    25_B     0.974     0    0.055   0.148     1.695   86.071   86.012
LGA    R    26_B      R    26_B     0.581     0    0.045   0.959     3.898   92.857   73.853
LGA    L    27_B      L    27_B     1.953     0    0.615   1.442     7.233   71.071   51.786
LGA    E    28_B      E    28_B     1.616     0    0.628   1.313     5.770   65.476   53.492
LGA    G    29_B      G    29_B     1.724     0    0.358   0.358     1.724   75.000   75.000
LGA    F    30_B      F    30_B     1.574     0    0.090   1.322     7.231   70.833   50.260
LGA    K    31_B      K    31_B     2.084     0    0.182   0.863     8.052   66.786   42.646
LGA    V    32_B      V    32_B     2.073     0    0.026   0.190     3.188   59.167   60.476
LGA    T    33_B      T    33_B     3.492     0    0.217   0.968     5.837   55.357   45.374
LGA    F    34_B      F    34_B     1.825     0    0.155   1.359     7.237   63.095   48.918
LGA    A    35_B      A    35_B     3.352     0    0.152   0.152     5.510   41.905   43.524
LGA    D    36_B      D    36_B     5.710     0    0.502   1.404    10.094   31.905   19.048
LGA    G    37_B      G    37_B     3.814     0    0.012   0.012     4.775   55.238   55.238
LGA    E    38_B      E    38_B     2.136     0    0.075   1.263     7.605   64.881   43.228
LGA    R    39_B      R    39_B     1.431     0    0.082   1.423     6.129   73.452   59.264
LGA    K    40_B      K    40_B     4.151     0    0.308   1.138     4.911   40.357   37.354
LGA    M    41_B      M    41_B     5.845     0    0.048   0.255     7.515   17.024   17.143
LGA    P    42_B      P    42_B     8.139     0    0.044   0.354     8.970    5.119    8.503
LGA    T    43_B      T    43_B    10.468     0    0.040   0.050    11.431    0.119    0.068
LGA    R    44_B      R    44_B    12.037     0    0.594   1.356    18.023    0.000    0.000
LGA    E    45_B      E    45_B    12.106     0    0.469   1.153    13.030    0.000    0.000
LGA    E    46_B      E    46_B     8.008     0    0.608   1.411    11.385    1.548    6.032
LGA    V    47_B      V    47_B    13.238     0    0.435   1.404    15.768    0.000    0.000

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       43     172    172  100.00     346    346  100.00                43
SUMMARY(RMSD_GDC):     4.074          4.088                  4.963           53.430   46.383

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     33    2.47    63.953    63.400     1.284

LGA_LOCAL      RMSD:   2.469  Number of atoms:   33  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.861  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   4.074  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.637050 * X  +  -0.620451 * Y  +  -0.457393 * Z  +  26.920403
  Y_new =   0.766031 * X  +  -0.575646 * Y  +  -0.286057 * Z  + -59.277241
  Z_new =  -0.085812 * X  +  -0.532609 * Y  +   0.842000 * Z  +  19.851009 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.264525  0.085918 -0.564012   [DEG:  129.7477    4.9227  -32.3155 ]
ZXZ: -1.011904  0.569817 -2.981849   [DEG:  -57.9778   32.6481 -170.8474 ]
 
# END of job
