
#######################################################
#                                                     #
#                        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:    17      12_A - 28_A        4.90    11.31
  LONGEST_CONTINUOUS_SEGMENT:    17      13_A - 29_A        4.57    10.81
  LONGEST_CONTINUOUS_SEGMENT:    17      14_A - 30_A        4.92     9.70
  LCS_AVERAGE:     44.98

LCS - RMSD CUTOFF   2.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     6      20_A - 25_A        1.83    11.01
  LONGEST_CONTINUOUS_SEGMENT:     6      23_A - 28_A        1.76    18.88
  LCS_AVERAGE:     14.04

LCS - RMSD CUTOFF   1.00      length       segment         l_RMS    g_RMS
  LONGEST_CONTINUOUS_SEGMENT:     5       7_A - 11_A        0.48    20.84
  LONGEST_CONTINUOUS_SEGMENT:     5      24_A - 28_A        0.58    16.45
  LCS_AVERAGE:     11.02

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      3    4   12      3    3    3    7    8    9    9    9   10   12   14   16   17   19   20   21   24   25   25   26 
LCS_GDT     D     2_A     D     2_A      3    4   12      3    3    3    7    8    9    9    9   10   12   14   16   17   19   21   22   24   25   25   26 
LCS_GDT     E     3_A     E     3_A      3    4   12      3    3    3    7    8    9    9    9   10   12   14   16   17   19   21   22   24   25   25   26 
LCS_GDT     M     4_A     M     4_A      3    4   12      3    3    3    4    4    5    6    8   10   11   15   16   18   19   21   22   24   26   27   27 
LCS_GDT     W     5_A     W     5_A      3    3   12      0    3    3    4    4    5    8   10   12   15   17   18   19   21   22   23   26   27   28   30 
LCS_GDT     F     6_A     F     6_A      3    3   14      3    3    3    4    7    8   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     C     7_A     C     7_A      5    5   16      4    5    5    6    7    8   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     E     8_A     E     8_A      5    5   16      4    5    5    5    5    5    6    7   10   13   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     T     9_A     T     9_A      5    5   16      4    5    5    7    7    7    7   10   11   13   15   19   19   22   24   25   27   28   28   30 
LCS_GDT     L    10_A     L    10_A      5    5   16      4    5    6    7    7    7    7   10   11   13   16   19   20   22   24   25   27   28   28   30 
LCS_GDT     R    11_A     R    11_A      5    5   16      4    5    5    5    5    5    6    7    8    9   16   16   18   21   24   25   27   28   28   30 
LCS_GDT     R    12_A     R    12_A      3    4   17      3    3    3    3    4    6    8    8   11   13   16   16   18   21   24   25   27   28   28   30 
LCS_GDT     L    13_A     L    13_A      3    4   17      3    3    3    4    4    6    8   10   12   14   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     L    14_A     L    14_A      4    4   17      4    4    5    5    6    7    9   10   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     C    15_A     C    15_A      4    4   17      4    4    5    6    7    8   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     P    16_A     P    16_A      4    5   17      4    4    5    5    6    8    8   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     K    17_A     K    17_A      4    5   17      4    4    5    6    7    8   10   11   13   16   18   19   20   22   24   25   26   28   28   30 
LCS_GDT     S    18_A     S    18_A      3    5   17      3    3    4    5    5    8    9   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     C    19_A     C    19_A      3    5   17      3    3    5    6    7    8   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     S    20_A     S    20_A      3    6   17      3    3    4    7    8    9    9   10   12   13   14   17   19   22   24   24   26   27   28   30 
LCS_GDT     I    21_A     I    21_A      3    6   17      3    4    4    5    6    9   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     E    22_A     E    22_A      4    6   17      3    4    4    7    8    9   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     G    23_A     G    23_A      4    6   17      3    3    4    7    8    9    9   10   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     G    24_A     G    24_A      5    6   17      4    5    6    7    8    9    9   10   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     C    25_A     C    25_A      5    6   17      4    5    6    7    8    9    9   10   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     P    26_A     P    26_A      5    6   17      4    5    6    7    7    7    8   10   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     E    27_A     E    27_A      5    6   17      4    5    6    7    7    8   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     V    28_A     V    28_A      5    6   17      3    5    6    7    7    8   10   11   13   16   18   19   20   22   24   25   27   28   28   30 
LCS_GDT     C    29_A     C    29_A      3    5   17      3    3    3    4    6    8   10   11   13   15   17   19   20   22   24   25   27   28   28   30 
LCS_GDT     S    30_A     S    30_A      4    5   17      3    3    4    4    5    8    8    9   11   13   16   16   19   21   23   25   27   28   28   30 
LCS_GDT     H    31_A     H    31_A      4    5   16      3    3    5    5    5    8    8    9   11   13   16   16   19   20   23   25   27   28   28   30 
LCS_GDT     M    32_A     M    32_A      4    5   16      3    3    4    4    4    7    7    8   11   13   16   16   19   21   23   25   27   28   28   30 
LCS_GDT     C    33_A     C    33_A      4    5   16      0    3    4    4    4    7    7    8    9   13   16   16   17   20   21   24   27   28   28   30 
LCS_GDT     P    34_A     P    34_A      3    5   13      0    3    3    4    4    7    7    8    8   13   16   16   17   20   22   24   27   28   28   30 
LCS_GDT     L    35_A     L    35_A      3    5   13      0    3    3    4    4    7    7    8    8   12   16   16   17   20   21   24   26   27   28   30 
LCS_AVERAGE  LCS_A:  23.35  (  11.02   14.04   44.98 )

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      4      5      6      7      8      9     10     11     13     16     18     19     20     22     24     25     27     28     28     30 
GDT PERCENT_AT  11.43  14.29  17.14  20.00  22.86  25.71  28.57  31.43  37.14  45.71  51.43  54.29  57.14  62.86  68.57  71.43  77.14  80.00  80.00  85.71
GDT RMS_LOCAL    0.14   0.48   0.74   1.28   1.84   2.04   2.69   2.80   3.18   3.88   4.24   4.36   4.63   5.02   5.34   5.71   6.39   6.49   6.24   6.83
GDT RMS_ALL_AT  15.26  20.84  14.60  13.84  11.32  11.00   9.99  10.33  10.36  10.50  10.73  10.49  10.90  11.26  11.44  10.82  10.44  10.29  10.28  10.17

# Checking swapping
#   possible swapping detected:  D     2_A      D     2_A
#   possible swapping detected:  E     3_A      E     3_A
#   possible swapping detected:  F     6_A      F     6_A

#      Molecule1      Molecule2  DISTANCE    Mis    MC     All    Dist_max   GDC_mc  GDC_all
LGA    S     1_A      S     1_A    23.703     0    0.471   0.456    26.270    0.000    0.000
LGA    D     2_A      D     2_A    18.989     0    0.310   1.073    21.391    0.000    0.000
LGA    E     3_A      E     3_A    16.721     0    0.560   0.778    21.646    0.000    0.000
LGA    M     4_A      M     4_A    13.749     0    0.622   1.099    21.354    0.000    0.000
LGA    W     5_A      W     5_A     7.278     0    0.568   1.171     9.848   17.024   23.231
LGA    F     6_A      F     6_A     3.082     0    0.597   1.314     4.713   61.190   60.303
LGA    C     7_A      C     7_A     1.147     0    0.582   0.514     4.409   62.500   62.143
LGA    E     8_A      E     8_A     7.096     0    0.070   0.864    11.326   12.500    6.878
LGA    T     9_A      T     9_A    10.977     0    0.030   0.187    14.314    1.190    0.680
LGA    L    10_A      L    10_A     9.979     0    0.164   0.157    12.686    0.357    1.012
LGA    R    11_A      R    11_A    10.116     0    0.457   0.463    17.620    0.357    0.130
LGA    R    12_A      R    12_A    10.570     0    0.660   1.338    21.571    0.238    0.087
LGA    L    13_A      L    13_A     7.118     0    0.622   1.036     8.882    9.762   10.298
LGA    L    14_A      L    14_A     4.906     0    0.651   0.586     9.542   33.095   19.821
LGA    C    15_A      C    15_A     1.634     0    0.047   0.777     4.844   72.857   65.952
LGA    P    16_A      P    16_A     3.588     0    0.029   0.078     6.951   50.357   36.871
LGA    K    17_A      K    17_A     1.872     0    0.208   0.669     7.512   64.405   43.915
LGA    S    18_A      S    18_A     3.866     0    0.268   0.253     6.570   52.143   40.556
LGA    C    19_A      C    19_A     1.688     0    0.547   0.838     4.709   70.238   59.286
LGA    S    20_A      S    20_A     5.259     0    0.608   0.908     9.524   35.952   25.238
LGA    I    21_A      I    21_A     3.516     0    0.392   0.367     4.856   43.333   39.583
LGA    E    22_A      E    22_A     5.572     0    0.505   0.708    11.263   25.119   13.545
LGA    G    23_A      G    23_A     8.074     0    0.721   0.721    11.260    4.048    4.048
LGA    G    24_A      G    24_A     9.414     0    0.507   0.507     9.692    2.024    2.024
LGA    C    25_A      C    25_A     8.724     0    0.087   0.755     8.902    9.286    7.143
LGA    P    26_A      P    26_A     6.924     0    0.050   0.059     9.131   22.262   13.810
LGA    E    27_A      E    27_A     3.065     0    0.640   1.224     4.622   43.929   40.899
LGA    V    28_A      V    28_A     2.411     0    0.627   0.894     6.383   63.333   48.435
LGA    C    29_A      C    29_A     3.301     0    0.564   0.630     6.501   41.548   38.492
LGA    S    30_A      S    30_A     8.628     0    0.425   0.393    12.005    5.119    3.889
LGA    H    31_A      H    31_A    10.531     0    0.229   1.125    12.035    1.071    0.476
LGA    M    32_A      M    32_A     9.745     0    0.590   1.387    12.766    0.238    3.988
LGA    C    33_A      C    33_A    16.323     0    0.264   0.309    19.006    0.000    0.000
LGA    P    34_A      P    34_A    18.650     0    0.431   0.468    20.737    0.000    0.000
LGA    L    35_A      L    35_A    20.303     0    0.398   0.677    24.155    0.000    0.000

# 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):     8.697          8.758                  9.604           23.014   19.221

#CA            N1   N2   DIST      N    RMSD    GDT_TS    LGA_S3     LGA_Q 
SUMMARY(GDT)   35   35    4.0     11    2.80    34.286    29.651     0.380

LGA_LOCAL      RMSD:   2.798  Number of atoms:   11  under DIST:   4.00
LGA_ASGN_ATOMS RMSD:  10.327  Number of assigned atoms:   35 
Std_ASGN_ATOMS RMSD:   8.697  Standard rmsd on all 35 assigned CA atoms 

Unitary ROTATION matrix and the SHIFT vector superimpose molecules  (1=>2)
  X_new =  -0.688521 * X  +   0.717400 * Y  +  -0.106184 * Z  +   1.065932
  Y_new =  -0.243946 * X  +  -0.366992 * Y  +  -0.897668 * Z  +   2.906486
  Z_new =  -0.682956 * X  +  -0.592160 * Y  +   0.427689 * Z  +   1.007892 

Euler angles from the ROTATION matrix. Conventions XYZ and ZXZ:
           Phi     Theta       Psi   [DEG:       Phi     Theta       Psi ]
XYZ: -2.801088  0.751801 -0.945292   [DEG: -160.4905   43.0751  -54.1612 ]
ZXZ: -0.117742  1.128862 -2.285109   [DEG:   -6.7461   64.6790 -130.9271 ]
 
# END of job
