
#######################################################
#                                                     #
#                        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        3.70     3.70
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       5_B - 39_B        1.89     4.72
  LCS_AVERAGE:     73.50

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    29       5_B - 33_B        0.82     4.32
  LCS_AVERAGE:     53.92

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     29   35   43      4   16   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     L     6_B     L     6_B     29   35   43     20   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     E     7_B     E     7_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     T     8_B     T     8_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     K     9_B     K     9_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     K    10_B     K    10_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     A    11_B     A    11_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     Y    12_B     Y    12_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     A    13_B     A    13_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     A    14_B     A    14_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     R    15_B     R    15_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     T    16_B     T    16_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     R    17_B     R    17_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     R    18_B     R    18_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     S    19_B     S    19_B     29   35   43     20   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     N    20_B     N    20_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     Y    21_B     Y    21_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     A    22_B     A    22_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     A    23_B     A    23_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     S    24_B     S    24_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     L    25_B     L    25_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     R    26_B     R    26_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     L    27_B     L    27_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     E    28_B     E    28_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     G    29_B     G    29_B     29   35   43     19   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     F    30_B     F    30_B     29   35   43     21   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     K    31_B     K    31_B     29   35   43     16   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     V    32_B     V    32_B     29   35   43     10   26   27   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     T    33_B     T    33_B     29   35   43      6   11   25   29   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     F    34_B     F    34_B     14   35   43      6   11   14   21   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     A    35_B     A    35_B     14   35   43      6   11   20   28   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     D    36_B     D    36_B     14   35   43      6   11   14   27   32   32   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     G    37_B     G    37_B     14   35   43      6   11   14   16   18   22   33   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     E    38_B     E    38_B     14   35   43      4   11   14   16   18   20   27   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     R    39_B     R    39_B     14   35   43      3   11   14   16   18   20   28   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     K    40_B     K    40_B     14   22   43      6   11   14   16   18   20   23   35   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     M    41_B     M    41_B     14   22   43      3   10   14   16   18   19   22   26   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     P    42_B     P    42_B     14   22   43      4    8   14   15   18   19   22   25   33   39   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     T    43_B     T    43_B     10   21   43      4    6   10   14   16   19   20   24   28   33   40   40   42   42   43   43   43   43   43   43 
LCS_GDT     R    44_B     R    44_B      7   19   43      4    6    8   12   13   16   18   20   24   30   32   38   42   42   43   43   43   43   43   43 
LCS_GDT     E    45_B     E    45_B      7   16   43      4    5    7   10   13   14   17   19   21   30   32   38   42   42   43   43   43   43   43   43 
LCS_GDT     E    46_B     E    46_B      3    9   43      3    3    3    3    6    8   10   12   15   19   23   26   37   39   43   43   43   43   43   43 
LCS_GDT     V    47_B     V    47_B      3    3   43      3    3    3    3   13   31   33   34   37   39   40   40   42   42   43   43   43   43   43   43 
LCS_AVERAGE  LCS_A:  75.81  (  53.92   73.50  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     21     26     27     29     32     32     33     35     37     39     40     40     42     42     43     43     43     43     43     43 
GDT PERCENT_AT  48.84  60.47  62.79  67.44  74.42  74.42  76.74  81.40  86.05  90.70  93.02  93.02  97.67  97.67 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.34   0.41   0.50   0.82   1.31   1.31   1.50   1.89   2.30   2.74   2.99   2.99   3.48   3.48   3.70   3.70   3.70   3.70   3.70   3.70
GDT RMS_ALL_AT   4.45   4.48   4.41   4.32   4.52   4.52   4.58   4.72   4.54   4.01   3.89   3.89   3.73   3.73   3.70   3.70   3.70   3.70   3.70   3.70

# Checking swapping
#   possible swapping detected:  Y    12_B      Y    12_B
#   possible swapping detected:  Y    21_B      Y    21_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:  E    45_B      E    45_B
#   possible swapping detected:  E    46_B      E    46_B

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     5_B      S     5_B     2.352     0    0.610   0.916     4.925   72.976   60.079
LGA    L     6_B      L     6_B     1.377     0    0.052   1.208     3.917   83.810   75.714
LGA    E     7_B      E     7_B     0.508     0    0.056   1.120     4.629   92.857   80.159
LGA    T     8_B      T     8_B     1.049     0    0.032   1.218     2.755   85.952   76.939
LGA    K     9_B      K     9_B     0.914     0    0.018   0.104     2.393   90.476   79.841
LGA    K    10_B      K    10_B     0.577     0    0.046   0.923     4.284   92.857   79.683
LGA    A    11_B      A    11_B     1.145     0    0.024   0.039     1.441   83.690   83.238
LGA    Y    12_B      Y    12_B     1.408     0    0.020   0.061     2.896   79.286   69.722
LGA    A    13_B      A    13_B     0.734     0    0.019   0.032     0.901   90.476   90.476
LGA    A    14_B      A    14_B     1.203     0    0.057   0.068     1.658   81.548   79.810
LGA    R    15_B      R    15_B     1.973     0    0.028   0.866     3.888   70.833   62.251
LGA    T    16_B      T    16_B     1.888     0    0.035   0.042     2.620   77.143   71.905
LGA    R    17_B      R    17_B     0.498     0    0.035   1.046     4.980   90.595   76.537
LGA    R    18_B      R    18_B     1.862     0    0.025   0.621     2.466   75.000   69.221
LGA    S    19_B      S    19_B     2.428     0    0.032   0.642     3.618   64.762   59.921
LGA    N    20_B      N    20_B     1.524     0    0.085   0.491     1.927   79.405   79.345
LGA    Y    21_B      Y    21_B     0.278     0    0.048   0.163     3.264   95.238   78.651
LGA    A    22_B      A    22_B     1.324     0    0.091   0.090     1.730   81.429   79.714
LGA    A    23_B      A    23_B     1.718     0    0.038   0.044     2.052   77.143   74.667
LGA    S    24_B      S    24_B     1.109     0    0.085   0.727     1.356   85.952   84.444
LGA    L    25_B      L    25_B     0.156     0    0.022   0.071     0.742  100.000   97.619
LGA    R    26_B      R    26_B     0.965     0    0.019   0.994     4.467   85.952   74.545
LGA    L    27_B      L    27_B     1.535     0    0.062   0.189     3.001   77.143   69.167
LGA    E    28_B      E    28_B     1.181     0    0.066   0.513     2.676   83.690   76.878
LGA    G    29_B      G    29_B     0.176     0    0.034   0.034     0.514   97.619   97.619
LGA    F    30_B      F    30_B     0.771     0    0.078   0.110     1.671   88.333   84.848
LGA    K    31_B      K    31_B     1.858     0    0.034   0.626     6.929   72.857   51.905
LGA    V    32_B      V    32_B     0.883     0    0.042   1.210     3.046   85.952   78.435
LGA    T    33_B      T    33_B     1.240     0    0.071   1.064     2.911   81.548   76.803
LGA    F    34_B      F    34_B     2.269     0    0.018   1.059     3.942   64.881   62.468
LGA    A    35_B      A    35_B     1.646     0    0.045   0.042     2.678   66.905   69.810
LGA    D    36_B      D    36_B     2.148     0    0.021   0.027     3.424   61.190   70.298
LGA    G    37_B      G    37_B     3.908     0    0.018   0.018     5.107   39.167   39.167
LGA    E    38_B      E    38_B     4.796     0    0.037   0.811     6.392   30.357   27.672
LGA    R    39_B      R    39_B     4.787     0    0.134   1.375     6.025   27.619   31.602
LGA    K    40_B      K    40_B     5.853     0    0.065   1.232     7.014   20.476   21.376
LGA    M    41_B      M    41_B     6.446     0    0.024   0.334     7.846   12.857   13.333
LGA    P    42_B      P    42_B     7.824     0    0.048   0.054     8.699    5.714    8.095
LGA    T    43_B      T    43_B    10.164     0    0.019   0.151    10.909    0.357    0.204
LGA    R    44_B      R    44_B    11.799     0    0.600   0.831    19.004    0.000    0.000
LGA    E    45_B      E    45_B    12.829     0    0.463   1.562    13.007    0.000    0.159
LGA    E    46_B      E    46_B    14.406     0    0.587   1.454    18.893    0.000    0.000
LGA    V    47_B      V    47_B     9.094     0    0.408   1.363    11.419    0.357    9.864

# 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):     3.704          3.707                  4.166           64.056   59.865

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   62   43    4.0     35    1.89    77.326    77.902     1.756

LGA_LOCAL      RMSD:   1.893  Number of atoms:   35  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   4.724  Number of assigned atoms:   43 
Std_ASGN_ATOMS RMSD:   3.704  Standard rmsd on all 43 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =   0.486053 * X  +  -0.775225 * Y  +   0.403459 * Z  +  22.341444
  Y_new =  -0.618695 * X  +   0.020820 * Y  +   0.785356 * Z  + -32.753204
  Z_new =  -0.617227 * X  +  -0.631343 * Y  +  -0.469508 * Z  +  21.872026 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -0.904891  0.665213 -2.210231   [DEG:  -51.8464   38.1139 -126.6369 ]
ZXZ:  2.667023  2.059530 -2.367500   [DEG:  152.8092  118.0024 -135.6477 ]
 
# END of job
