
#######################################################
#                                                     #
#                        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   35 (  269),  selected   35 , name one
# Molecule2: number of CA atoms   35 (  269),  selected   35 , 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       1_A - 35_A        2.00     2.00
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    35       1_A - 35_A        2.00     2.00
  LCS_AVERAGE:    100.00

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:    19       1_A - 19_A        0.99     2.42
  LCS_AVERAGE:     41.88

LCS_GDT    MOLECULE-1    MOLECULE-2     LCS_DETAILS     GDT_DETAILS                                                    TOTAL NUMBER OF RESIDUE PAIRS:   35
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     1_A     S     1_A     19   35   35      3    5   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     D     2_A     D     2_A     19   35   35      4    6   19   26   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E     3_A     E     3_A     19   35   35      5   14   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     M     4_A     M     4_A     19   35   35      4   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     W     5_A     W     5_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     F     6_A     F     6_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     C     7_A     C     7_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E     8_A     E     8_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     T     9_A     T     9_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    10_A     L    10_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     R    11_A     R    11_A     19   35   35      7   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     R    12_A     R    12_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    13_A     L    13_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    14_A     L    14_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     C    15_A     C    15_A     19   35   35      3   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     P    16_A     P    16_A     19   35   35      7   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     K    17_A     K    17_A     19   35   35      5   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     S    18_A     S    18_A     19   35   35      9   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     C    19_A     C    19_A     19   35   35      5   12   22   26   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     S    20_A     S    20_A      6   35   35      5    5    8   11   15   29   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     I    21_A     I    21_A      6   35   35      5    5   11   18   28   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    22_A     E    22_A      6   35   35      5    5   11   22   28   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     G    23_A     G    23_A     10   35   35      3    5   11   19   28   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     G    24_A     G    24_A     11   35   35      3   10   21   26   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     C    25_A     C    25_A     11   35   35      7   16   21   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     P    26_A     P    26_A     11   35   35      3    9   19   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     E    27_A     E    27_A     11   35   35      5    9   20   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     V    28_A     V    28_A     11   35   35      5    9   21   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     C    29_A     C    29_A     11   35   35      5   16   21   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     S    30_A     S    30_A     11   35   35      5   14   21   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     H    31_A     H    31_A     11   35   35      4   12   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     M    32_A     M    32_A     11   35   35      5   11   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     C    33_A     C    33_A     11   35   35      4   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     P    34_A     P    34_A     11   35   35      4   16   22   27   30   33   34   34   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_GDT     L    35_A     L    35_A      3   35   35      3    3    3   11   13   21   29   33   35   35   35   35   35   35   35   35   35   35   35   35 
LCS_AVERAGE  LCS_A:  80.63  (  41.88  100.00  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      9     16     22     27     30     33     34     34     35     35     35     35     35     35     35     35     35     35     35     35 
GDT PERCENT_AT  25.71  45.71  62.86  77.14  85.71  94.29  97.14  97.14 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00 100.00
GDT RMS_LOCAL    0.37   0.65   0.94   1.22   1.39   1.65   1.76   1.76   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00
GDT RMS_ALL_AT   2.53   2.19   2.34   2.11   2.09   2.03   2.03   2.03   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00   2.00

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E    22_A      E    22_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A     2.161     0    0.501   0.919     4.019   55.952   58.968
LGA    D     2_A      D     2_A     2.282     0    0.198   0.990     5.013   70.833   52.679
LGA    E     3_A      E     3_A     2.176     0    0.047   0.726     4.362   68.810   55.556
LGA    M     4_A      M     4_A     1.716     0    0.084   1.033     4.213   75.000   68.452
LGA    W     5_A      W     5_A     0.938     0    0.034   0.271     2.565   85.952   78.061
LGA    F     6_A      F     6_A     0.627     0    0.026   0.218     0.929   90.476   90.476
LGA    C     7_A      C     7_A     1.059     0    0.000   0.113     2.020   83.690   80.159
LGA    E     8_A      E     8_A     1.402     0    0.097   0.590     4.924   81.429   60.847
LGA    T     9_A      T     9_A     0.936     0    0.060   0.358     1.599   88.214   85.374
LGA    L    10_A      L    10_A     0.630     0    0.039   1.422     3.268   90.476   79.048
LGA    R    11_A      R    11_A     0.616     0    0.084   1.197     3.661   92.857   74.719
LGA    R    12_A      R    12_A     0.776     0    0.029   1.090     5.782   90.476   68.745
LGA    L    13_A      L    13_A     0.648     0    0.016   0.985     3.250   92.857   83.393
LGA    L    14_A      L    14_A     0.216     0    0.107   0.108     2.100   92.976   85.179
LGA    C    15_A      C    15_A     1.362     0    0.016   0.807     2.611   85.952   78.968
LGA    P    16_A      P    16_A     1.865     0    0.125   0.180     2.676   72.857   67.211
LGA    K    17_A      K    17_A     1.307     0    0.159   0.793     3.105   85.952   74.444
LGA    S    18_A      S    18_A     0.896     0    0.119   0.115     1.715   85.952   83.016
LGA    C    19_A      C    19_A     2.523     0    0.062   0.620     6.005   59.048   50.556
LGA    S    20_A      S    20_A     3.781     0    0.143   0.648     5.143   43.452   39.524
LGA    I    21_A      I    21_A     3.137     0    0.089   0.315     3.791   50.119   52.738
LGA    E    22_A      E    22_A     2.849     0    0.108   0.829     6.021   57.143   47.249
LGA    G    23_A      G    23_A     3.138     0    0.667   0.667     5.173   45.833   45.833
LGA    G    24_A      G    24_A     2.099     0    0.086   0.086     2.105   70.952   70.952
LGA    C    25_A      C    25_A     0.385     0    0.318   0.815     4.528   86.429   76.429
LGA    P    26_A      P    26_A     2.058     0    0.141   0.576     2.938   66.786   63.741
LGA    E    27_A      E    27_A     1.972     0    0.087   0.336     2.880   72.976   64.180
LGA    V    28_A      V    28_A     1.378     0    0.080   1.122     3.311   81.548   73.401
LGA    C    29_A      C    29_A     0.749     0    0.039   0.645     1.368   88.214   85.952
LGA    S    30_A      S    30_A     1.023     0    0.243   0.579     1.767   83.810   83.095
LGA    H    31_A      H    31_A     1.116     0    0.300   0.955     4.036   85.952   70.714
LGA    M    32_A      M    32_A     1.446     0    0.074   0.991     5.338   79.286   67.202
LGA    C    33_A      C    33_A     1.785     0    0.565   0.881     2.827   68.929   67.540
LGA    P    34_A      P    34_A     1.238     0    0.206   0.436     4.043   71.190   63.537
LGA    L    35_A      L    35_A     6.221     0    0.272   0.336     9.673   17.143   11.667

# RMSD_GDC results:       CA      MC common percent     ALL common percent   GDC_mc  GDC_all
NUMBER_OF_ATOMS_AA:       35     140    140  100.00     269    269  100.00                35
SUMMARY(RMSD_GDC):     1.998          2.066                  2.636           74.844   67.417

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     34    1.76    80.000    89.737     1.829

LGA_LOCAL      RMSD:   1.759  Number of atoms:   34  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:   2.028  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   1.998  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.241374 * X  +   0.960939 * Y  +   0.135405 * Z  + -134.197632
  Y_new =   0.216516 * X  +  -0.082686 * Y  +   0.972771 * Z  + -199.757767
  Z_new =   0.945970 * X  +   0.264119 * Y  +  -0.188100 * Z  + -181.192551 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ:  2.410430 -1.240574  2.189650   [DEG:  138.1075  -71.0796  125.4577 ]
ZXZ:  3.003287  1.760024  1.298526   [DEG:  172.0757  100.8419   74.4000 ]
 
# END of job
